PHI Prophage-Host Interaction Toolkit report
Toolkit for the Detection, Comparison, and Annotation of Prophages in Bacterial Genomes.
September 30, 2025
1 Summary
This table provides sample-by-sample information on detected viruses and key host genome statistics. It includes taxonomy, virus count, genome quality classification, CheckM2 metrics (completeness and contamination), and genome assembly statistics such as size and N50.
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Host Genome Quality
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CheckM Metrics
|
Statistics
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|---|---|---|---|---|---|---|---|---|---|
| # | Sample | GTDB Taxonomy | Virus_Count | Quality_Score | Genome_Quality | Completeness | Contamination | Genome size (bp) | N50 (contigs) |
| 1 | NC_000913 | Escherichia coli | 5 | 99.3 | High-quality draft |
|
|
4.6M | 4.6M |
| 2 | NC_002737 | Streptococcus pyogenes | 3 | 97.6 | High-quality draft |
|
|
1.9M | 1.9M |
| 3 | NC_003450 | Corynebacterium glutamicum | 1 | 98.5 | High-quality draft |
|
|
3.3M | 3.3M |
| 4 | NC_008261 | Sarcina perfringens | 2 | 99.3 | High-quality draft |
|
|
3.3M | 3.3M |
| 5 | NC_009012 | Hungateiclostridium thermocellum | 5 | 94.5 | High-quality draft |
|
|
3.8M | 3.8M |
| 6 | NC_012982 | Hirschia baltica | 0 | 99.8 | High-quality draft |
|
|
3.5M | 3.5M |
| 7 | NC_014008 | Coraliomargarita akajimensis | 0 | 99.9 | High-quality draft |
|
|
3.8M | 3.8M |
| 8 | NC_014168 | Segniliparus rotundus | 2 | 99.8 | High-quality draft |
|
|
3.2M | 3.2M |
| 9 | NC_014211 | Nocardiopsis dassonvillei | 0 | 14.0 | Low-quality draft |
|
|
775.4K | 775.4K |
| 10 | NC_014212 | Allomeiothermus silvanus | 3 | 99.2 | High-quality draft |
|
|
3.2M | 3.2M |
| 11 | NC_014363 | Olsenella uli | 0 | 98.0 | High-quality draft |
|
|
2.1M | 2.1M |
| 12 | NC_014364 | Sediminispirochaeta smaragdinae | 4 | 90.6 | High-quality draft |
|
|
4.7M | 4.7M |
| 13 | NC_015761 | Salmonella bongori | 3 | 99.3 | High-quality draft |
|
|
4.5M | 4.5M |
| 14 | NC_017033 | Frateuria aurantia | 3 | 99.8 | High-quality draft |
|
|
3.6M | 3.6M |
| 15 | NC_017095 | Fervidobacterium pennivorans | 0 | 86.6 | High-quality draft |
|
|
2.2M | 2.2M |
| 16 | NC_018014 | Terriglobus roseus | 0 | 53.1 | Medium-quality draft |
|
|
5.2M | 5.2M |
| 17 | NC_018068 | Desulfosporosinus acidiphilus | 2 | 97.9 | High-quality draft |
|
|
4.9M | 4.9M |
| 18 | NC_018515 | Desulfosporosinus meridiei | 2 | 90.8 | High-quality draft |
|
|
4.9M | 4.9M |
| 19 | NC_019897 | Thermobacillus xylanilyticus | 0 | 98.2 | High-quality draft |
|
|
4.2M | 4.2M |
| 20 | NC_019904 | Echinicola vietnamensis | 0 | 98.8 | High-quality draft |
|
|
5.6M | 5.6M |
| 21 | NC_019936 | Stutzerimonas stutzeri_AE | 3 | 99.3 | High-quality draft |
|
|
4.6M | 4.6M |
| 22 | NC_021184 | Sporotomaculum gibsoniae | 3 | 84.8 | High-quality draft |
|
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4.9M | 4.9M |
2 Results
Select sample to show:
2.1 NC_000913
2.1.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 4641652 | 100 | 0.13 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_000913.3_Lit_3 | Lit | Lit | NC_000913.3_1111 | NC_000913.3_1111 | NC_000913.3_1111 | 1 | Lit__Lit |
| NC_000913.3_RM_Type_IV_9 | RM | RM_Type_IV | NC_000913.3_1130 | NC_000913.3_1130 | NC_000913.3_1130 | 1 | RM_Type_IV__Type_IV_05 |
| NC_000913.3_Hachiman_1 | Hachiman | Hachiman | NC_000913.3_2589 | NC_000913.3_2590 | NC_000913.3_2589,NC_000913.3_2590 | 2 | Hachiman__HamA_2,Hachiman__HamB |
| NC_000913.3_RnlAB_6 | RnlAB | RnlAB | NC_000913.3_2591 | NC_000913.3_2592 | NC_000913.3_2591,NC_000913.3_2592 | 2 | RnlAB__RnlA,RnlAB__RnlB |
| NC_000913.3_CAS_Class1-Subtype-I-E_11 | Cas | CAS_Class1-Subtype-I-E | NC_000913.3_2706 | NC_000913.3_2713 | NC_000913.3_2706,NC_000913.3_2707,NC_000913.3_2708,NC_000913.3_2709,NC_000913.3_2710,NC_000913.3_2711,NC_000913.3_2712,NC_000913.3_2713 | 8 | cas1_I-E_1,cas2_I-E_2,cas3_I_5,cas5_I-E_3,cas6e_I_II_III_IV_V_VI_1,cas7_I-E_2,cas8e_I-E_1,cse2gr11_I-E_1 |
| NC_000913.3_MazEF_4 | MazEF | MazEF | NC_000913.3_2734 | NC_000913.3_2735 | NC_000913.3_2734,NC_000913.3_2735 | 2 | MazEF__MazE,MazEF__MazF |
| NC_000913.3_MazEF_5 | MazEF | MazEF | NC_000913.3_4140 | NC_000913.3_4141 | NC_000913.3_4140,NC_000913.3_4141 | 2 | MazEF__MazE,MazEF__MazF |
| NC_000913.3_RM_Type_IV_10 | RM | RM_Type_IV | NC_000913.3_4262 | NC_000913.3_4263 | NC_000913.3_4262,NC_000913.3_4263 | 2 | RM_Type_IV__FAM_1,RM_Type_IV__FAM_2 |
| NC_000913.3_RM_Type_I_8 | RM | RM_Type_I | NC_000913.3_4265 | NC_000913.3_4267 | NC_000913.3_4265,NC_000913.3_4266,NC_000913.3_4267 | 3 | RM__Type_I_MTases_FAM_2,RM__Type_I_REases_FAM_2.einsi_trimmed,RM__Type_I_S_52 |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_000913.3|provirus_1196867_1213107 | 16241 | 24 | 9 | Low-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1196867-1213107 |
| NC_000913.3|provirus_1412000_1434224 | 22225 | 27 | 13 | Low-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1412000-1434224 |
| NC_000913.3|provirus_2463012_2476510 | 13499 | 19 | 12 | Low-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 2463012-2476510 |
| NC_000913.3|provirus_563848_584430 | 20583 | 32 | 13 | Low-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 563848-584430 |
| NC_000913.3|provirus_1627517_1656149 | 28633 | 44 | 10 | Low-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1627517-1656149 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.1.2 Prophages
Select prophage to show:
2.1.2.1 Phage ID: NC_000913.3|provirus_1196867_1213107
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_000913.3|provirus_1196867_1213107_1105 | 666 | NA | NA | NA |
| NC_000913.3|provirus_1196867_1213107_1106 | 696 | NA | NA | NA |
| NC_000913.3|provirus_1196867_1213107_1107 | 894 | GENOMAD.088167.PP | PF10463;COG2856 | Peptidase U49 |
| NC_000913.3|provirus_1196867_1213107_1108 | 1128 | GENOMAD.195357.VP | PF09003;K21039 | Bacteriophage lambda integrase, Arm DNA-binding domain |
| NC_000913.3|provirus_1196867_1213107_1109 | 246 | GENOMAD.095038.VV | PF07825 | Excisionase-like protein |
| NC_000913.3|provirus_1196867_1213107_1110 | 342 | GENOMAD.226053.VP | PF11080;K18840 | Endoribonuclease GhoS |
| NC_000913.3|provirus_1196867_1213107_1111 | 309 | GENOMAD.226995.VP | NA | NA |
| NC_000913.3|provirus_1196867_1213107_1112 | 675 | NA | NA | NA |
| NC_000913.3|provirus_1196867_1213107_1113 | 201 | GENOMAD.218084.VP | PF15943;COG4197 | NA |
| NC_000913.3|provirus_1196867_1213107_1114 | 558 | GENOMAD.058510.VV | PF06892 | Phage regulatory protein CII (CP76) |
| NC_000913.3|provirus_1196867_1213107_1115 | 339 | GENOMAD.102216.VV | NA | NA |
| NC_000913.3|provirus_1196867_1213107_1116 | 1368 | GENOMAD.159591.VP | NA | NA |
| NC_000913.3|provirus_1196867_1213107_1117 | 183 | GENOMAD.088953.VV | PF10003 | NA |
| NC_000913.3|provirus_1196867_1213107_1118 | 474 | GENOMAD.044416.VV | TIGR01537 | NA |
| NC_000913.3|provirus_1196867_1213107_1119 | 750 | GENOMAD.110264.VV | PF04865;COG3948 | Phage-related baseplate assembly protein |
| NC_000913.3|provirus_1196867_1213107_1120 | 585 | GENOMAD.113504.VP | PF10076;COG3778 | Uncharacterized protein YmfQ in lambdoid prophage, DUF2313 family |
| NC_000913.3|provirus_1196867_1213107_1121 | 630 | GENOMAD.044962.VV | PF21882 | Putative tail fiber protein gp53-like, C-terminal |
| NC_000913.3|provirus_1196867_1213107_1122 | 375 | GENOMAD.045203.VV | PF02413 | Caudovirales tail fibre assembly protein, lambda gpK |
| NC_000913.3|provirus_1196867_1213107_1123 | 603 | GENOMAD.140378.VP | PF02413 | NA |
| NC_000913.3|provirus_1196867_1213107_1124 | 537 | GENOMAD.191048.VP | COG4675 | Microcystin-dependent protein (function unknown) |
| NC_000913.3|provirus_1196867_1213107_1125 | 555 | NA | NA | NA |
| NC_000913.3|provirus_1196867_1213107_1126 | 834 | GENOMAD.139104.VV | PF13395 | NA |
| NC_000913.3|provirus_1196867_1213107_1127 | 165 | NA | NA | NA |
| NC_000913.3|provirus_1196867_1213107_1128 | 405 | GENOMAD.227190.VP | PF07166;COG5562 | Prophage-encoded protein YbcV, DUF1398 family |
2.1.2.2 Phage ID: NC_000913.3|provirus_1412000_1434224
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_000913.3|provirus_1412000_1434224_1320 | 1236 | GENOMAD.159447.VP | PF12167;K14059;TIGR01634;COG4385 | phage tail protein, P2 protein I family |
| NC_000913.3|provirus_1412000_1434224_1321 | 216 | GENOMAD.114098.VV | PF06806 | Putative excisionase (DUF1233) |
| NC_000913.3|provirus_1412000_1434224_1322 | 210 | GENOMAD.223267.VP | PF06688;K19780 | NA |
| NC_000913.3|provirus_1412000_1434224_1323 | 810 | GENOMAD.127355.VP | PF03837;TIGR00616;COG3723 | recombinase, phage RecT family |
| NC_000913.3|provirus_1412000_1434224_1324 | 2601 | GENOMAD.084315.VV | PF06630;K10906 | Enterobacterial exodeoxyribonuclease VIII |
| NC_000913.3|provirus_1412000_1434224_1325 | 276 | NA | NA | NA |
| NC_000913.3|provirus_1412000_1434224_1326 | 171 | GENOMAD.110847.VV | PF04181 | NA |
| NC_000913.3|provirus_1412000_1434224_1327 | 222 | GENOMAD.074955.VV | NA | NA |
| NC_000913.3|provirus_1412000_1434224_1328 | 612 | NA | NA | NA |
| NC_000913.3|provirus_1412000_1434224_1329 | 156 | GENOMAD.222124.VP | PF07151 | NA |
| NC_000913.3|provirus_1412000_1434224_1330 | 135 | NA | NA | NA |
| NC_000913.3|provirus_1412000_1434224_1331 | 477 | GENOMAD.115833.VV | PF00376;COG5606;TIGR00673;K10123 | MerR family regulatory protein |
| NC_000913.3|provirus_1412000_1434224_1332 | 297 | GENOMAD.054651.VV | PF15943;COG4197 | DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily |
| NC_000913.3|provirus_1412000_1434224_1333 | 423 | GENOMAD.072359.VV | PF06254 | Putative bacterial toxin ydaT |
| NC_000913.3|provirus_1412000_1434224_1334 | 858 | GENOMAD.195765.VP | PF07120;COG3756 | Uncharacterized conserved protein YdaU, DUF1376 family |
| NC_000913.3|provirus_1412000_1434224_1335 | 747 | GENOMAD.047125.VV | PF16463;COG5437;TIGR02126 | Phage tail tube protein family |
| NC_000913.3|provirus_1412000_1434224_1336 | 561 | GENOMAD.144793.VV | PF07789 | NA |
| NC_000913.3|provirus_1412000_1434224_1337 | 300 | GENOMAD.219285.VP | PF03245 | Bacteriophage Rz lysis protein |
| NC_000913.3|provirus_1412000_1434224_1338 | 1425 | NA | NA | NA |
| NC_000913.3|provirus_1412000_1434224_1339 | 264 | GENOMAD.159709.VV | NA | NA |
| NC_000913.3|provirus_1412000_1434224_1340 | 360 | NA | NA | NA |
| NC_000913.3|provirus_1412000_1434224_1341 | 1029 | GENOMAD.120741.VP | COG5281 | Phage-related minor tail protein |
| NC_000913.3|provirus_1412000_1434224_1342 | 132 | NA | NA | NA |
| NC_000913.3|provirus_1412000_1434224_1343 | 981 | NA | NA | NA |
| NC_000913.3|provirus_1412000_1434224_1344 | 3363 | GENOMAD.020617.VV | NA | NA |
| NC_000913.3|provirus_1412000_1434224_1345 | 576 | GENOMAD.167268.VP | PF02413 | Caudovirales tail fibre assembly protein, lambda gpK |
| NC_000913.3|provirus_1412000_1434224_1346 | 591 | NA | NA | NA |
| NC_000913.3|provirus_1412000_1434224_1347 | 234 | GENOMAD.221767.PV | PF10965 | Biofilm development protein YmgB/AriR |
2.1.2.3 Phage ID: NC_000913.3|provirus_2463012_2476510
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_000913.3|provirus_2463012_2476510_2314 | 1059 | NA | NA | NA |
| NC_000913.3|provirus_2463012_2476510_2315 | 756 | NA | NA | NA |
| NC_000913.3|provirus_2463012_2476510_2316 | 933 | NA | NA | NA |
| NC_000913.3|provirus_2463012_2476510_2317 | 1158 | NA | NA | NA |
| NC_000913.3|provirus_2463012_2476510_2318 | 921 | NA | NA | NA |
| NC_000913.3|provirus_2463012_2476510_2319 | 1332 | NA | NA | NA |
| NC_000913.3|provirus_2463012_2476510_2320 | 303 | GENOMAD.167268.VP | PF02413 | Caudovirales tail fibre assembly protein, lambda gpK |
| NC_000913.3|provirus_2463012_2476510_2321 | 441 | GENOMAD.045203.VV | PF02413 | Caudovirales tail fibre assembly protein, lambda gpK |
| NC_000913.3|provirus_2463012_2476510_2322 | 603 | GENOMAD.044962.VV | PF21882 | Putative tail fiber protein gp53-like, C-terminal |
| NC_000913.3|provirus_2463012_2476510_2323 | 276 | GENOMAD.178309.VP | PF05869;TIGR01712 | phage N-6-adenine-methyltransferase |
| NC_000913.3|provirus_2463012_2476510_2324 | 495 | GENOMAD.225234.VP | PF06069 | PerC transcriptional activator |
| NC_000913.3|provirus_2463012_2476510_2325 | 369 | GENOMAD.086968.VV | NA | NA |
| NC_000913.3|provirus_2463012_2476510_2326 | 363 | GENOMAD.056235.VV | NA | NA |
| NC_000913.3|provirus_2463012_2476510_2327 | 825 | GENOMAD.052651.VV | PF10065;COG5532 | Uncharacterized conserved protein YfdQ, DUF2303 family |
| NC_000913.3|provirus_2463012_2476510_2328 | 537 | GENOMAD.172054.VC | NA | NA |
| NC_000913.3|provirus_2463012_2476510_2329 | 363 | GENOMAD.067358.VV | NA | NA |
| NC_000913.3|provirus_2463012_2476510_2330 | 306 | GENOMAD.222350.VP | NA | NA |
| NC_000913.3|provirus_2463012_2476510_2331 | 201 | GENOMAD.195460.VP | COG2452 | NA |
2.1.2.4 Phage ID: NC_000913.3|provirus_563848_584430
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_000913.3|provirus_563848_584430_520 | 633 | NA | NA | NA |
| NC_000913.3|provirus_563848_584430_521 | 1164 | GENOMAD.133037.VP | NA | NA |
| NC_000913.3|provirus_563848_584430_522 | 264 | GENOMAD.095346.VP | PF09588;K01143;COG5377;TIGR03033 | Phage-related protein, predicted endonuclease |
| NC_000913.3|provirus_563848_584430_523 | 96 | GENOMAD.086130.VV | PF08222;TIGR00373;COG4519 | CodY helix-turn-helix domain |
| NC_000913.3|provirus_563848_584430_524 | 300 | NA | NA | NA |
| NC_000913.3|provirus_563848_584430_525 | 867 | NA | NA | NA |
| NC_000913.3|provirus_563848_584430_526 | 333 | NA | NA | NA |
| NC_000913.3|provirus_563848_584430_527 | 1527 | NA | NA | NA |
| NC_000913.3|provirus_563848_584430_528 | 552 | GENOMAD.189584.CP | PF01161;COG1881;TIGR00481 | Phosphatidylethanolamine-binding protein |
| NC_000913.3|provirus_563848_584430_529 | 798 | GENOMAD.166602.PC | PF06719;PF12833;TIGR02297;K18991;COG2207 | 4-hydroxyphenylacetate catabolism regulatory protein HpaA |
| NC_000913.3|provirus_563848_584430_530 | 456 | GENOMAD.022699.VV | PF05772 | NinB protein |
| NC_000913.3|provirus_563848_584430_531 | 171 | GENOMAD.177576.VP | PF05322 | NINE Protein |
| NC_000913.3|provirus_563848_584430_532 | 291 | GENOMAD.038211.VV | PF07102 | Putative nuclease YbcO |
| NC_000913.3|provirus_563848_584430_533 | 363 | GENOMAD.154527.VP | PF05866;K01160;COG4570 | Holliday junction resolvase RusA (prophage-encoded endonuclease) |
| NC_000913.3|provirus_563848_584430_534 | 138 | GENOMAD.073918.VV | NA | NA |
| NC_000913.3|provirus_563848_584430_535 | 384 | GENOMAD.054312.VV | PF06576 | Phage antitermination protein Q |
| NC_000913.3|provirus_563848_584430_536 | 219 | NA | NA | NA |
| NC_000913.3|provirus_563848_584430_537 | 981 | NA | NA | NA |
| NC_000913.3|provirus_563848_584430_538 | 1068 | NA | NA | NA |
| NC_000913.3|provirus_563848_584430_539 | 216 | GENOMAD.208385.VP | PF04971 | Bacteriophage P21 holin S |
| NC_000913.3|provirus_563848_584430_540 | 498 | GENOMAD.171676.VP | PF00959;COG3772 | Phage-related lysozyme (muramidase), GH24 family |
| NC_000913.3|provirus_563848_584430_541 | 462 | GENOMAD.219285.VP | PF03245 | Bacteriophage Rz lysis protein |
| NC_000913.3|provirus_563848_584430_542 | 294 | NA | NA | NA |
| NC_000913.3|provirus_563848_584430_543 | 411 | GENOMAD.227189.VP | NA | NA |
| NC_000913.3|provirus_563848_584430_544 | 207 | GENOMAD.227340.VP | NA | NA |
| NC_000913.3|provirus_563848_584430_545 | 546 | GENOMAD.161251.VP | PF07471;K22014;COG4220 | Phage DNA packaging protein, Nu1 subunit of terminase |
| NC_000913.3|provirus_563848_584430_546 | 744 | GENOMAD.167268.VP | PF02413 | Caudovirales tail fibre assembly protein, lambda gpK |
| NC_000913.3|provirus_563848_584430_547 | 432 | NA | NA | NA |
| NC_000913.3|provirus_563848_584430_548 | 186 | GENOMAD.178075.VP | PF02413 | Caudovirales tail fibre assembly protein, lambda gpK |
| NC_000913.3|provirus_563848_584430_549 | 750 | NA | NA | NA |
2.1.2.5 Phage ID: NC_000913.3|provirus_1627517_1656149
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_000913.3|provirus_1627517_1656149_1513 | 747 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1514 | 687 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1515 | 204 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1516 | 1461 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1517 | 1284 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1518 | 234 | GENOMAD.221767.PV | PF10965 | Biofilm development protein YmgB/AriR |
| NC_000913.3|provirus_1627517_1656149_1519 | 591 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1520 | 576 | GENOMAD.167268.VP | PF02413 | Caudovirales tail fibre assembly protein, lambda gpK |
| NC_000913.3|provirus_1627517_1656149_1521 | 963 | GENOMAD.211480.VP | COG5301 | Phage-related tail fibre protein |
| NC_000913.3|provirus_1627517_1656149_1522 | 570 | GENOMAD.161251.VP | PF07471;K22014;COG4220 | Phage DNA packaging protein, Nu1 subunit of terminase |
| NC_000913.3|provirus_1627517_1656149_1523 | 411 | GENOMAD.227189.VP | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1524 | 174 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1525 | 213 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1526 | 498 | GENOMAD.062288.VV | PF10721 | NA |
| NC_000913.3|provirus_1627517_1656149_1527 | 534 | GENOMAD.171676.VP | PF00959;COG3772 | Phage-related lysozyme (muramidase), GH24 family |
| NC_000913.3|provirus_1627517_1656149_1528 | 312 | GENOMAD.225519.VP | PF07041 | NA |
| NC_000913.3|provirus_1627517_1656149_1529 | 207 | GENOMAD.208385.VP | PF04971 | Bacteriophage P21 holin S |
| NC_000913.3|provirus_1627517_1656149_1530 | 120 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1531 | 216 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1532 | 213 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1533 | 753 | GENOMAD.136613.VP | PF03589;TIGR02642 | Antitermination protein |
| NC_000913.3|provirus_1627517_1656149_1534 | 1050 | GENOMAD.196019.VP | PF06147 | dATP/dGTP pyrophosphohydrolase |
| NC_000913.3|provirus_1627517_1656149_1535 | 252 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1536 | 156 | GENOMAD.136858.PV | PF01848;K18919 | Hok/gef family |
| NC_000913.3|provirus_1627517_1656149_1537 | 288 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1538 | 240 | GENOMAD.151401.PV | PF04221;TIGR02384;COG3077;K07473 | addiction module antitoxin, RelB/DinJ family |
| NC_000913.3|provirus_1627517_1656149_1539 | 333 | GENOMAD.078672.PP | PF14282 | FlxA-like protein |
| NC_000913.3|provirus_1627517_1656149_1540 | 228 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1541 | 291 | GENOMAD.150946.VV | PF06254 | Putative bacterial toxin ydaT |
| NC_000913.3|provirus_1627517_1656149_1542 | 231 | GENOMAD.108381.VV | K22302 | NA |
| NC_000913.3|provirus_1627517_1656149_1543 | 408 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1544 | 156 | GENOMAD.222124.VP | PF07151 | NA |
| NC_000913.3|provirus_1627517_1656149_1545 | 129 | GENOMAD.136713.VV | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1546 | 219 | GENOMAD.180239.VV | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1547 | 165 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1548 | 189 | GENOMAD.189052.VV | PF05358;K22304 | DicB protein |
| NC_000913.3|provirus_1627517_1656149_1549 | 192 | GENOMAD.094923.VV | PF07358 | NA |
| NC_000913.3|provirus_1627517_1656149_1550 | 921 | GENOMAD.075680.VV | K10906 | NA |
| NC_000913.3|provirus_1627517_1656149_1551 | 543 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1552 | 1197 | GENOMAD.099267.VV | PF00589;TIGR02224;COG4973;K03733 | tyrosine recombinase XerC |
| NC_000913.3|provirus_1627517_1656149_1553 | 111 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1554 | 1020 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1555 | 1215 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1556 | 327 | NA | NA | NA |
| NC_000913.3|provirus_1627517_1656149_1557 | 342 | NA | NA | NA |
2.1.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_000913.3|provirus_1196867_1213107 | sequence_000002.fasta.fasta | 1_0 | 0.05 | average | ANImf | 1 |
| NC_000913.3|provirus_1412000_1434224 | sequence_000003.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
| NC_000913.3|provirus_2463012_2476510 | sequence_000000.fasta.fasta | 3_0 | 0.05 | average | ANImf | 3 |
| NC_000913.3|provirus_563848_584430 | sequence_000001.fasta.fasta | 4_0 | 0.05 | average | ANImf | 4 |
| NC_000913.3|provirus_1627517_1656149 | sequence_000004.fasta.fasta | 5_0 | 0.05 | average | ANImf | 5 |
Primary clustering plot
2.1.4 Virulence Genes
Screening of virulence genes present in the prophage contigs.
| sequence | start | end | strand | gene | coverage | coverage_map | gaps | percent_coverage | percent_identity | database | accession | product | resistance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NC_000913.3|provirus_2463012_2476510 | 4844 | 5206 |
|
gtrA | 1-363/363 | =============== | 0/0 | 100.00 | 88.70 | vfdb | NP_706257 | (gtrA) bactoprenol-linked glucose translocase/flippase [LPS (VF0124)] [Shigella flexneri 2a str. 301] | NA |
| NC_000913.3|provirus_2463012_2476510 | 5203 | 6107 |
|
gtrB | 1-905/930 | =============== | 0/0 | 97.31 | 80.66 | vfdb | NP_706258 | (gtrB) bactoprenol glucosyl transferase [LPS (VF0124)] [Shigella flexneri 2a str. 301] | NA |
2.1.5 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_000913.3|provirus_1196867_1213107 | GB_GCA_021307345.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia ruysiae | blast | 96.9 | iPHoP-RF;92.80 |
| NC_000913.3|provirus_1196867_1213107 | RS_GCF_000026225.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia fergusonii | blast | 96.9 | iPHoP-RF;92.40 |
| NC_000913.3|provirus_1196867_1213107 | RS_GCF_000759775.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia albertii | blast | 96.9 | iPHoP-RF;93.40 |
| NC_000913.3|provirus_1196867_1213107 | RS_GCF_002900365.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia marmotae | blast | 96.9 | iPHoP-RF;96.40 |
| NC_000913.3|provirus_1196867_1213107 | RS_GCF_003697165.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli | blast | 96.9 | iPHoP-RF;93.70 |
| NC_000913.3|provirus_1196867_1213107 | RS_GCF_004211955.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp004211955 | iPHoP-RF | 96.4 | None |
| NC_000913.3|provirus_1196867_1213107 | RS_GCF_005843885.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp005843885 | iPHoP-RF | 96.4 | None |
| NC_000913.3|provirus_1196867_1213107 | RS_GCF_011881725.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli_E | iPHoP-RF | 96.4 | None |
| NC_000913.3|provirus_1196867_1213107 | RS_GCF_002965065.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp002965065 | iPHoP-RF | 96.1 | None |
| NC_000913.3|provirus_1196867_1213107 | RS_GCF_014836715.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia whittamii | iPHoP-RF | 95.1 | None |
| NC_000913.3|provirus_1412000_1434224 | GB_GCA_021307345.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia ruysiae | blast | 96.9 | iPHoP-RF;93.70 |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_000759775.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia albertii | blast | 96.9 | iPHoP-RF;93.10 |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_002075345.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter;s__Citrobacter braakii | blast | 96.9 | None |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_002900365.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia marmotae | blast | 96.9 | iPHoP-RF;95.40 |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_002925905.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;s__Klebsiella michiganensis | blast | 96.9 | None |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_003697165.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli | blast | 96.9 | iPHoP-RF;95.40 |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_005843885.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp005843885 | iPHoP-RF | 96.1 | None |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_002965065.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp002965065 | iPHoP-RF | 95.4 | None |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_014836715.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia whittamii | iPHoP-RF | 95.4 | None |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_000026225.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia fergusonii | iPHoP-RF | 95.1 | None |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_011881725.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli_E | iPHoP-RF | 95.1 | None |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_002042885.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter;s__Citrobacter portucalensis | blast | 94.9 | None |
| NC_000913.3|provirus_1412000_1434224 | RS_GCF_004211955.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp004211955 | iPHoP-RF | 92.4 | None |
| NC_000913.3|provirus_1627517_1656149 | GB_GCA_021307345.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia ruysiae | blast | 96.9 | iPHoP-RF;93.10 |
| NC_000913.3|provirus_1627517_1656149 | RS_GCF_000759775.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia albertii | blast | 96.9 | iPHoP-RF;93.10 |
| NC_000913.3|provirus_1627517_1656149 | RS_GCF_002900365.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia marmotae | blast | 96.9 | iPHoP-RF;96.40 |
| NC_000913.3|provirus_1627517_1656149 | RS_GCF_003697165.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli | blast | 96.9 | iPHoP-RF;95.70 |
| NC_000913.3|provirus_1627517_1656149 | RS_GCF_011881725.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli_E | blast | 96.9 | iPHoP-RF;95.40 |
| NC_000913.3|provirus_1627517_1656149 | RS_GCF_005843885.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp005843885 | iPHoP-RF | 96.1 | None |
| NC_000913.3|provirus_1627517_1656149 | RS_GCF_002965065.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp002965065 | iPHoP-RF | 95.7 | None |
| NC_000913.3|provirus_1627517_1656149 | RS_GCF_004211955.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp004211955 | iPHoP-RF | 95.1 | None |
| NC_000913.3|provirus_1627517_1656149 | RS_GCF_000026225.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia fergusonii | iPHoP-RF | 94.4 | None |
| NC_000913.3|provirus_1627517_1656149 | RS_GCF_014836715.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia whittamii | iPHoP-RF | 92.8 | None |
| NC_000913.3|provirus_2463012_2476510 | GB_GCA_021307345.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia ruysiae | blast | 96.9 | iPHoP-RF;93.40 |
| NC_000913.3|provirus_2463012_2476510 | RS_GCF_000026225.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia fergusonii | blast | 96.9 | iPHoP-RF;92.10 |
| NC_000913.3|provirus_2463012_2476510 | RS_GCF_000759775.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia albertii | blast | 96.9 | iPHoP-RF;96.70 |
| NC_000913.3|provirus_2463012_2476510 | RS_GCF_002900365.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia marmotae | blast | 96.9 | iPHoP-RF;94.70 |
| NC_000913.3|provirus_2463012_2476510 | RS_GCF_003697165.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli | blast | 96.9 | iPHoP-RF;94.10 |
| NC_000913.3|provirus_2463012_2476510 | RS_GCF_004211955.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp004211955 | blast | 96.9 | iPHoP-RF;94.70 |
| NC_000913.3|provirus_2463012_2476510 | RS_GCF_011881725.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli_E | blast | 96.9 | iPHoP-RF;94.10 |
| NC_000913.3|provirus_2463012_2476510 | RS_GCF_005843885.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp005843885 | iPHoP-RF | 94.7 | None |
| NC_000913.3|provirus_2463012_2476510 | RS_GCF_002965065.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia sp002965065 | iPHoP-RF | 93.7 | None |
| NC_000913.3|provirus_2463012_2476510 | RS_GCF_014836715.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia whittamii | iPHoP-RF | 92.8 | None |
| NC_000913.3|provirus_563848_584430 | GB_GCA_021307345.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia ruysiae | blast | 96.9 | iPHoP-RF;88.20 |
| NC_000913.3|provirus_563848_584430 | RS_GCF_000759775.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia albertii | blast | 96.9 | iPHoP-RF;89.20 |
| NC_000913.3|provirus_563848_584430 | RS_GCF_002900365.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia marmotae | blast | 96.9 | iPHoP-RF;88.50 |
| NC_000913.3|provirus_563848_584430 | RS_GCF_002925905.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;s__Klebsiella michiganensis | blast | 96.9 | None |
| NC_000913.3|provirus_563848_584430 | RS_GCF_003697165.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli | blast | 96.9 | iPHoP-RF;87.00 |
| NC_000913.3|provirus_563848_584430 | RS_GCF_002075345.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter;s__Citrobacter braakii | blast | 96.5 | None |
2.1.6 AMG Predictions
Prediction of auxiliary metabolic genes in the prophage contigs.
| protein | scaffold | amg_ko | amg_ko_name | pfam | pfam_name |
|---|---|---|---|---|---|
| NC_000913.3|provirus_1196867_1213107_23 | NC_000913.3|provirus_1196867_1213107 | K00031 | IDH1, IDH2, icd; isocitrate dehydrogenase [EC:1.1.1.42] | PF00180.20 | Isocitrate/isopropylmalate dehydrogenase |
2.2 NC_002737
2.2.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus pyogenes |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 1852433 | 99.99 | 0.48 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_002737.2_AbiAlpha_1 | AbiAlpha | AbiAlpha | NC_002737.2_745 | NC_002737.2_745 | NC_002737.2_745 | 1 | AbiAlpha__AbiAlpha |
| NC_002737.2_VP1853_2 | VP1853 | VP1853 | NC_002737.2_750 | NC_002737.2_750 | NC_002737.2_750 | 1 | VP1853__VP1853 |
| NC_002737.2_CAS_Class2-Subtype-II-A_7 | Cas | CAS_Class2-Subtype-II-A | NC_002737.2_832 | NC_002737.2_835 | NC_002737.2_832,NC_002737.2_833,NC_002737.2_834,NC_002737.2_835 | 4 | cas1_I_II_III_IV_V_VI_5,cas2_I_II_III_IV_V_VI_6,cas9_II-A_II-B_II-C_3,csn2_II-A_4 |
| NC_002737.2_CAS_Class1-Subtype-I-C_5 | Cas | CAS_Class1-Subtype-I-C | NC_002737.2_1263 | NC_002737.2_1269 | NC_002737.2_1263,NC_002737.2_1264,NC_002737.2_1265,NC_002737.2_1266,NC_002737.2_1267,NC_002737.2_1268,NC_002737.2_1269 | 7 | cas1_I_II_III_IV_V_VI_6,cas2_I_II_III_IV_V_VI_5,cas3_I_5,cas4_I_II_III_IV_V_VI_4,cas5_I-C_11,cas7_I-C_13,cas8c_I-C_1 |
| NC_002737.2_RM_Type_I_4 | RM | RM_Type_I | NC_002737.2_1533 | NC_002737.2_1535 | NC_002737.2_1533,NC_002737.2_1534,NC_002737.2_1535 | 3 | RM__Type_I_MTases_FAM_0,RM__Type_I_REases_FAM_0.einsi_trimmed,RM__Type_I_S_51 |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_002737.2|provirus_529627_569283 | 39657 | 46 | 41 | High-quality | High-quality | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 529627-569283 |
| NC_002737.2|provirus_777501_820593 | 43093 | 65 | 42 | High-quality | High-quality | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 777501-820593 |
| NC_002737.2|provirus_1186916_1222544 | 35629 | 52 | 39 | High-quality | High-quality | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1186916-1222544 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.2.2 Prophages
Select prophage to show:
2.2.2.1 Phage ID: NC_002737.2|provirus_529627_569283
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_002737.2|provirus_529627_569283_517 | 1416 | GENOMAD.022372.VV | PF04708;COG1961;K14060 | Site-specific DNA recombinase related to the DNA invertase Pin |
| NC_002737.2|provirus_529627_569283_518 | 366 | GENOMAD.142683.VV | PF11446;TIGR04165;COG4888 | Cys-rich peptide, TIGR04165 family |
| NC_002737.2|provirus_529627_569283_519 | 762 | GENOMAD.108504.VP | PF05866;PF00717;COG4570;TIGR02754 | Endodeoxyribonuclease RusA; Peptidase S24-like |
| NC_002737.2|provirus_529627_569283_520 | 231 | NA | NA | NA |
| NC_002737.2|provirus_529627_569283_521 | 138 | NA | NA | NA |
| NC_002737.2|provirus_529627_569283_522 | 126 | GENOMAD.129654.VV | NA | NA |
| NC_002737.2|provirus_529627_569283_523 | 228 | GENOMAD.108243.VV | NA | NA |
| NC_002737.2|provirus_529627_569283_524 | 1320 | GENOMAD.010825.VV | PF13175;TIGR00634;COG4717;K03546 | DNA repair protein RecN |
| NC_002737.2|provirus_529627_569283_525 | 1092 | GENOMAD.141036.VV | PF13479;TIGR01618;K04484;COG0468 | phage nucleotide-binding protein |
| NC_002737.2|provirus_529627_569283_526 | 423 | GENOMAD.092954.VV | NA | NA |
| NC_002737.2|provirus_529627_569283_527 | 735 | GENOMAD.014438.VV | NA | NA |
| NC_002737.2|provirus_529627_569283_528 | 636 | GENOMAD.005320.VV | PF05037 | NA |
| NC_002737.2|provirus_529627_569283_529 | 1584 | NA | NA | NA |
| NC_002737.2|provirus_529627_569283_530 | 630 | GENOMAD.116271.VP | PF07768 | PVL ORF-50-like family |
| NC_002737.2|provirus_529627_569283_531 | 2274 | GENOMAD.168744.VP | K07505 | NA |
| NC_002737.2|provirus_529627_569283_532 | 219 | GENOMAD.004447.VV | PF21825 | crAss001_48 related protein |
| NC_002737.2|provirus_529627_569283_533 | 396 | GENOMAD.028440.VV | PF05866;COG4570;K01160 | Holliday junction resolvase RusA (prophage-encoded endonuclease) |
| NC_002737.2|provirus_529627_569283_534 | 222 | GENOMAD.053518.VV | NA | NA |
| NC_002737.2|provirus_529627_569283_535 | 273 | GENOMAD.072347.VV | TIGR02209 | NA |
| NC_002737.2|provirus_529627_569283_536 | 636 | GENOMAD.138295.VP | TIGR02987;COG0827 | NA |
| NC_002737.2|provirus_529627_569283_537 | 435 | GENOMAD.111673.VV | PF05263;TIGR01637 | phage transcriptional regulator, ArpU family |
| NC_002737.2|provirus_529627_569283_538 | 1167 | GENOMAD.038338.VV | COG3392 | NA |
| NC_002737.2|provirus_529627_569283_539 | 477 | GENOMAD.003239.VV | PF05133;TIGR01538 | phage portal protein, SPP1 family |
| NC_002737.2|provirus_529627_569283_540 | 1212 | GENOMAD.064889.VV | PF04466;PF17288;TIGR01547;COG1783;K06909 | phage terminase, large subunit, PBSX family |
| NC_002737.2|provirus_529627_569283_541 | 1503 | GENOMAD.003916.VV | PF05133;TIGR01542 | phage portal protein, putative, A118 family |
| NC_002737.2|provirus_529627_569283_542 | 1494 | GENOMAD.063181.VV | PF06152;TIGR01641 | Phage minor capsid protein 2 |
| NC_002737.2|provirus_529627_569283_543 | 228 | GENOMAD.148778.VV | NA | NA |
| NC_002737.2|provirus_529627_569283_544 | 267 | GENOMAD.076597.VV | NA | NA |
| NC_002737.2|provirus_529627_569283_545 | 609 | GENOMAD.041104.VV | NA | NA |
| NC_002737.2|provirus_529627_569283_546 | 819 | GENOMAD.013974.VV | PF20036;TIGR04387 | major capsid protein, N4-gp56 family |
| NC_002737.2|provirus_529627_569283_547 | 417 | GENOMAD.034545.VV | PF11436 | NA |
| NC_002737.2|provirus_529627_569283_548 | 333 | GENOMAD.114565.VV | PF10665 | Minor capsid protein |
| NC_002737.2|provirus_529627_569283_549 | 357 | GENOMAD.008261.VV | PF11114 | Minor capsid protein |
| NC_002737.2|provirus_529627_569283_550 | 399 | GENOMAD.034546.VV | PF12691 | Bacteriophage minor capsid protein |
| NC_002737.2|provirus_529627_569283_551 | 471 | GENOMAD.028171.VV | PF16461;COG5437 | Lambda phage tail tube protein, TTP |
| NC_002737.2|provirus_529627_569283_552 | 435 | GENOMAD.064813.VV | PF10666 | Phage tail assembly chaperone protein Gp14 ()A118 |
| NC_002737.2|provirus_529627_569283_553 | 582 | GENOMAD.013935.VV | PF06854 | Bacteriophage Gp15 protein |
| NC_002737.2|provirus_529627_569283_554 | 3261 | GENOMAD.002456.VV | COG3941 | NA |
| NC_002737.2|provirus_529627_569283_555 | 717 | GENOMAD.006390.VV | PF20195;COG4722;TIGR01633 | Phage-related protein |
| NC_002737.2|provirus_529627_569283_556 | 2145 | GENOMAD.049306.VV | COG4926 | Phage-related protein |
| NC_002737.2|provirus_529627_569283_557 | 1014 | GENOMAD.093524.VV | PF07212 | Hyaluronidase protein (HylP) |
| NC_002737.2|provirus_529627_569283_558 | 1887 | GENOMAD.033709.VV | PF07902 | gp58-like protein |
| NC_002737.2|provirus_529627_569283_559 | 432 | GENOMAD.073534.VV | PF07761 | NA |
| NC_002737.2|provirus_529627_569283_560 | 618 | GENOMAD.024672.VV | PF07104 | NA |
| NC_002737.2|provirus_529627_569283_561 | 276 | GENOMAD.039653.VV | PF24073 | NA |
| NC_002737.2|provirus_529627_569283_562 | 228 | GENOMAD.126098.VV | COG5546 | NA |
| NC_002737.2|provirus_529627_569283_563 | 111 | GENOMAD.102275.VV | NA | NA |
| NC_002737.2|provirus_529627_569283_564 | 1203 | GENOMAD.133734.VP | NA | NA |
| NC_002737.2|provirus_529627_569283_565 | 708 | GENOMAD.223462.VP | PF02876;PF01123;K11040 | Staphylococcal/Streptococcal toxin, beta-grasp domain; Staphylococcal/Streptococcal toxin, OB-fold domain |
2.2.2.2 Phage ID: NC_002737.2|provirus_777501_820593
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_002737.2|provirus_777501_820593_756 | 1041 | NA | NA | NA |
| NC_002737.2|provirus_777501_820593_757 | 1140 | GENOMAD.111131.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_758 | 810 | GENOMAD.221704.VP | PF02452;COG3692;K18841 | Uncharacterized protein YifN, PemK superfamily |
| NC_002737.2|provirus_777501_820593_759 | 747 | NA | NA | NA |
| NC_002737.2|provirus_777501_820593_760 | 159 | GENOMAD.097925.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_761 | 168 | GENOMAD.116752.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_762 | 840 | NA | NA | NA |
| NC_002737.2|provirus_777501_820593_763 | 228 | NA | NA | NA |
| NC_002737.2|provirus_777501_820593_764 | 207 | NA | NA | NA |
| NC_002737.2|provirus_777501_820593_765 | 729 | GENOMAD.133073.VP | PF03374;COG3645 | Phage antirepressor protein YoqD, KilAC domain |
| NC_002737.2|provirus_777501_820593_766 | 267 | GENOMAD.133830.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_767 | 807 | NA | NA | NA |
| NC_002737.2|provirus_777501_820593_768 | 237 | GENOMAD.153962.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_769 | 240 | GENOMAD.050216.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_770 | 186 | GENOMAD.105558.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_771 | 240 | GENOMAD.136142.VP | PF13730;TIGR00373;COG4738;K07721 | transcription factor E |
| NC_002737.2|provirus_777501_820593_772 | 387 | NA | NA | NA |
| NC_002737.2|provirus_777501_820593_773 | 234 | GENOMAD.100896.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_774 | 141 | GENOMAD.079484.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_775 | 207 | GENOMAD.114751.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_776 | 330 | GENOMAD.040347.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_777 | 792 | GENOMAD.177891.VP | PF03837;TIGR01913;COG3723 | phage recombination protein Bet |
| NC_002737.2|provirus_777501_820593_778 | 666 | GENOMAD.012371.VV | PF07083 | NA |
| NC_002737.2|provirus_777501_820593_779 | 360 | GENOMAD.012371.VV | PF07083 | NA |
| NC_002737.2|provirus_777501_820593_780 | 339 | GENOMAD.060064.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_781 | 513 | NA | NA | NA |
| NC_002737.2|provirus_777501_820593_782 | 195 | GENOMAD.100776.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_783 | 246 | GENOMAD.105486.VP | PF09643;TIGR01671 | phage uncharacterized protein TIGR01671 |
| NC_002737.2|provirus_777501_820593_784 | 462 | GENOMAD.003865.VV | PF11753;PF07852 | Protein of unknwon function (DUF3310) |
| NC_002737.2|provirus_777501_820593_785 | 171 | GENOMAD.094280.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_786 | 441 | GENOMAD.111673.VV | PF05263;TIGR01637 | phage transcriptional regulator, ArpU family |
| NC_002737.2|provirus_777501_820593_787 | 204 | NA | NA | NA |
| NC_002737.2|provirus_777501_820593_788 | 915 | GENOMAD.141545.VV | PF20505 | Intracellular sensor of Lambda phage, Abi component |
| NC_002737.2|provirus_777501_820593_789 | 462 | GENOMAD.146805.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_790 | 483 | GENOMAD.160265.VP | PF03592;COG3728;K07474 | Phage terminase, small subunit |
| NC_002737.2|provirus_777501_820593_791 | 1290 | GENOMAD.113336.VP | PF04466;TIGR01547;COG1783 | phage terminase, large subunit, PBSX family |
| NC_002737.2|provirus_777501_820593_792 | 363 | GENOMAD.033166.VV | PF05133;TIGR01538 | phage portal protein, SPP1 family |
| NC_002737.2|provirus_777501_820593_793 | 1029 | GENOMAD.100877.VP | NA | NA |
| NC_002737.2|provirus_777501_820593_794 | 1626 | GENOMAD.004769.VV | PF04233;COG5585;TIGR01641 | NAD+–asparagine ADP-ribosyltransferase |
| NC_002737.2|provirus_777501_820593_795 | 180 | GENOMAD.137178.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_796 | 270 | GENOMAD.076597.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_797 | 171 | GENOMAD.179672.VV | PF16777;COG4453;TIGR04563 | Transcriptional regulator, RHH-like, CopG |
| NC_002737.2|provirus_777501_820593_798 | 249 | GENOMAD.106940.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_799 | 747 | NA | NA | NA |
| NC_002737.2|provirus_777501_820593_800 | 534 | GENOMAD.010937.VV | PF14265 | NA |
| NC_002737.2|provirus_777501_820593_801 | 381 | GENOMAD.010435.VV | PF02924 | NA |
| NC_002737.2|provirus_777501_820593_802 | 1050 | GENOMAD.004151.VV | PF03864 | Phage major capsid protein E |
| NC_002737.2|provirus_777501_820593_803 | 267 | NA | NA | NA |
| NC_002737.2|provirus_777501_820593_804 | 354 | GENOMAD.020971.VV | PF11436;TIGR01560 | NA |
| NC_002737.2|provirus_777501_820593_805 | 309 | GENOMAD.042575.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_806 | 366 | GENOMAD.011013.VV | PF11114;TIGR01725;COG5005 | phage protein, HK97 gp10 family |
| NC_002737.2|provirus_777501_820593_807 | 390 | GENOMAD.023411.VV | PF16807 | NA |
| NC_002737.2|provirus_777501_820593_808 | 654 | GENOMAD.018762.VV | TIGR02126;COG5437 | phage major tail protein, TP901-1 family |
| NC_002737.2|provirus_777501_820593_809 | 354 | GENOMAD.019874.VV | PF12363 | Phage tail assembly chaperone protein, TAC |
| NC_002737.2|provirus_777501_820593_810 | 330 | GENOMAD.025799.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_811 | 3636 | GENOMAD.013432.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_812 | 780 | GENOMAD.016670.VV | PF20195;TIGR01633;COG4722 | putative phage tail component, N-terminal domain |
| NC_002737.2|provirus_777501_820593_813 | 2049 | GENOMAD.130674.VP | COG4926 | Phage-related protein |
| NC_002737.2|provirus_777501_820593_814 | 1119 | GENOMAD.093524.VV | PF07212 | Hyaluronidase protein (HylP) |
| NC_002737.2|provirus_777501_820593_815 | 1911 | GENOMAD.033709.VV | PF07902 | gp58-like protein |
| NC_002737.2|provirus_777501_820593_816 | 162 | GENOMAD.181912.VC | NA | NA |
| NC_002737.2|provirus_777501_820593_817 | 612 | GENOMAD.024672.VV | PF07104 | NA |
| NC_002737.2|provirus_777501_820593_818 | 297 | GENOMAD.084276.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_819 | 186 | GENOMAD.004934.VV | PF16945 | Putative lactococcus lactis phage r1t holin |
| NC_002737.2|provirus_777501_820593_820 | 108 | GENOMAD.102275.VV | NA | NA |
| NC_002737.2|provirus_777501_820593_821 | 1335 | GENOMAD.006162.VV | K07273;COG3757 | Lyzozyme M1 (1,4-beta-N-acetylmuramidase), GH25 family |
| NC_002737.2|provirus_777501_820593_822 | 678 | GENOMAD.223611.VP | PF02876;PF01123;K11040 | Staphylococcal/Streptococcal toxin, beta-grasp domain; Staphylococcal/Streptococcal toxin, OB-fold domain |
| NC_002737.2|provirus_777501_820593_823 | 711 | GENOMAD.224010.VP | PF02876 | Staphylococcal/Streptococcal toxin, beta-grasp domain |
2.2.2.3 Phage ID: NC_002737.2|provirus_1186916_1222544
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_002737.2|provirus_1186916_1222544_1181 | 1863 | NA | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1182 | 183 | GENOMAD.222241.VP | PF24313 | Paratox |
| NC_002737.2|provirus_1186916_1222544_1183 | 801 | NA | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1184 | 486 | NA | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1185 | 1206 | GENOMAD.133734.VP | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1186 | 111 | GENOMAD.102275.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1187 | 228 | GENOMAD.126098.VV | COG5546 | NA |
| NC_002737.2|provirus_1186916_1222544_1188 | 276 | GENOMAD.039653.VV | PF24073 | NA |
| NC_002737.2|provirus_1186916_1222544_1189 | 618 | GENOMAD.024672.VV | PF07104 | NA |
| NC_002737.2|provirus_1186916_1222544_1190 | 432 | GENOMAD.073534.VV | PF07761 | NA |
| NC_002737.2|provirus_1186916_1222544_1191 | 1785 | GENOMAD.033709.VV | PF07902 | gp58-like protein |
| NC_002737.2|provirus_1186916_1222544_1192 | 1113 | GENOMAD.093524.VV | PF07212 | Hyaluronidase protein (HylP) |
| NC_002737.2|provirus_1186916_1222544_1193 | 1959 | GENOMAD.010194.VV | PF06605;COG4926 | Phage-related protein |
| NC_002737.2|provirus_1186916_1222544_1194 | 696 | GENOMAD.004911.VV | PF20195;COG4722;TIGR01633 | Phage-related protein |
| NC_002737.2|provirus_1186916_1222544_1195 | 2358 | GENOMAD.003531.VV | COG5412 | Phage-related protein |
| NC_002737.2|provirus_1186916_1222544_1196 | 372 | GENOMAD.024158.VV | PF17318 | NA |
| NC_002737.2|provirus_1186916_1222544_1197 | 264 | GENOMAD.021224.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1198 | 594 | GENOMAD.073691.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1199 | 336 | GENOMAD.019860.VV | PF16807 | NA |
| NC_002737.2|provirus_1186916_1222544_1200 | 237 | GENOMAD.017784.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1201 | 339 | GENOMAD.018809.VV | PF10665 | Minor capsid protein |
| NC_002737.2|provirus_1186916_1222544_1202 | 423 | GENOMAD.076853.VV | PF09355 | Phage protein Gp19/Gp15/Gp42 |
| NC_002737.2|provirus_1186916_1222544_1203 | 201 | GENOMAD.069443.VV | PF09124 | T4 recombination endonuclease VII, dimerisation |
| NC_002737.2|provirus_1186916_1222544_1204 | 912 | GENOMAD.013457.VV | PF05065;TIGR01554;COG4653 | Phage capsid family |
| NC_002737.2|provirus_1186916_1222544_1205 | 462 | GENOMAD.083647.VV | PF14265 | NA |
| NC_002737.2|provirus_1186916_1222544_1206 | 1416 | GENOMAD.003419.VV | PF20441;PF03354;COG4626;TIGR01547;K17677 | Phage terminase-like protein, large subunit, contains N-terminal HTH domain |
| NC_002737.2|provirus_1186916_1222544_1207 | 267 | GENOMAD.076597.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1208 | 180 | NA | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1209 | 225 | GENOMAD.193246.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1210 | 1494 | GENOMAD.003531.VV | COG5412 | Phage-related protein |
| NC_002737.2|provirus_1186916_1222544_1211 | 1269 | GENOMAD.076853.VV | PF09355 | Phage protein Gp19/Gp15/Gp42 |
| NC_002737.2|provirus_1186916_1222544_1212 | 357 | GENOMAD.072475.VV | PF12855;COG4338 | ECL1/2/3 zinc binding proteins |
| NC_002737.2|provirus_1186916_1222544_1213 | 345 | GENOMAD.108097.VV | PF13395 | HNH endonuclease |
| NC_002737.2|provirus_1186916_1222544_1214 | 420 | GENOMAD.024790.VV | PF07374;TIGR01636;COG2739 | phage transcriptional activator, RinA family |
| NC_002737.2|provirus_1186916_1222544_1215 | 636 | GENOMAD.138295.VP | TIGR02987;COG0827 | NA |
| NC_002737.2|provirus_1186916_1222544_1216 | 270 | GENOMAD.072347.VV | TIGR02209 | NA |
| NC_002737.2|provirus_1186916_1222544_1217 | 513 | NA | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1218 | 393 | GENOMAD.060064.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1219 | 798 | GENOMAD.161534.VP | PF12684;TIGR01896 | PDDEXK-like domain of unknown function (DUF3799) |
| NC_002737.2|provirus_1186916_1222544_1220 | 201 | GENOMAD.148606.VV | PF06289 | NA |
| NC_002737.2|provirus_1186916_1222544_1221 | 990 | GENOMAD.091877.VP | PF03837;COG3723;K07455;TIGR00616 | Recombinational DNA repair protein RecT |
| NC_002737.2|provirus_1186916_1222544_1222 | 333 | GENOMAD.040347.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1223 | 207 | GENOMAD.114751.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1224 | 141 | GENOMAD.079484.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1225 | 234 | GENOMAD.100896.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1226 | 387 | NA | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1227 | 255 | GENOMAD.136142.VP | PF13730;TIGR00373;COG4738;K07721 | transcription factor E |
| NC_002737.2|provirus_1186916_1222544_1228 | 186 | GENOMAD.105558.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1229 | 312 | GENOMAD.050216.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1230 | 132 | GENOMAD.114759.VV | NA | NA |
| NC_002737.2|provirus_1186916_1222544_1231 | 213 | GENOMAD.225776.VP | PF05339;TIGR00673;COG3620;K22299 | cyanase |
| NC_002737.2|provirus_1186916_1222544_1232 | 756 | GENOMAD.091877.VP | PF03837;COG3723;K07455;TIGR00616 | Recombinational DNA repair protein RecT |
| NC_002737.2|provirus_1186916_1222544_1233 | 519 | GENOMAD.064488.VV | PF08797 | HIRAN domain |
| NC_002737.2|provirus_1186916_1222544_1234 | 1143 | GENOMAD.111131.VV | NA | NA |
2.2.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_002737.2|provirus_529627_569283 | sequence_000001.fasta.fasta | 1_0 | 0.05 | average | ANImf | 1 |
| NC_002737.2|provirus_777501_820593 | sequence_000002.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
| NC_002737.2|provirus_1186916_1222544 | sequence_000000.fasta.fasta | 3_0 | 0.05 | average | ANImf | 3 |
Primary clustering plot
2.2.4 Virulence Genes
Screening of virulence genes present in the prophage contigs.
| sequence | start | end | strand | gene | coverage | coverage_map | gaps | percent_coverage | percent_identity | database | accession | product | resistance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NC_002737.2|provirus_1186916_1222544 | 2808 | 3614 |
|
mf3 | 1-807/807 | =============== | 0/0 | 100 | 100.00 | vfdb | NP_269520 | (mf3) deoxyribonuclease [DNase (VF0252)] [Streptococcus pyogenes M1 GAS] | NA |
| NC_002737.2|provirus_1186916_1222544 | 9081 | 10193 |
|
hylP | 1-1113/1113 | =============== | 0/0 | 100 | 100.00 | vfdb | NP_269528 | (hylP) hyaluronidase phage associated [Hyaluronidase (VF0246)] [Streptococcus pyogenes M1 GAS] | NA |
| NC_002737.2|provirus_529627_569283 | 33078 | 34091 |
|
hylP | 1-1014/1014 | =============== | 0/0 | 100 | 100.00 | vfdb | NP_268936 | (hylP) hyaluronidase phage associated [Hyaluronidase (VF0246)] [Streptococcus pyogenes M1 GAS] | NA |
| NC_002737.2|provirus_529627_569283 | 38950 | 39657 |
|
spec | 1-708/708 | =============== | 0/0 | 100 | 100.00 | vfdb | NP_268943 | (spec) streptococcal exotoxin C precursor phage associated [Spes (VF0248)] [Streptococcus pyogenes M1 GAS] | NA |
| NC_002737.2|provirus_777501_820593 | 35641 | 36759 |
|
hylP | 1-1119/1119 | =============== | 0/0 | 100 | 100.00 | vfdb | NP_269179 | (hylP) hyaluronidase phage associated [Hyaluronidase (VF0246)] [Streptococcus pyogenes M1 GAS] | NA |
| NC_002737.2|provirus_777501_820593 | 41680 | 42357 |
|
spei | 1-678/678 | =============== | 0/0 | 100 | 99.85 | vfdb | NP_269185 | (spei) streptococcal exotoxin I precursor [Spes (VF0248)] [Streptococcus pyogenes M1 GAS] | NA |
| NC_002737.2|provirus_777501_820593 | 42383 | 43093 |
|
speh | 1-711/711 | =============== | 0/0 | 100 | 100.00 | vfdb | NP_269186 | (speh) streptococcal exotoxin H precursor [Spes (VF0248)] [Streptococcus pyogenes M1 GAS] | NA |
2.2.5 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_000186445.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus agalactiae | CRISPR | 97.8 | blast;91.00 iPHoP-RF;88.90 |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_900459225.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus dysgalactiae | iPHoP-RF | 97.1 | blast;96.90 |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_002055535.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus pyogenes | blast | 96.9 | iPHoP-RF;96.40 |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_022354845.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis_AA | CRISPR | 96.8 | None |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_900459405.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus hyointestinalis | CRISPR | 96.8 | iPHoP-RF;89.50 |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_900636575.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus canis | iPHoP-RF | 96.7 | blast;96.60 |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_000425025.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus castoreus | iPHoP-RF | 94.7 | None |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_001598035.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus halotolerans | iPHoP-RF | 93.7 | None |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_000154985.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus infantarius | iPHoP-RF | 93.4 | None |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_900475675.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus lutetiensis | iPHoP-RF | 93.1 | None |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_000187265.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus equinus | iPHoP-RF | 92.8 | None |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_900101445.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus equinus_B | iPHoP-RF | 92.8 | None |
| NC_002737.2|provirus_1186916_1222544 | GB_GCA_000283635.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus macedonicus | iPHoP-RF | 92.4 | None |
| NC_002737.2|provirus_1186916_1222544 | GB_GCA_934196125.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp934196125 | iPHoP-RF | 92.4 | None |
| NC_002737.2|provirus_1186916_1222544 | GB_GCA_900637675.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus equi | iPHoP-RF | 92.1 | blast;62.80 |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_004843545.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus pasteurianus | iPHoP-RF | 91.8 | None |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_003337175.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus gallolyticus_B | iPHoP-RF | 91.4 | None |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_009870755.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus halichoeri | iPHoP-RF | 91.1 | None |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_002000985.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus gallolyticus | iPHoP-RF | 90.8 | None |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_000188015.2 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus ictaluri | iPHoP-RF | 90.5 | blast;62.80 |
| NC_002737.2|provirus_1186916_1222544 | RS_GCF_000188055.2 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus urinalis | iPHoP-RF | 90.5 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000960035.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus oralis_G | CRISPR | 98.6 | iPHoP-RF;97.10 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_002055535.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus pyogenes | CRISPR | 98.6 | blast;97.50 iPHoP-RF;96.10 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_002093545.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus oralis_C | CRISPR | 98.6 | iPHoP-RF;96.10 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_900636575.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus canis | CRISPR | 98.4 | iPHoP-RF;97.10 blast;96.70 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_001937065.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp001937065 | CRISPR | 98.2 | iPHoP-RF;96.70 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_902729355.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp902729355 | CRISPR | 98.1 | iPHoP-RF;95.40 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000186445.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus agalactiae | CRISPR | 97.6 | iPHoP-RF;91.40 blast;67.70 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000188035.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus pseudoporcinus | CRISPR | 97.6 | iPHoP-RF;96.40 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000220065.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp000220065 | iPHoP-RF | 97.1 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000379985.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus caballi | iPHoP-RF | 97.1 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000380105.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus orisratti | iPHoP-RF | 97.1 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000380125.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus ovis | iPHoP-RF | 97.1 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_900459225.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus dysgalactiae | blast | 96.9 | iPHoP-RF;93.10 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000423745.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus plurextorum | iPHoP-RF | 96.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_002953735.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus pluranimalium | iPHoP-RF | 96.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_006739205.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus mutans | iPHoP-RF | 96.7 | None |
| NC_002737.2|provirus_529627_569283 | GB_GCA_945876895.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp945876895 | iPHoP-RF | 96.4 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000425025.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus castoreus | iPHoP-RF | 96.4 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_002000985.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus gallolyticus | iPHoP-RF | 96.4 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_002355215.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus troglodytae | iPHoP-RF | 96.4 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_003337175.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus gallolyticus_B | iPHoP-RF | 96.4 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_900475415.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus porcinus | iPHoP-RF | 96.4 | None |
| NC_002737.2|provirus_529627_569283 | GB_GCA_900637675.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus equi | iPHoP-RF | 96.1 | blast;78.70 |
| NC_002737.2|provirus_529627_569283 | GB_GCA_934196125.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp934196125 | iPHoP-RF | 96.1 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000420785.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus hyovaginalis | iPHoP-RF | 96.1 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_004843545.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus pasteurianus | iPHoP-RF | 96.1 | None |
| NC_002737.2|provirus_529627_569283 | GB_GCA_000283635.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus macedonicus | iPHoP-RF | 95.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000423765.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus porci | iPHoP-RF | 95.7 | blast;72.00 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_003686955.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus hillyeri | iPHoP-RF | 95.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_011039275.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus hyointestinalis_A | iPHoP-RF | 95.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_012277075.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus alactolyticus | iPHoP-RF | 95.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_900459405.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus hyointestinalis | iPHoP-RF | 95.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_901542335.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus porcinus_A | iPHoP-RF | 95.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000187995.2 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus macacae | iPHoP-RF | 95.4 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000380145.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus thoraltensis | iPHoP-RF | 95.4 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_012396585.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus ovuberis | iPHoP-RF | 95.4 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_016908655.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus saliviloxodontae | iPHoP-RF | 95.4 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000188055.2 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus urinalis | iPHoP-RF | 95.1 | blast;66.30 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_001598035.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus halotolerans | iPHoP-RF | 95.1 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_009870755.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus halichoeri | iPHoP-RF | 95.1 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_024814375.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp024814375 | iPHoP-RF | 95.1 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_011421425.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus catagoni | iPHoP-RF | 94.7 | blast;66.30 |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000380085.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus merionis | iPHoP-RF | 93.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_000785785.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus uberis_A | iPHoP-RF | 93.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_003674745.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus iniae | iPHoP-RF | 93.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_900475595.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus uberis | iPHoP-RF | 93.7 | None |
| NC_002737.2|provirus_529627_569283 | RS_GCF_019794555.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis_AB | iPHoP-RF | 91.1 | None |
| NC_002737.2|provirus_777501_820593 | MGYG000003717 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;gStreptococcus;s | CRISPR | 98.4 | iPHoP-RF;96.70 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_004843545.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus pasteurianus | CRISPR | 98.4 | iPHoP-RF;94.10 |
| NC_002737.2|provirus_777501_820593 | GB_GCA_000283635.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus macedonicus | CRISPR | 98.3 | iPHoP-RF;88.50 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000186445.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus agalactiae | CRISPR | 98.3 | iPHoP-RF;80.30 blast;76.70 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_002055535.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus pyogenes | blast | 98.0 | iPHoP-RF;93.70 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_900636575.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus canis | CRISPR | 98.0 | blast;96.50 iPHoP-RF;95.40 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_010120595.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus thermophilus | CRISPR | 97.9 | iPHoP-RF;96.10 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000220065.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp000220065 | iPHoP-RF | 97.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_001697145.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus anginosus_C | iPHoP-RF | 97.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_009717815.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus parasanguinis_F | iPHoP-RF | 97.1 | blast;83.70 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_016648925.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp900766505 | iPHoP-RF | 97.1 | blast;83.70 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_900636475.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus anginosus | iPHoP-RF | 97.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_902167705.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus constellatus_A | iPHoP-RF | 97.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_943193075.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus parasanguinis_E | iPHoP-RF | 97.1 | blast;83.70 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_900459225.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus dysgalactiae | blast | 96.9 | iPHoP-RF;95.10 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000380125.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus ovis | iPHoP-RF | 96.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000423765.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus porci | iPHoP-RF | 96.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_001598035.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus halotolerans | iPHoP-RF | 96.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_023109675.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus parasanguinis_I | iPHoP-RF | 96.7 | blast;83.70 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_023167545.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus constellatus | iPHoP-RF | 96.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000423745.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus plurextorum | iPHoP-RF | 96.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_003686955.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus hillyeri | iPHoP-RF | 96.4 | blast;70.10 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_011039275.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus hyointestinalis_A | iPHoP-RF | 96.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000380025.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus entericus | iPHoP-RF | 96.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000380145.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus thoraltensis | iPHoP-RF | 96.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_900475675.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus lutetiensis | iPHoP-RF | 96.1 | blast;68.90 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000154985.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus infantarius | iPHoP-RF | 95.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000420785.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus hyovaginalis | iPHoP-RF | 95.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000425025.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus castoreus | iPHoP-RF | 95.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_002000985.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus gallolyticus | iPHoP-RF | 95.4 | blast;68.90 |
| NC_002737.2|provirus_777501_820593 | GB_GCA_000440235.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis_F | iPHoP-RF | 95.1 | None |
| NC_002737.2|provirus_777501_820593 | GB_GCA_934196125.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp934196125 | iPHoP-RF | 95.1 | None |
| NC_002737.2|provirus_777501_820593 | GB_GCA_002831545.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis_P | iPHoP-RF | 94.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000785515.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus salivarius | iPHoP-RF | 94.7 | blast;68.90 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_003337175.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus gallolyticus_B | iPHoP-RF | 94.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_900101445.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus equinus_B | iPHoP-RF | 94.7 | None |
| NC_002737.2|provirus_777501_820593 | GB_GCA_945876895.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp945876895 | iPHoP-RF | 94.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_002760245.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis_I | iPHoP-RF | 94.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_002953735.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus pluranimalium | iPHoP-RF | 94.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000380105.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus orisratti | iPHoP-RF | 94.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_902702775.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis_W | iPHoP-RF | 94.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_902729355.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp902729355 | iPHoP-RF | 94.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000376985.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus henryi | iPHoP-RF | 93.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_012396585.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus ovuberis | iPHoP-RF | 93.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_016743335.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis_Y | iPHoP-RF | 93.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_900459405.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus hyointestinalis | iPHoP-RF | 93.7 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000294495.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis | iPHoP-RF | 93.4 | blast;65.20 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000380085.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus merionis | iPHoP-RF | 93.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_001302265.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus phocae | iPHoP-RF | 93.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_016908655.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus saliviloxodontae | iPHoP-RF | 93.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_019794555.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis_AB | iPHoP-RF | 93.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_021654455.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus parasuis | iPHoP-RF | 93.4 | None |
| NC_002737.2|provirus_777501_820593 | GB_GCA_900637675.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus equi | iPHoP-RF | 93.1 | blast;70.70 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000440115.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis_L | iPHoP-RF | 93.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_003595525.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus respiraculi | iPHoP-RF | 93.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_015594605.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp015594605 | iPHoP-RF | 92.8 | blast;68.90 |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000188055.2 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus urinalis | iPHoP-RF | 92.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_012277075.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus alactolyticus | iPHoP-RF | 92.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_001578805.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp001578805 | iPHoP-RF | 91.8 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000785785.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus uberis_A | iPHoP-RF | 91.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_022354845.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus suis_AA | iPHoP-RF | 91.4 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_900475595.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus uberis | iPHoP-RF | 91.1 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_003674745.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus iniae | iPHoP-RF | 90.8 | None |
| NC_002737.2|provirus_777501_820593 | RS_GCF_000188035.1 | d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus pseudoporcinus | iPHoP-RF | 90.5 | None |
2.2.6 AMG Predictions
Prediction of auxiliary metabolic genes in the prophage contigs.
| protein | scaffold | amg_ko | amg_ko_name | pfam | pfam_name |
|---|---|---|---|---|---|
| NC_002737.2|provirus_777501_820593_1 | NC_002737.2|provirus_777501_820593 | K01710 | E4.2.1.46, rfbB, rffG; dTDP-glucose 4,6-dehydratase [EC:4.2.1.46] | PF16363.5 | GDP-mannose 4,6 dehydratase |
2.3 NC_003450
2.3.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Actinomycetota;c__Actinomycetes;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium;s__Corynebacterium glutamicum |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 3309401 | 100 | 0.29 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_003450.3_RM_Type_IIG_2_7 | RM | RM_Type_IIG_2 | NC_003450.3_730 | NC_003450.3_730 | NC_003450.3_730 | 1 | RM_Type_IIG__Type_IIG_FAM_0.einsi_trimmed |
| NC_003450.3_Uzume_1 | Uzume | Uzume | NC_003450.3_1364 | NC_003450.3_1364 | NC_003450.3_1364 | 1 | Uzume__UzuA |
| NC_003450.3_RM_Type_II_4 | RM | RM_Type_II | NC_003450.3_1762 | NC_003450.3_1764 | NC_003450.3_1762,NC_003450.3_1763,NC_003450.3_1764 | 3 | RM_Type_II__Type_II_MTases_FAM_0,RM_Type_II__Type_II_REase29,RM_Type_II__Type_II_REase38 |
| NC_003450.3_Wadjet_I_3 | Wadjet | Wadjet_I | NC_003450.3_2782 | NC_003450.3_2785 | NC_003450.3_2782,NC_003450.3_2783,NC_003450.3_2784,NC_003450.3_2785 | 4 | Wadjet__JetA_I,Wadjet__JetB_I,Wadjet__JetC_I,Wadjet__JetD_I |
| NC_003450.3_RM_Type_IIG_6 | RM | RM_Type_IIG | NC_003450.3_3041 | NC_003450.3_3041 | NC_003450.3_3041 | 1 | RM_Type_IIG__Type_IIG_FAM_2.einsi_trimmed |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_003450.3|provirus_1777332_1987821 | 210490 | 195 | 13 | High-quality | High-quality | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;;Herelleviridae | Provirus | 1777332-1987821 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.3.2 Prophages
Select prophage to show:
2.3.2.1 Phage ID: NC_003450.3|provirus_1777332_1987821
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_003450.3|provirus_1777332_1987821_1641 | 318 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1642 | 126 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1643 | 1410 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1644 | 564 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1645 | 174 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1646 | 564 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1647 | 870 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1648 | 2583 | GENOMAD.055261.VV | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1649 | 1116 | GENOMAD.055261.VV | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1650 | 1926 | GENOMAD.100223.VV | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1651 | 486 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1652 | 192 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1653 | 228 | GENOMAD.189071.VV | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1654 | 432 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1655 | 600 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1656 | 1002 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1657 | 156 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1658 | 1110 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1659 | 423 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1660 | 561 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1661 | 867 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1662 | 423 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1663 | 738 | GENOMAD.207798.PC | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1664 | 252 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1665 | 228 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1666 | 897 | GENOMAD.222424.VP | PF14243 | NA |
| NC_003450.3|provirus_1777332_1987821_1667 | 141 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1668 | 132 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1669 | 438 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1670 | 600 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1671 | 426 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1672 | 534 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1673 | 336 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1674 | 468 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1675 | 615 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1676 | 915 | GENOMAD.138073.VV | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1677 | 156 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1678 | 459 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1679 | 684 | GENOMAD.094320.VV | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1680 | 288 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1681 | 336 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1682 | 615 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1683 | 996 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1684 | 378 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1685 | 480 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1686 | 729 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1687 | 741 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1688 | 768 | GENOMAD.215962.PC | PF00110 | wnt family |
| NC_003450.3|provirus_1777332_1987821_1689 | 459 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1690 | 189 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1691 | 675 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1692 | 420 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1693 | 306 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1694 | 372 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1695 | 210 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1696 | 2205 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1697 | 1698 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1698 | 222 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1699 | 432 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1700 | 897 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1701 | 297 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1702 | 216 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1703 | 1302 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1704 | 1863 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1705 | 783 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1706 | 1776 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1707 | 3792 | GENOMAD.224017.VP | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1708 | 450 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1709 | 420 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1710 | 1842 | GENOMAD.007224.VV | PF00176;K14440;COG1061;TIGR04095 | Superfamily II DNA or RNA helicase |
| NC_003450.3|provirus_1777332_1987821_1711 | 378 | GENOMAD.222568.VP | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1712 | 339 | GENOMAD.168436.VP | PF14359;COG3613;TIGR03646 | Nucleoside 2-deoxyribosyltransferase |
| NC_003450.3|provirus_1777332_1987821_1713 | 351 | GENOMAD.224423.VP | PF11774 | Lsr2 |
| NC_003450.3|provirus_1777332_1987821_1714 | 621 | GENOMAD.221383.VP | PF07443 | HepA-related protein (HARP) |
| NC_003450.3|provirus_1777332_1987821_1715 | 540 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1716 | 531 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1717 | 750 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1718 | 189 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1719 | 336 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1720 | 579 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1721 | 1224 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1722 | 1281 | GENOMAD.226101.VP | PF08800;COG4983 | Uncharacterized protein, contains Primase-polymerase (Primpol) domain |
| NC_003450.3|provirus_1777332_1987821_1723 | 576 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1724 | 183 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1725 | 1260 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1726 | 1827 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1727 | 1968 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1728 | 477 | GENOMAD.159467.VP | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1729 | 3768 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1730 | 378 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1731 | 381 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1732 | 468 | GENOMAD.218177.VP | PF06892;K22299;TIGR00673;COG5606 | cyanase |
| NC_003450.3|provirus_1777332_1987821_1733 | 267 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1734 | 780 | GENOMAD.162261.CP | PF16262;K13355;COG4119;TIGR02150 | Predicted NTP pyrophosphohydrolase, NUDIX family |
| NC_003450.3|provirus_1777332_1987821_1735 | 705 | GENOMAD.148006.VV | PF04275;K19797;TIGR01223;COG1102 | phosphomevalonate kinase, animal type |
| NC_003450.3|provirus_1777332_1987821_1736 | 228 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1737 | 2160 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1738 | 234 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1739 | 6510 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1740 | 1092 | GENOMAD.136632.VV | PF00145;TIGR00675;K00558;COG0270 | DNA-methyltransferase (dcm) |
| NC_003450.3|provirus_1777332_1987821_1741 | 1077 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1742 | 1899 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1743 | 1524 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1744 | 672 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1745 | 1821 | GENOMAD.218864.VV | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1746 | 189 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1747 | 354 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1748 | 1218 | GENOMAD.189350.VP | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1749 | 1674 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1750 | 1209 | GENOMAD.080614.VV | PF08722 | NA |
| NC_003450.3|provirus_1777332_1987821_1751 | 1248 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1752 | 2496 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1753 | 1788 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1754 | 579 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1755 | 1116 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1756 | 849 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1757 | 882 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1758 | 2769 | GENOMAD.161127.PV | PF18555 | MobL relaxases |
| NC_003450.3|provirus_1777332_1987821_1759 | 603 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1760 | 1254 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1761 | 699 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1762 | 717 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1763 | 1011 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1764 | 1662 | GENOMAD.214492.VP | PF21822 | Phage tail assembly chaperone protein, TAC |
| NC_003450.3|provirus_1777332_1987821_1765 | 1464 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1766 | 360 | GENOMAD.222537.PV | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1767 | 1512 | GENOMAD.179757.VP | PF01541;COG2827;TIGR01453 | Predicted endonuclease, GIY-YIG superfamily |
| NC_003450.3|provirus_1777332_1987821_1768 | 363 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1769 | 225 | GENOMAD.098687.PP | PF09954 | NA |
| NC_003450.3|provirus_1777332_1987821_1770 | 294 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1771 | 510 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1772 | 762 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1773 | 552 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1774 | 933 | GENOMAD.225221.VP | PF12686 | NA |
| NC_003450.3|provirus_1777332_1987821_1775 | 4467 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1776 | 582 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1777 | 936 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1778 | 138 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1779 | 378 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1780 | 1824 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1781 | 204 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1782 | 462 | GENOMAD.223777.PV | PF02556;TIGR00809;COG1952;K03071 | protein-export chaperone SecB |
| NC_003450.3|provirus_1777332_1987821_1783 | 360 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1784 | 408 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1785 | 732 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1786 | 945 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1787 | 561 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1788 | 213 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1789 | 537 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1790 | 537 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1791 | 945 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1792 | 591 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1793 | 447 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1794 | 702 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1795 | 297 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1796 | 219 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1797 | 135 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1798 | 777 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1799 | 831 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1800 | 276 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1801 | 381 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1802 | 432 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1803 | 1584 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1804 | 2433 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1805 | 870 | GENOMAD.207947.PV | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1806 | 2280 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1807 | 2088 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1808 | 894 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1809 | 435 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1810 | 747 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1811 | 1857 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1812 | 294 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1813 | 1221 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1814 | 1179 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1815 | 333 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1816 | 639 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1817 | 120 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1818 | 144 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1819 | 567 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1820 | 1455 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1821 | 462 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1822 | 1143 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1823 | 150 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1824 | 1422 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1825 | 594 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1826 | 399 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1827 | 240 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1828 | 627 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1829 | 582 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1830 | 465 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1831 | 510 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1832 | 561 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1833 | 336 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1834 | 483 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1835 | 573 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1836 | 915 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1837 | 696 | GENOMAD.178028.VP | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1838 | 369 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1839 | 645 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1840 | 366 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1841 | 276 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1842 | 267 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1843 | 237 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1844 | 237 | GENOMAD.082277.VV | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1845 | 276 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1846 | 1086 | NA | NA | NA |
| NC_003450.3|provirus_1777332_1987821_1847 | 318 | NA | NA | NA |
2.3.3 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_003450.3|provirus_1777332_1987821 | RS_GCF_000011325.1 | d__Bacteria;p__Actinomycetota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium;s__Corynebacterium glutamicum | blast | 96.8 | iPHoP-RF;52.80 |
| NC_003450.3|provirus_1777332_1987821 | RS_GCF_002355155.1 | d__Bacteria;p__Actinomycetota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium;s__Corynebacterium suranareeae | blast | 96.3 | None |
| NC_003450.3|provirus_1777332_1987821 | RS_GCF_001643015.1 | d__Bacteria;p__Actinomycetota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium;s__Corynebacterium crudilactis | blast | 95.9 | None |
2.4 NC_008261
2.4.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Bacillota_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Sarcina;s__Sarcina perfringens |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 3256683 | 100 | 0.14 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_008261.1_RM_Type_II_5 | RM | RM_Type_II | NC_008261.1_127 | NC_008261.1_128 | NC_008261.1_127,NC_008261.1_128 | 2 | RM_Type_II__Type_II_MTases_FAM_0,RM_Type_II__Type_II_REase18 |
| NC_008261.1_RM_Type_III_7 | RM | RM_Type_III | NC_008261.1_340 | NC_008261.1_341 | NC_008261.1_340,NC_008261.1_341 | 2 | RM_Type_III__Type_III_MTases_FAM_0,RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed |
| NC_008261.1_RM_Type_IV_8 | RM | RM_Type_IV | NC_008261.1_962 | NC_008261.1_963 | NC_008261.1_962,NC_008261.1_963 | 2 | RM_Type_IV__FAM_1,RM_Type_IV__FAM_2 |
| NC_008261.1_DRT_2_1 | DRT | DRT_2 | NC_008261.1_983 | NC_008261.1_983 | NC_008261.1_983 | 1 | DRT2__DRT2 |
| NC_008261.1_RM_Type_II_6 | RM | RM_Type_II | NC_008261.1_985 | NC_008261.1_987 | NC_008261.1_985,NC_008261.1_986,NC_008261.1_987 | 3 | RM_Type_II__Type_II_MTases_FAM_0,RM_Type_II__Type_II_MTases_FAM_22,RM_Type_II__Type_II_REase34 |
| NC_008261.1_PD-Lambda-5_2 | PD-Lambda-5 | PD-Lambda-5 | NC_008261.1_1563 | NC_008261.1_1564 | NC_008261.1_1563,NC_008261.1_1564 | 2 | PD-Lambda-5__PD-Lambda-5_A,PD-Lambda-5__PD-Lambda-5_B |
| NC_008261.1_RM_Type_I_4 | RM | RM_Type_I | NC_008261.1_2512 | NC_008261.1_2515 | NC_008261.1_2512,NC_008261.1_2514,NC_008261.1_2515 | 3 | RM__Type_I_MTases_FAM_0,RM__Type_I_REases_FAM_0.einsi_trimmed,RM__Type_I_S_51 |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_008261.1|provirus_1084498_1127691 | 43194 | 55 | 25 | High-quality | High-quality | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1084498-1127691 |
| NC_008261.1|provirus_1784095_1821197 | 37103 | 44 | 21 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1784095-1821197 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.4.2 Prophages
Select prophage to show:
2.4.2.1 Phage ID: NC_008261.1|provirus_1084498_1127691
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_008261.1|provirus_1084498_1127691_890 | 489 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_891 | 1761 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_892 | 459 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_893 | 723 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_894 | 219 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_895 | 1065 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_896 | 465 | GENOMAD.123021.VV | PF06114;COG2856 | IrrE N-terminal-like domain |
| NC_008261.1|provirus_1084498_1127691_897 | 504 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_898 | 237 | GENOMAD.069056.VV | PF06892;TIGR00673;COG1974;K07727 | cyanase |
| NC_008261.1|provirus_1084498_1127691_899 | 732 | GENOMAD.119058.VP | PF10552 | ORF6C domain |
| NC_008261.1|provirus_1084498_1127691_900 | 255 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_901 | 672 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_902 | 303 | GENOMAD.061044.VV | PF13411;COG4220;TIGR02054 | Phage DNA packaging protein, Nu1 subunit of terminase |
| NC_008261.1|provirus_1084498_1127691_903 | 180 | GENOMAD.164182.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_904 | 183 | GENOMAD.117872.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_905 | 108 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_906 | 186 | GENOMAD.172161.VC | NA | NA |
| NC_008261.1|provirus_1084498_1127691_907 | 912 | GENOMAD.077205.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_908 | 870 | GENOMAD.100145.VP | PF03837;COG3723;K07455;TIGR00616 | Recombinational DNA repair protein RecT |
| NC_008261.1|provirus_1084498_1127691_909 | 714 | GENOMAD.178290.VP | PF04492;TIGR01714;COG2188 | Bacteriophage replication protein O |
| NC_008261.1|provirus_1084498_1127691_910 | 174 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_911 | 387 | GENOMAD.177634.VP | PF05866;COG4570 | Endodeoxyribonuclease RusA |
| NC_008261.1|provirus_1084498_1127691_912 | 648 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_913 | 474 | GENOMAD.062141.VV | PF05263;TIGR01636 | phage transcriptional activator, RinA family |
| NC_008261.1|provirus_1084498_1127691_914 | 1176 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_915 | 468 | GENOMAD.026460.VV | PF03592;COG3728;K07474 | Phage terminase, small subunit |
| NC_008261.1|provirus_1084498_1127691_916 | 1365 | GENOMAD.017640.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_917 | 768 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_918 | 1521 | GENOMAD.016130.VV | PF05133;TIGR01542 | phage portal protein, putative, A118 family |
| NC_008261.1|provirus_1084498_1127691_919 | 1638 | GENOMAD.015690.VV | PF06152;TIGR01641 | Phage minor capsid protein 2 |
| NC_008261.1|provirus_1084498_1127691_920 | 225 | GENOMAD.093339.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_921 | 618 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_922 | 606 | GENOMAD.041104.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_923 | 906 | GENOMAD.075076.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_924 | 270 | GENOMAD.050526.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_925 | 363 | GENOMAD.020431.VV | PF11436 | Putative DnaT-like ssDNA binding protein |
| NC_008261.1|provirus_1084498_1127691_926 | 327 | GENOMAD.024076.VV | PF10665 | Minor capsid protein |
| NC_008261.1|provirus_1084498_1127691_927 | 384 | GENOMAD.019595.VV | PF11114 | Minor capsid protein |
| NC_008261.1|provirus_1084498_1127691_928 | 387 | GENOMAD.028696.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_929 | 459 | GENOMAD.019307.VV | PF16461;COG5437 | Predicted secreted protein |
| NC_008261.1|provirus_1084498_1127691_930 | 369 | GENOMAD.052890.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_931 | 363 | GENOMAD.015650.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_932 | 3213 | GENOMAD.171590.VP | NA | NA |
| NC_008261.1|provirus_1084498_1127691_933 | 354 | GENOMAD.012935.VV | PF20458 | NA |
| NC_008261.1|provirus_1084498_1127691_934 | 267 | GENOMAD.163907.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_935 | 381 | GENOMAD.016019.VV | PF07761 | NA |
| NC_008261.1|provirus_1084498_1127691_936 | 5109 | GENOMAD.141397.VP | PF06605;PF00149;TIGR01665;K01517;COG4926 | phage minor structural protein, N-terminal region |
| NC_008261.1|provirus_1084498_1127691_937 | 249 | GENOMAD.113645.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_938 | 417 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_939 | 417 | GENOMAD.224084.VP | NA | NA |
| NC_008261.1|provirus_1084498_1127691_940 | 1029 | GENOMAD.169358.VC | PF06725;PF18348;COG3584;K11060;TIGR04211 | 3D (Asp-Asp-Asp) domain |
| NC_008261.1|provirus_1084498_1127691_941 | 663 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_942 | 1089 | GENOMAD.129207.VV | NA | NA |
| NC_008261.1|provirus_1084498_1127691_943 | 342 | NA | NA | NA |
| NC_008261.1|provirus_1084498_1127691_944 | 726 | GENOMAD.129093.VV | NA | NA |
2.4.2.2 Phage ID: NC_008261.1|provirus_1784095_1821197
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_008261.1|provirus_1784095_1821197_1520 | 486 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1521 | 303 | GENOMAD.099786.VV | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1522 | 1029 | GENOMAD.169358.VC | PF06725;PF18348;COG3584;K11060;TIGR04211 | 3D (Asp-Asp-Asp) domain |
| NC_008261.1|provirus_1784095_1821197_1523 | 483 | GENOMAD.222318.VP | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1524 | 234 | GENOMAD.080405.VV | PF10779 | Haemolysin XhlA |
| NC_008261.1|provirus_1784095_1821197_1525 | 186 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1526 | 2499 | GENOMAD.033703.VV | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1527 | 1881 | GENOMAD.082024.VV | PF10651;PF15425 | BppU N-terminal domain |
| NC_008261.1|provirus_1784095_1821197_1528 | 3060 | GENOMAD.004842.VV | PF06605;PF18994;COG4926;TIGR01665 | Phage-related protein |
| NC_008261.1|provirus_1784095_1821197_1529 | 711 | GENOMAD.004006.VV | PF20195;COG4722;TIGR01633 | Phage-related protein |
| NC_008261.1|provirus_1784095_1821197_1530 | 3255 | GENOMAD.116638.VP | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1531 | 354 | GENOMAD.080513.VV | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1532 | 318 | GENOMAD.080540.VV | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1533 | 603 | GENOMAD.013991.VV | PF04630;TIGR01603 | phage major tail protein, phi13 family |
| NC_008261.1|provirus_1784095_1821197_1534 | 348 | GENOMAD.056191.VV | PF05657 | NA |
| NC_008261.1|provirus_1784095_1821197_1535 | 438 | GENOMAD.072939.VV | TIGR01725;COG5005 | phage protein, HK97 gp10 family |
| NC_008261.1|provirus_1784095_1821197_1536 | 330 | GENOMAD.078312.VV | PF05521;TIGR01563;COG5614 | phage head-tail adaptor, putative, SPP1 family |
| NC_008261.1|provirus_1784095_1821197_1537 | 279 | GENOMAD.034954.VV | PF05135;TIGR01560 | Phage gp6-like head-tail connector protein |
| NC_008261.1|provirus_1784095_1821197_1538 | 1185 | GENOMAD.014413.VV | PF05065;TIGR01554;COG4653 | phage major capsid protein, HK97 family |
| NC_008261.1|provirus_1784095_1821197_1539 | 606 | GENOMAD.126260.VV | PF04586;COG3740;K06904;TIGR01543 | Phage head maturation protease |
| NC_008261.1|provirus_1784095_1821197_1540 | 1248 | GENOMAD.126260.VV | PF04586;COG3740;K06904;TIGR01543 | Phage head maturation protease |
| NC_008261.1|provirus_1784095_1821197_1541 | 1740 | GENOMAD.192500.VP | PF18352;COG4626 | Phage terminase-like protein, large subunit, contains N-terminal HTH domain |
| NC_008261.1|provirus_1784095_1821197_1542 | 513 | GENOMAD.136127.VP | PF05119;COG3747;TIGR01558 | Phage terminase, small subunit |
| NC_008261.1|provirus_1784095_1821197_1543 | 822 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1544 | 549 | GENOMAD.027124.VV | PF07104 | NA |
| NC_008261.1|provirus_1784095_1821197_1545 | 354 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1546 | 207 | GENOMAD.117627.VV | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1547 | 462 | GENOMAD.062141.VV | PF05263;TIGR01636 | phage transcriptional activator, RinA family |
| NC_008261.1|provirus_1784095_1821197_1548 | 390 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1549 | 147 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1550 | 1284 | GENOMAD.068048.VV | PF20307;TIGR03600;K02314;COG0305 | phage replicative helicase, DnaB family, HK022 subfamily |
| NC_008261.1|provirus_1784095_1821197_1551 | 741 | GENOMAD.096239.VV | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1552 | 159 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1553 | 180 | GENOMAD.148814.VV | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1554 | 231 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1555 | 498 | GENOMAD.142555.VV | PF06892;TIGR02612;K22299;COG3620 | Phage regulatory protein CII (CP76) |
| NC_008261.1|provirus_1784095_1821197_1556 | 189 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1557 | 345 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1558 | 1590 | GENOMAD.219971.CV | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1559 | 855 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1560 | 498 | GENOMAD.123021.VV | PF06114;COG2856 | IrrE N-terminal-like domain |
| NC_008261.1|provirus_1784095_1821197_1561 | 1509 | GENOMAD.169508.VP | PF04708;PF13262;COG1961;K14060 | Site-specific DNA recombinase related to the DNA invertase Pin |
| NC_008261.1|provirus_1784095_1821197_1562 | 339 | NA | NA | NA |
| NC_008261.1|provirus_1784095_1821197_1563 | 378 | NA | NA | NA |
2.4.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_008261.1|provirus_1084498_1127691 | sequence_000000.fasta.fasta | 1_0 | 0.05 | average | ANImf | 1 |
| NC_008261.1|provirus_1784095_1821197 | sequence_000001.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
Primary clustering plot
2.4.4 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_008261.1|provirus_1084498_1127691 | RS_GCF_000013285.1 | d__Bacteria;p__Bacillota_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Sarcina;s__Sarcina perfringens | blast | 98.2 | iPHoP-RF;75.00 |
| NC_008261.1|provirus_1784095_1821197 | RS_GCF_000013285.1 | d__Bacteria;p__Bacillota_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Sarcina;s__Sarcina perfringens | blast | 96.9 | CRISPR;93.40 iPHoP-RF;85.40 |
2.5 NC_009012
2.5.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Bacillota_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium;s__Hungateiclostridium thermocellum |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 3843301 | 100 | 1.09 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_009012.1_RM_Type_III_8 | RM | RM_Type_III | NC_009012.1_532 | NC_009012.1_533 | NC_009012.1_532,NC_009012.1_533 | 2 | RM_Type_III__Type_III_MTases_FAM_0,RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed |
| NC_009012.1_SEFIR_3 | SEFIR | SEFIR | NC_009012.1_1184 | NC_009012.1_1184 | NC_009012.1_1184 | 1 | SEFIR__bSEFIR |
| NC_009012.1_RloC_2 | RloC | RloC | NC_009012.1_1211 | NC_009012.1_1211 | NC_009012.1_1211 | 1 | RloC__RloC |
| NC_009012.1_RM_Type_II_4 | RM | RM_Type_II | NC_009012.1_1577 | NC_009012.1_1579 | NC_009012.1_1577,NC_009012.1_1578,NC_009012.1_1579 | 3 | RM_Type_II__Type_II_MTases_FAM_38,RM_Type_II__Type_II_MTases_FAM_4,RM_Type_II__Type_II_REase32 |
| NC_009012.1_AbiU_1 | AbiU | AbiU | NC_009012.1_1698 | NC_009012.1_1698 | NC_009012.1_1698 | 1 | AbiU__AbiU |
| NC_009012.1_RM_Type_II_5 | RM | RM_Type_II | NC_009012.1_1826 | NC_009012.1_1827 | NC_009012.1_1826,NC_009012.1_1827 | 2 | RM_Type_II__Type_II_MTases_FAM_16,RM_Type_II__Type_II_REase01 |
| NC_009012.1_CAS_Class1-Subtype-III-D_11 | Cas | CAS_Class1-Subtype-III-D | NC_009012.1_2140 | NC_009012.1_2149 | NC_009012.1_2140,NC_009012.1_2141,NC_009012.1_2142,NC_009012.1_2143,NC_009012.1_2144,NC_009012.1_2145,NC_009012.1_2146,NC_009012.1_2147,NC_009012.1_2149 | 9 | cas10_III-D_3,csm2gr11_III-D_6,csm2gr11_III-D_7,csm3gr7_III-A_III-D_2,csm3gr7_III_1,csm3gr7_III_1,csm3gr7_III_IV,csx10gr5_III-D_2,csx1_III_9 |
| NC_009012.1_CAS_Class1-Subtype-I-B_9 | Cas | CAS_Class1-Subtype-I-B | NC_009012.1_2404 | NC_009012.1_2411 | NC_009012.1_2404,NC_009012.1_2405,NC_009012.1_2406,NC_009012.1_2407,NC_009012.1_2408,NC_009012.1_2409,NC_009012.1_2410,NC_009012.1_2411 | 8 | cas1_I_II_III_IV_V_VI_7,cas2_I_II_III_IV_V_VI_3,cas3_I_5,cas4_I_II_III_IV_V_VI_6,cas5_I-B_1,cas6_I_II_III_IV_V_VI_14,cas7_I-B_6,cas8b1_I-B_12 |
| NC_009012.1_RM_Type_II_6 | RM | RM_Type_II | NC_009012.1_2429 | NC_009012.1_2430 | NC_009012.1_2429,NC_009012.1_2430 | 2 | RM_Type_II__Type_II_MTases_FAM_2,RM_Type_II__Type_II_REase30 |
| NC_009012.1_RM_Type_II_7 | RM | RM_Type_II | NC_009012.1_2587 | NC_009012.1_2588 | NC_009012.1_2587,NC_009012.1_2588 | 2 | RM_Type_II__Type_II_MTases_FAM_4,RM_Type_II__Type_II_REase07 |
| NC_009012.1_CAS_Class1-Subtype-I-B_10 | Cas | CAS_Class1-Subtype-I-B | NC_009012.1_3357 | NC_009012.1_3361 | NC_009012.1_3357,NC_009012.1_3358,NC_009012.1_3359,NC_009012.1_3360,NC_009012.1_3361 | 5 | cas3_I_5,cas5_I-B_17,cas6_I_II_III_IV_V_VI_12,cas7_I-B_8,cas8b1_I-B_4 |
| NC_009012.1_CAS_Class1-Subtype-III-D_12 | Cas | CAS_Class1-Subtype-III-D | NC_009012.1_3361 | NC_009012.1_3378 | NC_009012.1_3361,NC_009012.1_3365,NC_009012.1_3366,NC_009012.1_3367,NC_009012.1_3368,NC_009012.1_3369,NC_009012.1_3370,NC_009012.1_3372,NC_009012.1_3375,NC_009012.1_3376,NC_009012.1_3377,NC_009012.1_3378 | 12 | cas10_III-D_3,cas1_I_II_III_IV_V_VI_10,cas2_I_II_III_IV_V_VI_3,cas4_I_II_III_IV_V_VI_1,cas6_I_II_III_IV_V_VI_12,csm3gr7_III-D_2,csm3gr7_III-D_3,csm3gr7_III_1,csx10gr5_III-D_3,csx19_III-D_11,csx1_III_21,csx1_III_9 |
| NC_009012.1_CAS_Class1-Subtype-III-D_12 | Cas | CAS_Class1-Subtype-III-D | NC_009012.1_3361 | NC_009012.1_3378 | NC_009012.1_3361,NC_009012.1_3365,NC_009012.1_3366,NC_009012.1_3367,NC_009012.1_3368,NC_009012.1_3369,NC_009012.1_3370,NC_009012.1_3372,NC_009012.1_3375,NC_009012.1_3376,NC_009012.1_3377,NC_009012.1_3378 | 12 | cas10_III-D_3,cas1_I_II_III_IV_V_VI_10,cas2_I_II_III_IV_V_VI_3,cas4_I_II_III_IV_V_VI_1,cas6_I_II_III_IV_V_VI_12,csm3gr7_III-D_2,csm3gr7_III-D_3,csm3gr7_III_1,csx10gr5_III-D_3,csx19_III-D_11,csx1_III_21,csx1_III_9 |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_009012.1|provirus_1938476_1983993 | 45518 | 52 | 23 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1938476-1983993 |
| NC_009012.1|provirus_2921887_2969530 | 47644 | 65 | 28 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 2921887-2969530 |
| NC_009012.1|provirus_2022140_2067593 | 45454 | 54 | 21 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 2022140-2067593 |
| NC_009012.1|provirus_3339258_3389798 | 50541 | 55 | 6 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 3339258-3389798 |
| NC_009012.1|provirus_2330336_2378640 | 48305 | 46 | 3 | Low-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 2330336-2378640 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.5.2 Prophages
Select prophage to show:
2.5.2.1 Phage ID: NC_009012.1|provirus_1938476_1983993
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_009012.1|provirus_1938476_1983993_1694 | 492 | NA | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1695 | 1569 | GENOMAD.097162.VV | PF20307;TIGR03600;COG0305;K18947 | phage replicative helicase, DnaB family, HK022 subfamily |
| NC_009012.1|provirus_1938476_1983993_1696 | 219 | GENOMAD.180442.VC | PF20612 | SHOCT domain |
| NC_009012.1|provirus_1938476_1983993_1697 | 1005 | GENOMAD.215835.VV | PF01510;COG5632;K11066 | N-acetylmuramoyl-L-alanine amidase CwlA |
| NC_009012.1|provirus_1938476_1983993_1698 | 420 | GENOMAD.083633.VV | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1699 | 2469 | GENOMAD.116546.VV | PF06605;TIGR01665;COG4926 | phage minor structural protein, N-terminal region |
| NC_009012.1|provirus_1938476_1983993_1700 | 576 | GENOMAD.066153.VV | PF06605;TIGR01665;COG4926 | phage minor structural protein, N-terminal region |
| NC_009012.1|provirus_1938476_1983993_1701 | 195 | GENOMAD.089015.VV | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1702 | 2523 | GENOMAD.116546.VV | PF06605;TIGR01665;COG4926 | phage minor structural protein, N-terminal region |
| NC_009012.1|provirus_1938476_1983993_1703 | 774 | GENOMAD.116614.VV | PF20195;COG4722;TIGR01633 | Phage-related protein |
| NC_009012.1|provirus_1938476_1983993_1704 | 2289 | GENOMAD.036973.VV | K02334;COG4722 | Phage-related protein |
| NC_009012.1|provirus_1938476_1983993_1705 | 273 | NA | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1706 | 405 | NA | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1707 | 192 | GENOMAD.223693.VP | PF09550;TIGR02216 | Phage tail assembly chaperone protein, TAC |
| NC_009012.1|provirus_1938476_1983993_1708 | 384 | GENOMAD.166825.VP | PF11836 | Phage tail tube protein, GTA-gp10 |
| NC_009012.1|provirus_1938476_1983993_1709 | 597 | GENOMAD.005050.VV | PF04630;TIGR01603 | phage major tail protein, phi13 family |
| NC_009012.1|provirus_1938476_1983993_1710 | 345 | GENOMAD.077616.VV | PF05657 | NA |
| NC_009012.1|provirus_1938476_1983993_1711 | 432 | GENOMAD.032585.VV | PF11114;COG5005;TIGR01725 | Mu-like prophage protein gpG |
| NC_009012.1|provirus_1938476_1983993_1712 | 336 | GENOMAD.040271.VV | PF05521;COG5614;TIGR01563 | Bacteriophage head-tail adaptor |
| NC_009012.1|provirus_1938476_1983993_1713 | 309 | GENOMAD.028909.VV | PF05135;TIGR01560 | Phage gp6-like head-tail connector protein |
| NC_009012.1|provirus_1938476_1983993_1714 | 1203 | GENOMAD.168658.VV | PF05065;PF04586;PF12518;COG4653;TIGR01554;K06904 | Predicted phage phi-C31 gp36 major capsid-like protein |
| NC_009012.1|provirus_1938476_1983993_1715 | 729 | GENOMAD.028909.VV | PF05135;TIGR01560 | Phage gp6-like head-tail connector protein |
| NC_009012.1|provirus_1938476_1983993_1716 | 1323 | GENOMAD.179073.VP | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1717 | 1785 | NA | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1718 | 1230 | GENOMAD.181434.VP | PF20441 | Terminase large subunit, endonuclease domain |
| NC_009012.1|provirus_1938476_1983993_1719 | 336 | NA | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1720 | 195 | GENOMAD.140940.VV | PF16468 | NA |
| NC_009012.1|provirus_1938476_1983993_1721 | 468 | GENOMAD.191984.VP | PF07128 | NA |
| NC_009012.1|provirus_1938476_1983993_1722 | 900 | GENOMAD.105515.VV | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1723 | 231 | NA | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1724 | 693 | GENOMAD.105515.VV | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1725 | 1254 | GENOMAD.208446.VP | PF01555;COG4725;K13581 | N6-adenosine-specific RNA methylase IME4 |
| NC_009012.1|provirus_1938476_1983993_1726 | 1299 | GENOMAD.005053.VV | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1727 | 183 | GENOMAD.195270.VP | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1728 | 552 | GENOMAD.098194.VV | PF05119;COG3747;TIGR01558 | Phage terminase, small subunit |
| NC_009012.1|provirus_1938476_1983993_1729 | 360 | GENOMAD.112725.VV | PF16786 | Recombination enhancement, RecA-dependent nuclease |
| NC_009012.1|provirus_1938476_1983993_1730 | 243 | GENOMAD.212426.VP | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1731 | 999 | NA | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1732 | 411 | NA | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1733 | 456 | GENOMAD.056402.VV | PF05263;TIGR01636 | phage transcriptional activator, RinA family |
| NC_009012.1|provirus_1938476_1983993_1734 | 303 | GENOMAD.138066.VP | PF03838;COG3331;TIGR00648 | Penicillin-binding protein-related factor A, putative recombinase |
| NC_009012.1|provirus_1938476_1983993_1735 | 2556 | NA | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1736 | 426 | GENOMAD.179451.VC | PF24963 | NA |
| NC_009012.1|provirus_1938476_1983993_1737 | 798 | GENOMAD.153366.VP | PF03374;COG3645 | Phage antirepressor protein YoqD, KilAC domain |
| NC_009012.1|provirus_1938476_1983993_1738 | 1923 | GENOMAD.166868.VC | PF00476;COG0749 | DNA polymerase I - 3’-5’ exonuclease and polymerase domains |
| NC_009012.1|provirus_1938476_1983993_1739 | 753 | GENOMAD.211539.VV | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1740 | 441 | GENOMAD.026103.VV | PF23984 | Pam3 gp33-like protein |
| NC_009012.1|provirus_1938476_1983993_1741 | 1359 | GENOMAD.003266.VV | PF00176;K14440;COG1061;TIGR04095 | Superfamily II DNA or RNA helicase |
| NC_009012.1|provirus_1938476_1983993_1742 | 183 | NA | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1743 | 1920 | GENOMAD.213960.VV | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1744 | 207 | NA | NA | NA |
| NC_009012.1|provirus_1938476_1983993_1745 | 948 | NA | NA | NA |
2.5.2.2 Phage ID: NC_009012.1|provirus_2921887_2969530
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_009012.1|provirus_2921887_2969530_2577 | 3264 | GENOMAD.064018.VV | PF13872;K14440;COG1111;TIGR04095 | ERCC4-related helicase |
| NC_009012.1|provirus_2921887_2969530_2578 | 1809 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2579 | 357 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2580 | 3129 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2581 | 1113 | GENOMAD.016861.VV | PF13671;COG2019;TIGR01359;K13829 | AAA domain |
| NC_009012.1|provirus_2921887_2969530_2582 | 423 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2583 | 207 | GENOMAD.087773.VV | PF14083 | PGDYG protein |
| NC_009012.1|provirus_2921887_2969530_2584 | 465 | GENOMAD.170160.VC | PF18184 | SMODS and SLOG-associating 2TM effector domain 3 |
| NC_009012.1|provirus_2921887_2969530_2585 | 441 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2586 | 429 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2587 | 240 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2588 | 747 | GENOMAD.132419.VP | PF03374;COG3645 | Phage antirepressor protein YoqD, KilAC domain |
| NC_009012.1|provirus_2921887_2969530_2589 | 219 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2590 | 213 | GENOMAD.209016.VC | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2591 | 174 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2592 | 219 | GENOMAD.088748.VV | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2593 | 552 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2594 | 906 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2595 | 288 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2596 | 189 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2597 | 1083 | GENOMAD.021533.VV | TIGR01714 | phage replisome organizer, putative, N-terminal region |
| NC_009012.1|provirus_2921887_2969530_2598 | 837 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2599 | 375 | GENOMAD.151656.VP | PF17288;K06909;TIGR01547;COG1783 | phage terminase, large subunit, PBSX family |
| NC_009012.1|provirus_2921887_2969530_2600 | 423 | GENOMAD.221128.VP | PF05263;TIGR01636;COG2739 | phage transcriptional activator, RinA family |
| NC_009012.1|provirus_2921887_2969530_2601 | 243 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2602 | 843 | GENOMAD.178342.VP | PF02086;PF06576;PF06147;K21507;TIGR00571;COG0338 | DNA adenine methylase (dam) |
| NC_009012.1|provirus_2921887_2969530_2603 | 1281 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2604 | 846 | GENOMAD.225783.VP | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2605 | 150 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2606 | 450 | GENOMAD.026460.VV | PF03592;COG3728;K07474 | Phage terminase, small subunit |
| NC_009012.1|provirus_2921887_2969530_2607 | 1248 | GENOMAD.141197.VP | PF17288;K06909;TIGR01547;COG1783 | Terminase RNAseH like domain |
| NC_009012.1|provirus_2921887_2969530_2608 | 1434 | GENOMAD.006049.VV | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2609 | 150 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2610 | 1410 | GENOMAD.003968.VV | PF06152;COG5585;TIGR01641 | NAD+–asparagine ADP-ribosyltransferase |
| NC_009012.1|provirus_2921887_2969530_2611 | 207 | GENOMAD.066155.VV | PF06372 | NA |
| NC_009012.1|provirus_2921887_2969530_2612 | 687 | GENOMAD.007545.VV | PF06810 | Phage minor structural protein GP20 |
| NC_009012.1|provirus_2921887_2969530_2613 | 924 | GENOMAD.092843.VP | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2614 | 147 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2615 | 402 | GENOMAD.047671.VV | PF11436 | NA |
| NC_009012.1|provirus_2921887_2969530_2616 | 336 | GENOMAD.074010.VV | PF12206 | NA |
| NC_009012.1|provirus_2921887_2969530_2617 | 411 | GENOMAD.019155.VV | PF11114;TIGR01725 | phage protein, HK97 gp10 family |
| NC_009012.1|provirus_2921887_2969530_2618 | 420 | GENOMAD.025660.VV | PF20765 | Phage tail terminator protein |
| NC_009012.1|provirus_2921887_2969530_2619 | 1290 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2620 | 1047 | GENOMAD.118787.VV | PF04984;PF17482;COG3497 | Phage tail sheath protein subtilisin-like domain; Phage tail sheath C-terminal domain |
| NC_009012.1|provirus_2921887_2969530_2621 | 477 | GENOMAD.018728.VV | PF09393 | Phage tail tube protein |
| NC_009012.1|provirus_2921887_2969530_2622 | 414 | GENOMAD.009389.VV | PF08890;PF17482 | Phage XkdN-like tail assembly chaperone protein, TAC; Phage tail sheath C-terminal domain |
| NC_009012.1|provirus_2921887_2969530_2623 | 192 | GENOMAD.059912.VV | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2624 | 1836 | GENOMAD.118787.VV | PF04984;PF17482;COG3497 | Phage tail sheath protein subtilisin-like domain; Phage tail sheath C-terminal domain |
| NC_009012.1|provirus_2921887_2969530_2625 | 660 | GENOMAD.017357.VV | PF06995;COG1652 | Nucleoid-associated protein YgaU, contains BON and LysM domains |
| NC_009012.1|provirus_2921887_2969530_2626 | 945 | GENOMAD.018966.VV | PF14594;COG4379;TIGR03361;K06905 | Mu-like prophage tail protein gpP |
| NC_009012.1|provirus_2921887_2969530_2627 | 234 | GENOMAD.096038.VV | PF10844 | NA |
| NC_009012.1|provirus_2921887_2969530_2628 | 396 | GENOMAD.016318.VV | PF10934;COG4381;TIGR03357 | Mu-like prophage protein gp46 |
| NC_009012.1|provirus_2921887_2969530_2629 | 1059 | GENOMAD.004833.VV | PF04865;COG3299 | Baseplate J-like protein |
| NC_009012.1|provirus_2921887_2969530_2630 | 603 | GENOMAD.015577.VV | PF10076;COG3778;TIGR02242 | Uncharacterized protein YmfQ in lambdoid prophage, DUF2313 family |
| NC_009012.1|provirus_2921887_2969530_2631 | 285 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2632 | 1383 | GENOMAD.087125.VV | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2633 | 261 | GENOMAD.213587.VP | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2634 | 153 | GENOMAD.065816.VV | PF09693;TIGR01669 | phage uncharacterized protein, XkdX family |
| NC_009012.1|provirus_2921887_2969530_2635 | 291 | GENOMAD.171716.VV | PF07439 | NA |
| NC_009012.1|provirus_2921887_2969530_2636 | 657 | GENOMAD.220135.VV | COG5632 | N-acetylmuramoyl-L-alanine amidase CwlA |
| NC_009012.1|provirus_2921887_2969530_2637 | 300 | GENOMAD.151236.VC | PF06946 | Bacteriophage A118-like holin, Hol118 |
| NC_009012.1|provirus_2921887_2969530_2638 | 636 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2639 | 432 | GENOMAD.206152.VV | PF01845;COG2337;K07171 | mRNA-degrading endonuclease, toxin component of the MazEF toxin-antitoxin module |
| NC_009012.1|provirus_2921887_2969530_2640 | 486 | NA | NA | NA |
| NC_009012.1|provirus_2921887_2969530_2641 | 165 | NA | NA | NA |
2.5.2.3 Phage ID: NC_009012.1|provirus_2022140_2067593
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_009012.1|provirus_2022140_2067593_1786 | 1329 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1787 | 1290 | GENOMAD.022372.VV | PF04708;COG1961;K14060 | Site-specific DNA recombinase related to the DNA invertase Pin |
| NC_009012.1|provirus_2022140_2067593_1788 | 672 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1789 | 486 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1790 | 411 | GENOMAD.083633.VV | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1791 | 1689 | GENOMAD.068767.VV | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1792 | 1158 | GENOMAD.222380.VP | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1793 | 1905 | GENOMAD.004340.VV | PF06605;PF18994;COG4926;TIGR01665 | Phage-related protein |
| NC_009012.1|provirus_2022140_2067593_1794 | 705 | GENOMAD.004006.VV | PF20195;COG4722;TIGR01633 | Phage-related protein |
| NC_009012.1|provirus_2022140_2067593_1795 | 2280 | GENOMAD.089120.VP | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1796 | 126 | GENOMAD.202970.VV | PF09550;TIGR02216 | NA |
| NC_009012.1|provirus_2022140_2067593_1797 | 324 | GENOMAD.136836.VV | PF16478 | Phage tail tube protein, GTA-gp10 |
| NC_009012.1|provirus_2022140_2067593_1798 | 441 | GENOMAD.053493.CC | PF14101 | NA |
| NC_009012.1|provirus_2022140_2067593_1799 | 1044 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1800 | 108 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1801 | 573 | GENOMAD.013991.VV | PF04630;TIGR01603 | phage major tail protein, phi13 family |
| NC_009012.1|provirus_2022140_2067593_1802 | 330 | GENOMAD.018077.VV | PF05657 | NA |
| NC_009012.1|provirus_2022140_2067593_1803 | 393 | GENOMAD.066487.VV | TIGR01725;COG5005 | phage protein, HK97 gp10 family |
| NC_009012.1|provirus_2022140_2067593_1804 | 327 | GENOMAD.124210.VP | PF05521;COG5614;TIGR01563 | Bacteriophage head-tail adaptor |
| NC_009012.1|provirus_2022140_2067593_1805 | 600 | GENOMAD.158311.VV | PF05135;TIGR02215 | phage conserved hypothetical protein, phiE125 gp8 family |
| NC_009012.1|provirus_2022140_2067593_1806 | 441 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1807 | 1290 | GENOMAD.093418.VV | PF05065;TIGR01554;COG4653 | phage major capsid protein, HK97 family |
| NC_009012.1|provirus_2022140_2067593_1808 | 744 | GENOMAD.158277.VP | PF00574;PF19602;K01358;TIGR00493;COG3904 | ATP-dependent Clp endopeptidase, proteolytic subunit ClpP |
| NC_009012.1|provirus_2022140_2067593_1809 | 1260 | GENOMAD.179073.VP | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1810 | 2550 | GENOMAD.181434.VP | PF20441 | Terminase large subunit, endonuclease domain |
| NC_009012.1|provirus_2022140_2067593_1811 | 483 | GENOMAD.168120.VP | PF05119;COG3747;TIGR01558 | Phage terminase, small subunit |
| NC_009012.1|provirus_2022140_2067593_1812 | 216 | GENOMAD.225559.VP | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1813 | 753 | GENOMAD.105515.VV | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1814 | 312 | GENOMAD.224340.VP | PF19854 | NA |
| NC_009012.1|provirus_2022140_2067593_1815 | 480 | GENOMAD.191984.VP | PF07128 | NA |
| NC_009012.1|provirus_2022140_2067593_1816 | 924 | GENOMAD.105515.VV | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1817 | 1452 | GENOMAD.136632.VV | PF00145;TIGR00675;K00558;COG0270 | DNA-methyltransferase (dcm) |
| NC_009012.1|provirus_2022140_2067593_1818 | 1236 | GENOMAD.038338.VV | COG3392 | NA |
| NC_009012.1|provirus_2022140_2067593_1819 | 426 | GENOMAD.133740.VV | PF07750;COG5352;K13583;TIGR00721 | GcrA cell cycle regulator |
| NC_009012.1|provirus_2022140_2067593_1820 | 381 | GENOMAD.219652.VP | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1821 | 246 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1822 | 405 | GENOMAD.159035.VP | PF07374;TIGR01636;COG2739 | phage transcriptional activator, RinA family |
| NC_009012.1|provirus_2022140_2067593_1823 | 303 | GENOMAD.212426.VP | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1824 | 1875 | GENOMAD.024099.VV | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1825 | 1692 | GENOMAD.102034.VP | TIGR01636 | NA |
| NC_009012.1|provirus_2022140_2067593_1826 | 459 | GENOMAD.031678.VV | PF05037 | NA |
| NC_009012.1|provirus_2022140_2067593_1827 | 1431 | GENOMAD.016341.VV | PF13479;PF12684;TIGR01618;K07465;COG1468 | phage nucleotide-binding protein |
| NC_009012.1|provirus_2022140_2067593_1828 | 366 | GENOMAD.010330.VV | PF03838;COG3331;TIGR00648 | Recombination protein U |
| NC_009012.1|provirus_2022140_2067593_1829 | 1179 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1830 | 90 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1831 | 765 | GENOMAD.107118.VP | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1832 | 252 | GENOMAD.222352.VV | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1833 | 324 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1834 | 228 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1835 | 711 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1836 | 369 | GENOMAD.213960.VV | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1837 | 381 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1838 | 789 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1839 | 417 | NA | NA | NA |
| NC_009012.1|provirus_2022140_2067593_1840 | 408 | NA | NA | NA |
2.5.2.4 Phage ID: NC_009012.1|provirus_3339258_3389798
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_009012.1|provirus_3339258_3389798_2977 | 240 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2978 | 807 | GENOMAD.169139.VV | PF09250 | Bifunctional DNA primase/polymerase, N-terminal |
| NC_009012.1|provirus_3339258_3389798_2979 | 1848 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2980 | 1239 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2981 | 138 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2982 | 330 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2983 | 471 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2984 | 405 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2985 | 759 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2986 | 1485 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2987 | 717 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2988 | 348 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2989 | 1686 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2990 | 579 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2991 | 390 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2992 | 138 | GENOMAD.223510.VP | PF10122;TIGR04104;COG4530 | Mu-like prophage protein Com |
| NC_009012.1|provirus_3339258_3389798_2993 | 552 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2994 | 1842 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2995 | 1239 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2996 | 345 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2997 | 435 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2998 | 345 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_2999 | 246 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3000 | 189 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3001 | 1206 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3002 | 288 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3003 | 390 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3004 | 141 | GENOMAD.223510.VP | PF10122;TIGR04104;COG4530 | Mu-like prophage protein Com |
| NC_009012.1|provirus_3339258_3389798_3005 | 2160 | GENOMAD.197438.VP | PF09250 | Bifunctional DNA primase/polymerase, N-terminal |
| NC_009012.1|provirus_3339258_3389798_3006 | 1314 | GENOMAD.093418.VV | PF05065;TIGR01554;COG4653 | phage major capsid protein, HK97 family |
| NC_009012.1|provirus_3339258_3389798_3007 | 303 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3008 | 1245 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3009 | 288 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3010 | 297 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3011 | 807 | GENOMAD.169139.VV | PF09250 | Bifunctional DNA primase/polymerase, N-terminal |
| NC_009012.1|provirus_3339258_3389798_3012 | 1848 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3013 | 1239 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3014 | 528 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3015 | 471 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3016 | 1137 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3017 | 348 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3018 | 780 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3019 | 930 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3020 | 243 | GENOMAD.227820.VP | PF15597 | Immunity protein 59 |
| NC_009012.1|provirus_3339258_3389798_3021 | 603 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3022 | 1005 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3023 | 237 | GENOMAD.218640.VC | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3024 | 390 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3025 | 138 | GENOMAD.223510.VP | PF10122;TIGR04104;COG4530 | Mu-like prophage protein Com |
| NC_009012.1|provirus_3339258_3389798_3026 | 2160 | GENOMAD.197438.VP | PF09250 | Bifunctional DNA primase/polymerase, N-terminal |
| NC_009012.1|provirus_3339258_3389798_3027 | 1314 | GENOMAD.061958.VV | PF05065 | Phage capsid family |
| NC_009012.1|provirus_3339258_3389798_3028 | 303 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3029 | 1245 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3030 | 186 | NA | NA | NA |
| NC_009012.1|provirus_3339258_3389798_3031 | 294 | NA | NA | NA |
2.5.2.5 Phage ID: NC_009012.1|provirus_2330336_2378640
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_009012.1|provirus_2330336_2378640_2057 | 933 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2058 | 1341 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2059 | 198 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2060 | 966 | GENOMAD.221871.VP | K13281;TIGR00629;COG4294 | UV damage endonuclease UvdE |
| NC_009012.1|provirus_2330336_2378640_2061 | 735 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2062 | 1083 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2063 | 2451 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2064 | 963 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2065 | 2514 | GENOMAD.208624.VC | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2066 | 1530 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2067 | 564 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2068 | 141 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2069 | 327 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2070 | 1737 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2071 | 3201 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2072 | 1380 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2073 | 306 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2074 | 330 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2075 | 321 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2076 | 1524 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2077 | 564 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2078 | 948 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2079 | 327 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2080 | 246 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2081 | 1353 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2082 | 807 | GENOMAD.197438.VP | PF09250 | Bifunctional DNA primase/polymerase, N-terminal |
| NC_009012.1|provirus_2330336_2378640_2083 | 138 | GENOMAD.223510.VP | PF10122;TIGR04104;COG4530 | Mu-like prophage protein Com |
| NC_009012.1|provirus_2330336_2378640_2084 | 390 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2085 | 243 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2086 | 1185 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2087 | 348 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2088 | 1272 | GENOMAD.061958.VV | PF05065 | Phage capsid family |
| NC_009012.1|provirus_2330336_2378640_2089 | 2160 | GENOMAD.197438.VP | PF09250 | Bifunctional DNA primase/polymerase, N-terminal |
| NC_009012.1|provirus_2330336_2378640_2090 | 138 | GENOMAD.223510.VP | PF10122;TIGR04104;COG4530 | Mu-like prophage protein Com |
| NC_009012.1|provirus_2330336_2378640_2091 | 390 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2092 | 279 | GENOMAD.218057.VV | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2093 | 894 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2094 | 780 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2095 | 348 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2096 | 987 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2097 | 948 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2098 | 351 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2099 | 1524 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2100 | 726 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2101 | 315 | NA | NA | NA |
| NC_009012.1|provirus_2330336_2378640_2102 | 771 | NA | NA | NA |
2.5.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_009012.1|provirus_1938476_1983993 | sequence_000002.fasta.fasta | 1_1 | 0.05 | average | ANImf | 1 |
| NC_009012.1|provirus_2921887_2969530 | sequence_000004.fasta.fasta | 1_2 | 0.05 | average | ANImf | 1 |
| NC_009012.1|provirus_2022140_2067593 | sequence_000000.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
| NC_009012.1|provirus_3339258_3389798 | sequence_000001.fasta.fasta | 3_0 | 0.05 | average | ANImf | 3 |
| NC_009012.1|provirus_2330336_2378640 | sequence_000003.fasta.fasta | 4_0 | 0.05 | average | ANImf | 4 |
Primary clustering plot
2.5.4 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_009012.1|provirus_1938476_1983993 | RS_GCF_000015865.1 | d__Bacteria;p__Bacillota_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium;s__Hungateiclostridium thermocellum | blast | 94.9 | iPHoP-RF;71.30 |
| NC_009012.1|provirus_2022140_2067593 | RS_GCF_000015865.1 | d__Bacteria;p__Bacillota_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium;s__Hungateiclostridium thermocellum | blast | 93.9 | None |
| NC_009012.1|provirus_2330336_2378640 | RS_GCF_000015865.1 | d__Bacteria;p__Bacillota_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium;s__Hungateiclostridium thermocellum | blast | 97.7 | iPHoP-RF;83.30 |
| NC_009012.1|provirus_2330336_2378640 | RS_GCF_004102745.1 | d__Bacteria;p__Bacillota_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium;s__Hungateiclostridium mesophilum | blast | 90.4 | None |
| NC_009012.1|provirus_2330336_2378640 | 3300025605_6 | d__Bacteria;p__Bacillota_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;gHungateiclostridium;s | blast | 90.0 | iPHoP-RF;50.70 |
| NC_009012.1|provirus_2921887_2969530 | RS_GCF_000015865.1 | d__Bacteria;p__Bacillota_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium;s__Hungateiclostridium thermocellum | blast | 93.1 | iPHoP-RF;51.50 |
| NC_009012.1|provirus_2921887_2969530 | 3300025605_6 | d__Bacteria;p__Bacillota_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;gHungateiclostridium;s | blast | 91.8 | None |
| NC_009012.1|provirus_3339258_3389798 | RS_GCF_000015865.1 | d__Bacteria;p__Bacillota_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium;s__Hungateiclostridium thermocellum | blast | 98.1 | iPHoP-RF;76.80 |
2.5.5 AMG Predictions
Prediction of auxiliary metabolic genes in the prophage contigs.
| protein | scaffold | amg_ko | amg_ko_name | pfam | pfam_name |
|---|---|---|---|---|---|
| NC_009012.1|provirus_2022140_2067593_32 | NC_009012.1|provirus_2022140_2067593 | K00558 | DNMT1, dcm; DNA (cytosine-5)-methyltransferase 1 [EC:2.1.1.37] | PF00145.17 | C-5 cytosine-specific DNA methylase |
2.6 NC_012982
2.6.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Pseudomonadota;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hirschia;s__Hirschia baltica |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 3455622 | 100 | 0.05 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_012982.1_AbiC_1 | AbiC | AbiC | NC_012982.1_420 | NC_012982.1_420 | NC_012982.1_420 | 1 | AbiC__AbiC |
| NC_012982.1_RM_Type_IIG_5 | RM | RM_Type_IIG | NC_012982.1_623 | NC_012982.1_623 | NC_012982.1_623 | 1 | RM_Type_IIG__Type_IIG_FAM_1.einsi_trimmed |
| NC_012982.1_RM_Type_III_6 | RM | RM_Type_III | NC_012982.1_1629 | NC_012982.1_1630 | NC_012982.1_1629,NC_012982.1_1630 | 2 | RM_Type_III__Type_III_MTases_FAM_0,RM_Type_III__Type_III_REases_FAM_1.einsi_trimmed |
| NC_012982.1_CBASS_I_3 | CBASS | CBASS_I | NC_012982.1_1825 | NC_012982.1_1826 | NC_012982.1_1825,NC_012982.1_1826 | 2 | CBASS__Cyclase_II,CBASS__Phospholipase |
| NC_012982.1_Rst_DUF4238_4 | Rst_DUF4238 | Rst_DUF4238 | NC_012982.1_2416 | NC_012982.1_2416 | NC_012982.1_2416 | 1 | Rst_DUF4238__DUF4238_Pers |
2.7 NC_014008
2.7.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Coraliomargaritaceae;g__Coraliomargarita;s__Coraliomargarita akajimensis |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 3750771 | 100 | 0.02 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_014008.1_RM_Type_I_6 | RM | RM_Type_I | NC_014008.1_1177 | NC_014008.1_1181 | NC_014008.1_1177,NC_014008.1_1180,NC_014008.1_1181 | 3 | RM__Type_I_MTases_FAM_3,RM__Type_I_REases_FAM_1.einsi_trimmed,RM__Type_I_S_52 |
| NC_014008.1_Viperin_3 | Viperin | Viperin | NC_014008.1_1182 | NC_014008.1_1182 | NC_014008.1_1182 | 1 | Viperin__pVip |
| NC_014008.1_dGTPase_4 | dGTPase | dGTPase | NC_014008.1_1769 | NC_014008.1_1769 | NC_014008.1_1769 | 1 | dGTPase__Sp_dGTPase |
| NC_014008.1_Ceres_1 | Ceres | Ceres | NC_014008.1_2641 | NC_014008.1_2641 | NC_014008.1_2641 | 1 | Ceres__CrsA1 |
| NC_014008.1_Gao_Mza_2 | Gao_Mza | Gao_Mza | NC_014008.1_2741 | NC_014008.1_2744 | NC_014008.1_2741,NC_014008.1_2743,NC_014008.1_2744 | 3 | Gao_Mza__MzaB,Gao_Mza__MzaC,Gao_Mza__MzaE |
2.8 NC_014168
2.8.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Actinomycetota;c__Actinomycetes;o__Mycobacteriales;f__Mycobacteriaceae;g__Segniliparus;s__Segniliparus rotundus |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 3157527 | 99.99 | 0.03 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_014168.1_RM_Type_II_2 | RM | RM_Type_II | NC_014168.1_1355 | NC_014168.1_1356 | NC_014168.1_1355,NC_014168.1_1356 | 2 | RM_Type_II__Type_II_MTases_FAM_41,RM_Type_II__Type_II_REase25 |
| NC_014168.1_RM_Type_IIG_3 | RM | RM_Type_IIG | NC_014168.1_1738 | NC_014168.1_1738 | NC_014168.1_1738 | 1 | RM_Type_IIG__Type_IIG_FAM_2.einsi_trimmed |
| NC_014168.1_DS-20_1 | DS-20 | DS-20 | NC_014168.1_2356 | NC_014168.1_2356 | NC_014168.1_2356 | 1 | DS-20__DS-20 |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_014168.1|provirus_27479_67296 | 39818 | 60 | 29 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 27479-67296 |
| NC_014168.1|provirus_1141631_1162952 | 21322 | 36 | 19 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1141631-1162952 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.8.2 Prophages
Select prophage to show:
2.8.2.1 Phage ID: NC_014168.1|provirus_27479_67296
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_014168.1|provirus_27479_67296_28 | 897 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_29 | 549 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_30 | 198 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_31 | 753 | GENOMAD.032144.VV | PF12684 | NA |
| NC_014168.1|provirus_27479_67296_32 | 657 | GENOMAD.124252.VP | PF03837;TIGR01913 | phage recombination protein Bet |
| NC_014168.1|provirus_27479_67296_33 | 402 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_34 | 354 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_35 | 153 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_36 | 420 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_37 | 516 | GENOMAD.033304.VV | PF13395 | NA |
| NC_014168.1|provirus_27479_67296_38 | 936 | GENOMAD.028141.VV | PF09681;TIGR01714 | N-terminal phage replisome organiser (Phage_rep_org_N) |
| NC_014168.1|provirus_27479_67296_39 | 366 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_40 | 387 | GENOMAD.018151.VV | PF01870;COG1591 | Holliday junction resolvase, archaeal type |
| NC_014168.1|provirus_27479_67296_41 | 201 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_42 | 312 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_43 | 213 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_44 | 237 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_45 | 321 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_46 | 471 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_47 | 429 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_48 | 579 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_49 | 312 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_50 | 780 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_51 | 222 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_52 | 1761 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_53 | 657 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_54 | 321 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_55 | 255 | GENOMAD.083226.VV | PF23850 | NA |
| NC_014168.1|provirus_27479_67296_56 | 384 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_57 | 480 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_58 | 369 | GENOMAD.215374.PC | PF13827 | NA |
| NC_014168.1|provirus_27479_67296_59 | 279 | GENOMAD.014408.VV | PF13395;TIGR02646 | HNH endonuclease |
| NC_014168.1|provirus_27479_67296_60 | 186 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_61 | 264 | GENOMAD.047538.VV | NA | NA |
| NC_014168.1|provirus_27479_67296_62 | 1416 | GENOMAD.002060.VV | PF20441;PF04466;COG4626;TIGR01547;K06909 | Phage terminase-like protein, large subunit, contains N-terminal HTH domain |
| NC_014168.1|provirus_27479_67296_63 | 1377 | GENOMAD.080886.VV | PF05133;TIGR01538 | phage portal protein, SPP1 family |
| NC_014168.1|provirus_27479_67296_64 | 684 | GENOMAD.097054.VV | PF04233;TIGR01641 | phage putative head morphogenesis protein, SPP1 gp7 family |
| NC_014168.1|provirus_27479_67296_65 | 477 | GENOMAD.040462.VV | NA | NA |
| NC_014168.1|provirus_27479_67296_66 | 909 | GENOMAD.013023.VV | PF05065;TIGR01554;COG4653 | phage major capsid protein, HK97 family |
| NC_014168.1|provirus_27479_67296_67 | 174 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_68 | 468 | GENOMAD.062537.VV | PF09355 | Phage protein Gp19/Gp15/Gp42 |
| NC_014168.1|provirus_27479_67296_69 | 342 | GENOMAD.038727.VV | PF12206;COG5614;TIGR01563 | Minor capsid protein |
| NC_014168.1|provirus_27479_67296_70 | 309 | GENOMAD.087122.VV | NA | NA |
| NC_014168.1|provirus_27479_67296_71 | 399 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_72 | 648 | GENOMAD.004252.VV | NA | NA |
| NC_014168.1|provirus_27479_67296_73 | 333 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_74 | 384 | GENOMAD.056037.VV | PF17318;PF08765;TIGR02417 | Mor transcription activator family |
| NC_014168.1|provirus_27479_67296_75 | 3723 | GENOMAD.016295.VV | COG3953 | SLT domain protein |
| NC_014168.1|provirus_27479_67296_76 | 1263 | GENOMAD.053786.VV | COG4722 | Phage-related protein |
| NC_014168.1|provirus_27479_67296_77 | 1773 | GENOMAD.019112.VV | NA | NA |
| NC_014168.1|provirus_27479_67296_78 | 252 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_79 | 1062 | GENOMAD.059914.VV | NA | NA |
| NC_014168.1|provirus_27479_67296_80 | 1266 | GENOMAD.079434.VV | NA | NA |
| NC_014168.1|provirus_27479_67296_81 | 1260 | GENOMAD.047467.VV | COG5632 | N-acetylmuramoyl-L-alanine amidase CwlA |
| NC_014168.1|provirus_27479_67296_82 | 357 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_83 | 276 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_84 | 207 | GENOMAD.158505.VV | PF24596 | NA |
| NC_014168.1|provirus_27479_67296_85 | 360 | GENOMAD.073706.VV | PF23778 | Putative phage holin family 2 |
| NC_014168.1|provirus_27479_67296_86 | 372 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_87 | 336 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_88 | 273 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_89 | 1263 | NA | NA | NA |
| NC_014168.1|provirus_27479_67296_90 | 1050 | NA | NA | NA |
2.8.2.2 Phage ID: NC_014168.1|provirus_1141631_1162952
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_014168.1|provirus_1141631_1162952_1152 | 318 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1153 | 360 | GENOMAD.082050.VV | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1154 | 333 | GENOMAD.076859.VV | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1155 | 312 | GENOMAD.103239.VV | PF10665;TIGR01563;COG5614 | Minor capsid protein |
| NC_014168.1|provirus_1141631_1162952_1156 | 237 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1157 | 510 | GENOMAD.028700.VV | TIGR02215 | phage conserved hypothetical protein, phiE125 gp8 family |
| NC_014168.1|provirus_1141631_1162952_1158 | 192 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1159 | 1281 | GENOMAD.098207.VP | PF06673;TIGR01554;COG1659 | Lactococcus lactis bacteriophage major capsid protein |
| NC_014168.1|provirus_1141631_1162952_1160 | 693 | GENOMAD.207278.VV | PF04586;COG3740;K06904;TIGR01543 | Phage head maturation protease |
| NC_014168.1|provirus_1141631_1162952_1161 | 1302 | GENOMAD.138175.VV | PF04860;TIGR01537;COG4695 | phage portal protein, HK97 family |
| NC_014168.1|provirus_1141631_1162952_1162 | 1497 | GENOMAD.037086.VV | PF20441;PF03354;COG4626;TIGR01547 | Phage terminase-like protein, large subunit, contains N-terminal HTH domain |
| NC_014168.1|provirus_1141631_1162952_1163 | 291 | GENOMAD.064187.VV | TIGR01558 | NA |
| NC_014168.1|provirus_1141631_1162952_1164 | 507 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1165 | 552 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1166 | 282 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1167 | 276 | GENOMAD.041582.VV | PF13395;TIGR02646 | TIGR02646 family protein |
| NC_014168.1|provirus_1141631_1162952_1168 | 1119 | GENOMAD.064801.VV | PF00145;TIGR00675;COG0270;K15336 | DNA-methyltransferase (dcm) |
| NC_014168.1|provirus_1141631_1162952_1169 | 657 | GENOMAD.066690.VV | PF10122;COG5349;TIGR01206 | Uncharacterized conserved protein, DUF983 family |
| NC_014168.1|provirus_1141631_1162952_1170 | 249 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1171 | 258 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1172 | 378 | GENOMAD.063447.VV | PF11417 | NA |
| NC_014168.1|provirus_1141631_1162952_1173 | 795 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1174 | 426 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1175 | 387 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1176 | 783 | GENOMAD.021092.VV | PF12684;TIGR00372;COG1468;K07465 | CRISPR-associated protein Cas4 |
| NC_014168.1|provirus_1141631_1162952_1177 | 291 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1178 | 228 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1179 | 375 | GENOMAD.067886.VV | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1180 | 843 | GENOMAD.161686.VP | PF20188 | NA |
| NC_014168.1|provirus_1141631_1162952_1181 | 921 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1182 | 255 | GENOMAD.222641.VP | PF08667;COG5606;TIGR02612;K07727 | Predicted DNA-binding protein, XRE-type HTH domain |
| NC_014168.1|provirus_1141631_1162952_1183 | 429 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1184 | 861 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1185 | 264 | NA | NA | NA |
| NC_014168.1|provirus_1141631_1162952_1186 | 1356 | NA | NA | NA |
2.8.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_014168.1|provirus_27479_67296 | sequence_000000.fasta.fasta | 1_0 | 0.05 | average | ANImf | 1 |
| NC_014168.1|provirus_1141631_1162952 | sequence_000001.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
Primary clustering plot
2.8.4 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_014168.1|provirus_1141631_1162952 | RS_GCF_000092825.1 | d__Bacteria;p__Actinomycetota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Segniliparus;s__Segniliparus rotundus | blast | 95.7 | iPHoP-RF;68.00 |
| NC_014168.1|provirus_27479_67296 | RS_GCF_000092825.1 | d__Bacteria;p__Actinomycetota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Segniliparus;s__Segniliparus rotundus | blast | 96.0 | iPHoP-RF;79.30 |
2.8.5 AMG Predictions
Prediction of auxiliary metabolic genes in the prophage contigs.
| protein | scaffold | amg_ko | amg_ko_name | pfam | pfam_name |
|---|---|---|---|---|---|
| NC_014168.1|provirus_1141631_1162952_17 | NC_014168.1|provirus_1141631_1162952 | K00558 | DNMT1, dcm; DNA (cytosine-5)-methyltransferase 1 [EC:2.1.1.37] | PF00145.17 | C-5 cytosine-specific DNA methylase |
2.9 NC_014211
2.9.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Actinomycetota;c__Actinomycetes;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis;s__Nocardiopsis dassonvillei |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 775354 | 14.07 | 0.01 |
No Defense-Finder systems detected.
2.10 NC_014212
2.10.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Allomeiothermus;s__Allomeiothermus silvanus |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 3249394 | 99.99 | 0.16 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_014212.1_Ceres_1 | Ceres | Ceres | NC_014212.1_142 | NC_014212.1_142 | NC_014212.1_142 | 1 | Ceres__CrsA1 |
| NC_014212.1_RM_Type_III_2 | RM | RM_Type_III | NC_014212.1_571 | NC_014212.1_572 | NC_014212.1_571,NC_014212.1_572 | 2 | RM_Type_III__Type_III_MTases_FAM_0,RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed |
| NC_014212.1_CAS_Class1-Subtype-III-A_4 | Cas | CAS_Class1-Subtype-III-A | NC_014212.1_712 | NC_014212.1_723 | NC_014212.1_712,NC_014212.1_713,NC_014212.1_714,NC_014212.1_715,NC_014212.1_716,NC_014212.1_719,NC_014212.1_720,NC_014212.1_721,NC_014212.1_722,NC_014212.1_723 | 10 | cas10_III-A_1,cas1_I_II_III_IV_V_VI_1,cas2_I_II_III_IV_V_VI_8,cas6_I_II_III_IV_V_VI_15,csm2gr11_III-A_1,csm3gr7_III-A_1,csm4gr5_III-A_2,csm5gr7_III-A_2,csx1_III_21,csx1_III_21 |
| NC_014212.1_CAS_Class1-Subtype-I-E_3 | Cas | CAS_Class1-Subtype-I-E | NC_014212.1_1246 | NC_014212.1_1255 | NC_014212.1_1246,NC_014212.1_1248,NC_014212.1_1249,NC_014212.1_1251,NC_014212.1_1252,NC_014212.1_1253,NC_014212.1_1254,NC_014212.1_1255 | 8 | cas1_I-E_1,cas2_I-E_1,cas3_I_2,cas5_I-E_2,cas6e_I_II_III_IV_V_VI_2,cas7_I-E_16,cas8e_I-E_5,cse2gr11_I-E_8 |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_014212.1|provirus_1746722_1764354 | 17633 | 38 | 3 | Medium-quality | Genome-fragment | Viruses;Varidnaviria;Helvetiavirae;Dividoviricota;Laserviricetes;Halopanivirales;Matsushitaviridae | Provirus | 1746722-1764354 |
| NC_014212.1|provirus_1892278_1921074 | 28797 | 40 | 6 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1892278-1921074 |
| NC_014212.1|provirus_1170297_1211081 | 40785 | 50 | 10 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1170297-1211081 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.10.2 Prophages
Select prophage to show:
2.10.2.1 Phage ID: NC_014212.1|provirus_1746722_1764354
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_014212.1|provirus_1746722_1764354_1776 | 981 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1777 | 570 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1778 | 708 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1779 | 189 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1780 | 207 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1781 | 171 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1782 | 279 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1783 | 123 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1784 | 93 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1785 | 300 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1786 | 345 | GENOMAD.138277.VP | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1787 | 333 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1788 | 1467 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1789 | 210 | GENOMAD.118491.VV | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1790 | 333 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1791 | 243 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1792 | 270 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1793 | 204 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1794 | 471 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1795 | 366 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1796 | 678 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1797 | 201 | GENOMAD.187456.VV | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1798 | 738 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1799 | 432 | GENOMAD.226936.VP | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1800 | 462 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1801 | 885 | GENOMAD.175220.VV | PF22210 | Large MCP VP17 central beta-barrel |
| NC_014212.1|provirus_1746722_1764354_1802 | 243 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1803 | 636 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1804 | 300 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1805 | 177 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1806 | 507 | GENOMAD.201673.VV | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1807 | 189 | GENOMAD.131894.VV | PF04531;TIGR01598;COG5546 | NA |
| NC_014212.1|provirus_1746722_1764354_1808 | 174 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1809 | 456 | GENOMAD.199413.VV | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1810 | 1050 | GENOMAD.107709.VV | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1811 | 1014 | GENOMAD.109373.VV | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1812 | 264 | NA | NA | NA |
| NC_014212.1|provirus_1746722_1764354_1813 | 750 | NA | NA | NA |
2.10.2.2 Phage ID: NC_014212.1|provirus_1892278_1921074
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_014212.1|provirus_1892278_1921074_1934 | 438 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1935 | 312 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1936 | 240 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1937 | 231 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1938 | 276 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1939 | 219 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1940 | 396 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1941 | 480 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1942 | 702 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1943 | 441 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1944 | 249 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1945 | 342 | GENOMAD.188989.VV | PF10711 | Hypothetical protein (DUF2513) |
| NC_014212.1|provirus_1892278_1921074_1946 | 321 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1947 | 462 | GENOMAD.102149.VV | PF11985 | Bacteriophage Mu, Gp27 |
| NC_014212.1|provirus_1892278_1921074_1948 | 1284 | GENOMAD.025283.VV | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1949 | 1536 | GENOMAD.116653.VV | PF06074;COG4383 | Mu-like prophage protein gp29 |
| NC_014212.1|provirus_1892278_1921074_1950 | 1173 | GENOMAD.169564.VP | COG2369 | Uncharacterized conserved protein, contains phage Mu gpF-like domain |
| NC_014212.1|provirus_1892278_1921074_1951 | 1200 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1952 | 453 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1953 | 540 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1954 | 447 | GENOMAD.191448.VP | PF05069;TIGR01635;COG5005 | phage virion morphogenesis (putative tail completion) protein |
| NC_014212.1|provirus_1892278_1921074_1955 | 501 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1956 | 213 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1957 | 1422 | GENOMAD.041181.VV | PF10758;COG3497 | Phage tail sheath protein FI |
| NC_014212.1|provirus_1892278_1921074_1958 | 432 | GENOMAD.115837.VV | PF10772 | Bacteriophage HP1, Orf24 |
| NC_014212.1|provirus_1892278_1921074_1959 | 375 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1960 | 132 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1961 | 2082 | GENOMAD.106657.VP | COG5280 | Phage-related minor tail protein |
| NC_014212.1|provirus_1892278_1921074_1962 | 579 | GENOMAD.163406.VV | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1963 | 666 | GENOMAD.068883.VV | TIGR03361;COG3500 | type VI secretion system Vgr family protein |
| NC_014212.1|provirus_1892278_1921074_1964 | 477 | GENOMAD.068883.VV | TIGR03361;COG3500 | type VI secretion system Vgr family protein |
| NC_014212.1|provirus_1892278_1921074_1965 | 375 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1966 | 1083 | GENOMAD.106861.VV | PF04865;COG3299 | Baseplate J-like protein |
| NC_014212.1|provirus_1892278_1921074_1967 | 612 | GENOMAD.067612.VV | PF10076;COG4385;TIGR01634 | Bacteriophage P2-related tail formation protein |
| NC_014212.1|provirus_1892278_1921074_1968 | 1155 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1969 | 177 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1970 | 501 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1971 | 1002 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1972 | 282 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1973 | 1392 | NA | NA | NA |
| NC_014212.1|provirus_1892278_1921074_1974 | 2181 | GENOMAD.090865.VV | PF13086;TIGR02785;COG1074;K19781 | helicase-exonuclease AddAB, AddA subunit, Firmicutes type |
2.10.2.3 Phage ID: NC_014212.1|provirus_1170297_1211081
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_014212.1|provirus_1170297_1211081_1203 | 1164 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1204 | 261 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1205 | 1200 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1206 | 453 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1207 | 654 | GENOMAD.212789.VC | PF08667;TIGR00673;COG1974;K22299 | cyanase |
| NC_014212.1|provirus_1170297_1211081_1208 | 180 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1209 | 231 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1210 | 189 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1211 | 273 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1212 | 123 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1213 | 219 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1214 | 618 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1215 | 1734 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1216 | 336 | GENOMAD.004598.VV | PF18743;COG1591 | REase_AHJR-like |
| NC_014212.1|provirus_1170297_1211081_1217 | 2694 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1218 | 243 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1219 | 837 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1220 | 468 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1221 | 456 | GENOMAD.172137.VP | PF07141;COG3728;TIGR02036 | Putative bacteriophage terminase small subunit |
| NC_014212.1|provirus_1170297_1211081_1222 | 1305 | GENOMAD.190694.VP | PF04466;PF17288;TIGR01547;COG1783;K06909 | phage terminase, large subunit, PBSX family |
| NC_014212.1|provirus_1170297_1211081_1223 | 1428 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1224 | 873 | GENOMAD.017886.VV | PF04233;TIGR01641 | phage putative head morphogenesis protein, SPP1 gp7 family |
| NC_014212.1|provirus_1170297_1211081_1225 | 180 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1226 | 1644 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1227 | 201 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1228 | 873 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1229 | 660 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1230 | 1653 | GENOMAD.196129.VP | PF05125;TIGR01551;COG4653 | phage major capsid protein, P2 family |
| NC_014212.1|provirus_1170297_1211081_1231 | 234 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1232 | 555 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1233 | 327 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1234 | 540 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1235 | 435 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1236 | 789 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1237 | 486 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1238 | 3738 | GENOMAD.183233.VP | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1239 | 441 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1240 | 1077 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1241 | 1905 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1242 | 543 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1243 | 540 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1244 | 312 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1245 | 1839 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1246 | 561 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1247 | 312 | GENOMAD.103334.VV | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1248 | 792 | GENOMAD.024392.VV | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1249 | 549 | GENOMAD.052331.VV | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1250 | 216 | GENOMAD.199026.VV | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1251 | 300 | NA | NA | NA |
| NC_014212.1|provirus_1170297_1211081_1252 | 1002 | NA | NA | NA |
2.10.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_014212.1|provirus_1746722_1764354 | sequence_000000.fasta.fasta | 1_0 | 0.05 | average | ANImf | 1 |
| NC_014212.1|provirus_1892278_1921074 | sequence_000002.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
| NC_014212.1|provirus_1170297_1211081 | sequence_000001.fasta.fasta | 3_0 | 0.05 | average | ANImf | 3 |
Primary clustering plot
2.10.4 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_014212.1|provirus_1170297_1211081 | RS_GCF_000092125.1 | d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus_B;s__Meiothermus_B silvanus | blast | 95.9 | iPHoP-RF;76.80 |
| NC_014212.1|provirus_1170297_1211081 | RS_GCF_003226535.1 | d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus_B;s__Meiothermus_B sp003226535 | blast | 92.4 | iPHoP-RF;74.60 |
| NC_014212.1|provirus_1170297_1211081 | RS_GCF_000430045.1 | d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus;s__Calidithermus chliarophilus | blast | 90.7 | CRISPR;76.20 iPHoP-RF;71.10 |
| NC_014212.1|provirus_1746722_1764354 | RS_GCF_000092125.1 | d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus_B;s__Meiothermus_B silvanus | blast | 95.2 | iPHoP-RF;86.00 |
| NC_014212.1|provirus_1892278_1921074 | RS_GCF_000092125.1 | d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus_B;s__Meiothermus_B silvanus | blast | 94.5 | iPHoP-RF;74.80 |
| NC_014212.1|provirus_1892278_1921074 | RS_GCF_000430045.1 | d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus;s__Calidithermus chliarophilus | blast | 92.9 | iPHoP-RF;63.50 |
| NC_014212.1|provirus_1892278_1921074 | RS_GCF_000373205.1 | d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus;s__Calidithermus timidus | blast | 90.9 | None |
| NC_014212.1|provirus_1892278_1921074 | RS_GCF_003574095.1 | d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus;s__Calidithermus roseus | blast | 90.6 | None |
| NC_014212.1|provirus_1892278_1921074 | RS_GCF_003574035.1 | d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus;s__Meiothermus hypogaeus | blast | 90.5 | iPHoP-RF;59.80 |
2.10.5 AMG Predictions
Prediction of auxiliary metabolic genes in the prophage contigs.
| protein | scaffold | amg_ko | amg_ko_name | pfam | pfam_name |
|---|---|---|---|---|---|
| NC_014212.1|provirus_1892278_1921074_39 | NC_014212.1|provirus_1892278_1921074 | K01840 | manB; phosphomannomutase [EC:5.4.2.8] | PF02878.16 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I |
2.11 NC_014363
2.11.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Actinomycetota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella;s__Olsenella uli |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 2051896 | 99.7 | 0.35 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_014363.1_AbiE_1 | AbiE | AbiE | NC_014363.1_207 | NC_014363.1_208 | NC_014363.1_207,NC_014363.1_208 | 2 | AbiEii__AbiEi_4,AbiEii__AbiEii |
| NC_014363.1_AbiE_2 | AbiE | AbiE | NC_014363.1_473 | NC_014363.1_474 | NC_014363.1_473,NC_014363.1_474 | 2 | AbiEii__AbiEi_4,AbiEii__AbiEii |
| NC_014363.1_VP1839_3 | VP1839 | VP1839 | NC_014363.1_1184 | NC_014363.1_1184 | NC_014363.1_1184 | 1 | VP1839__VP1839 |
| NC_014363.1_RM_Type_II_6 | RM | RM_Type_II | NC_014363.1_1186 | NC_014363.1_1187 | NC_014363.1_1186,NC_014363.1_1187 | 2 | RM_Type_II__Type_II_MTases_FAM_0,RM_Type_II__Type_II_REase15 |
| NC_014363.1_CAS_Class2-Subtype-II-A_7 | Cas | CAS_Class2-Subtype-II-A | NC_014363.1_1233 | NC_014363.1_1236 | NC_014363.1_1233,NC_014363.1_1234,NC_014363.1_1235,NC_014363.1_1236 | 4 | cas1_I_II_III_IV_V_VI_5,cas2_I_II_III_IV_V_VI_6,cas9_II-A_1,csn2_II-A_3 |
| NC_014363.1_RM_Type_I_5 | RM | RM_Type_I | NC_014363.1_1659 | NC_014363.1_1664 | NC_014363.1_1659,NC_014363.1_1662,NC_014363.1_1663,NC_014363.1_1664 | 4 | RM__Type_I_MTases_FAM_2,RM__Type_I_REases_FAM_2.einsi_trimmed,RM__Type_I_S_04,RM__Type_I_S_04 |
2.12 NC_014364
2.12.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-16054;f__Sediminispirochaetaceae;g__Sediminispirochaeta;s__Sediminispirochaeta smaragdinae |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 4653970 | 99.98 | 1.88 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_014364.1_TIR-IV_4 | TIR-IV | TIR-IV | NC_014364.1_392 | NC_014364.1_393 | NC_014364.1_392,NC_014364.1_393 | 2 | TIR-IV__TIR-IV_A,TIR-IV__TIR-IV_B |
| NC_014364.1_SoFic_3 | SoFIC | SoFic | NC_014364.1_418 | NC_014364.1_418 | NC_014364.1_418 | 1 | SoFic__SoFic |
| NC_014364.1_MazEF_2 | MazEF | MazEF | NC_014364.1_697 | NC_014364.1_698 | NC_014364.1_697,NC_014364.1_698 | 2 | MazEF__MazE,MazEF__MazF |
| NC_014364.1_CAS_Class1-Subtype-I-C_5 | Cas | CAS_Class1-Subtype-I-C | NC_014364.1_1062 | NC_014364.1_1069 | NC_014364.1_1062,NC_014364.1_1063,NC_014364.1_1064,NC_014364.1_1065,NC_014364.1_1066,NC_014364.1_1067,NC_014364.1_1068,NC_014364.1_1069 | 8 | WYL_I_II_III_IV_V_VI_4,cas1_I_II_III_IV_V_VI_6,cas2_I_II_III_IV_V_VI_3,cas3_I_5,cas4_I_II_III_IV_V_VI_6,cas5_I-C_11,cas7_I-C_7,cas8c_I-C_4 |
| NC_014364.1_CAS_Class1-Subtype-IV-B_6 | Cas | CAS_Class1-Subtype-IV-B | NC_014364.1_2494 | NC_014364.1_2499 | NC_014364.1_2494,NC_014364.1_2496,NC_014364.1_2497,NC_014364.1_2498,NC_014364.1_2499 | 5 | csf1gr8_IV-A_5,csf2gr7_IV_1,csf3gr5_IV-B_1,csf4gr11_IV-B_4,cysH_IV-B_1 |
| NC_014364.1_AbiE_1 | AbiE | AbiE | NC_014364.1_2619 | NC_014364.1_2620 | NC_014364.1_2619,NC_014364.1_2620 | 2 | AbiEii__AbiEi_4,AbiEii__AbiEii |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_014364.1|provirus_2666253_2703772 | 37520 | 56 | 15 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 2666253-2703772 |
| NC_014364.1|provirus_2976748_3014759 | 38012 | 44 | 12 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 2976748-3014759 |
| NC_014364.1|provirus_2119034_2157334 | 38301 | 47 | 12 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 2119034-2157334 |
| NC_014364.1|provirus_2329685_2350621 | 20937 | 29 | 6 | Low-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 2329685-2350621 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.12.2 Prophages
Select prophage to show:
2.12.2.1 Phage ID: NC_014364.1|provirus_2666253_2703772
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_014364.1|provirus_2666253_2703772_2490 | 1263 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2491 | 441 | GENOMAD.167054.PV | PF06892;TIGR02612;COG3655 | mobile mystery protein A |
| NC_014364.1|provirus_2666253_2703772_2492 | 384 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2493 | 249 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2494 | 417 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2495 | 561 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2496 | 426 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2497 | 249 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2498 | 102 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2499 | 372 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2500 | 234 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2501 | 612 | GENOMAD.008561.VV | PF16778 | Phage tail assembly chaperone protein |
| NC_014364.1|provirus_2666253_2703772_2502 | 3315 | GENOMAD.109300.VV | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2503 | 2178 | GENOMAD.040051.VV | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2504 | 276 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2505 | 402 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2506 | 756 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2507 | 399 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2508 | 426 | GENOMAD.060383.VV | PF04883;TIGR01725;COG5005 | phage protein, HK97 gp10 family |
| NC_014364.1|provirus_2666253_2703772_2509 | 558 | GENOMAD.080176.VV | PF11436;TIGR02215 | phage conserved hypothetical protein, phiE125 gp8 family |
| NC_014364.1|provirus_2666253_2703772_2510 | 414 | GENOMAD.210649.VV | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2511 | 1251 | GENOMAD.090434.VV | PF05065;TIGR01554;COG4653 | phage major capsid protein, HK97 family |
| NC_014364.1|provirus_2666253_2703772_2512 | 708 | GENOMAD.126169.VV | PF04586;K06904;COG3740;TIGR01543 | Phage head maturation protease |
| NC_014364.1|provirus_2666253_2703772_2513 | 1617 | GENOMAD.179073.VP | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2514 | 1725 | GENOMAD.194580.VP | PF03354;PF05521;PF20441;COG4626;TIGR01563 | Phage terminase-like protein, large subunit, contains N-terminal HTH domain |
| NC_014364.1|provirus_2666253_2703772_2515 | 510 | GENOMAD.170837.VV | PF05119;COG3747;TIGR01558 | Phage terminase, small subunit |
| NC_014364.1|provirus_2666253_2703772_2516 | 399 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2517 | 708 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2518 | 237 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2519 | 678 | GENOMAD.222821.VP | TIGR03116 | CRISPR type IV/AFERR-associated protein Csf3 |
| NC_014364.1|provirus_2666253_2703772_2520 | 942 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2521 | 354 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2522 | 741 | GENOMAD.222446.VP | TIGR03114 | CRISPR type AFERR-associated protein Csf1 |
| NC_014364.1|provirus_2666253_2703772_2523 | 186 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2524 | 192 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2525 | 219 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2526 | 402 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2527 | 1089 | GENOMAD.018355.VV | PF09681;TIGR01714 | phage replisome organizer, putative, N-terminal region |
| NC_014364.1|provirus_2666253_2703772_2528 | 597 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2529 | 414 | GENOMAD.002027.VV | PF05766 | Bacteriophage Lambda NinG protein |
| NC_014364.1|provirus_2666253_2703772_2530 | 2514 | GENOMAD.126436.VP | PF13872 | NA |
| NC_014364.1|provirus_2666253_2703772_2531 | 477 | GENOMAD.111167.VV | PF16784 | Putative HNHc nuclease |
| NC_014364.1|provirus_2666253_2703772_2532 | 606 | GENOMAD.176983.VP | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2533 | 813 | GENOMAD.177891.VP | PF03837;TIGR01913;COG3723 | phage recombination protein Bet |
| NC_014364.1|provirus_2666253_2703772_2534 | 756 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2535 | 204 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2536 | 735 | GENOMAD.014438.VV | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2537 | 348 | GENOMAD.100208.VV | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2538 | 264 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2539 | 342 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2540 | 423 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2541 | 219 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2542 | 348 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2543 | 504 | NA | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2544 | 291 | GENOMAD.219421.VC | NA | NA |
| NC_014364.1|provirus_2666253_2703772_2545 | 363 | GENOMAD.227798.VP | NA | NA |
2.12.2.2 Phage ID: NC_014364.1|provirus_2976748_3014759
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_014364.1|provirus_2976748_3014759_2796 | 1251 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2797 | 474 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2798 | 186 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2799 | 315 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2800 | 456 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2801 | 381 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2802 | 228 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2803 | 543 | GENOMAD.112664.VP | PF11195 | NA |
| NC_014364.1|provirus_2976748_3014759_2804 | 255 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2805 | 1092 | GENOMAD.032961.VV | PF13479;TIGR01618;COG2087;K04484 | phage nucleotide-binding protein |
| NC_014364.1|provirus_2976748_3014759_2806 | 651 | GENOMAD.025041.VV | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2807 | 639 | GENOMAD.067346.VV | PF06023;TIGR00372;COG4343 | CRISPR-associated protein Cas4 |
| NC_014364.1|provirus_2976748_3014759_2808 | 474 | GENOMAD.111167.VV | PF16784 | Putative HNHc nuclease |
| NC_014364.1|provirus_2976748_3014759_2809 | 447 | GENOMAD.002027.VV | PF05766 | Bacteriophage Lambda NinG protein |
| NC_014364.1|provirus_2976748_3014759_2810 | 543 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2811 | 1098 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2812 | 402 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2813 | 219 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2814 | 207 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2815 | 720 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2816 | 870 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2817 | 678 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2818 | 177 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2819 | 543 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2820 | 330 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2821 | 1683 | GENOMAD.060970.VV | PF12236 | Bacteriophage head to tail connecting protein |
| NC_014364.1|provirus_2976748_3014759_2822 | 303 | GENOMAD.118268.VV | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2823 | 807 | GENOMAD.072294.VV | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2824 | 987 | GENOMAD.004790.VV | PF19307 | Phage capsid-like protein |
| NC_014364.1|provirus_2976748_3014759_2825 | 375 | GENOMAD.013948.VV | PF21190 | Bbp16 |
| NC_014364.1|provirus_2976748_3014759_2826 | 315 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2827 | 594 | GENOMAD.061091.VV | PF17212 | Tail tubular protein |
| NC_014364.1|provirus_2976748_3014759_2828 | 1713 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2829 | 888 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2830 | 1947 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2831 | 6246 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2832 | 3657 | GENOMAD.089557.VV | K03987 | NA |
| NC_014364.1|provirus_2976748_3014759_2833 | 612 | GENOMAD.007262.VV | PF16778 | Phage tail assembly chaperone protein |
| NC_014364.1|provirus_2976748_3014759_2834 | 234 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2835 | 480 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2836 | 222 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2837 | 417 | NA | NA | NA |
| NC_014364.1|provirus_2976748_3014759_2838 | 1110 | NA | NA | NA |
2.12.2.3 Phage ID: NC_014364.1|provirus_2119034_2157334
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_014364.1|provirus_2119034_2157334_1977 | 765 | GENOMAD.168064.VC | TIGR02869 | spore cortex-lytic enzyme |
| NC_014364.1|provirus_2119034_2157334_1978 | 1188 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1979 | 282 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1980 | 1875 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1981 | 1542 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1982 | 1671 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1983 | 1191 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1984 | 219 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1985 | 369 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1986 | 189 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1987 | 489 | GENOMAD.053051.VV | PF10772;PF02086;TIGR00571;COG0338 | Bacteriophage HP1, Orf24; D12 class N6 adenine-specific DNA methyltransferase |
| NC_014364.1|provirus_2119034_2157334_1988 | 348 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1989 | 819 | GENOMAD.177891.VP | PF03837;TIGR01913;COG3723 | phage recombination protein Bet |
| NC_014364.1|provirus_2119034_2157334_1990 | 690 | GENOMAD.183319.VP | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1991 | 477 | GENOMAD.111167.VV | PF16784 | Putative HNHc nuclease |
| NC_014364.1|provirus_2119034_2157334_1992 | 393 | GENOMAD.002027.VV | PF05766 | Bacteriophage Lambda NinG protein |
| NC_014364.1|provirus_2119034_2157334_1993 | 603 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1994 | 1089 | GENOMAD.018355.VV | PF09681;TIGR01714 | phage replisome organizer, putative, N-terminal region |
| NC_014364.1|provirus_2119034_2157334_1995 | 402 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1996 | 219 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1997 | 435 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1998 | 729 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_1999 | 510 | GENOMAD.170837.VV | PF05119;COG3747;TIGR01558 | Phage terminase, small subunit |
| NC_014364.1|provirus_2119034_2157334_2000 | 1722 | GENOMAD.194580.VP | PF03354;PF05521;PF20441;COG4626;TIGR01563 | Phage terminase-like protein, large subunit, contains N-terminal HTH domain |
| NC_014364.1|provirus_2119034_2157334_2001 | 1242 | GENOMAD.179073.VP | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2002 | 834 | GENOMAD.096083.VP | PF00574;K01358;TIGR00493;COG0740 | ATP-dependent Clp endopeptidase, proteolytic subunit ClpP |
| NC_014364.1|provirus_2119034_2157334_2003 | 1200 | GENOMAD.080602.VV | PF05135;TIGR02215 | phage conserved hypothetical protein, phiE125 gp8 family |
| NC_014364.1|provirus_2119034_2157334_2004 | 423 | GENOMAD.129880.VV | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2005 | 558 | GENOMAD.080176.VV | PF11436;TIGR02215 | phage conserved hypothetical protein, phiE125 gp8 family |
| NC_014364.1|provirus_2119034_2157334_2006 | 453 | GENOMAD.060383.VV | PF04883;TIGR01725;COG5005 | phage protein, HK97 gp10 family |
| NC_014364.1|provirus_2119034_2157334_2007 | 399 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2008 | 696 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2009 | 402 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2010 | 276 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2011 | 2274 | GENOMAD.009561.VV | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2012 | 3279 | GENOMAD.109300.VV | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2013 | 612 | GENOMAD.008561.VV | PF16778 | Phage tail assembly chaperone protein |
| NC_014364.1|provirus_2119034_2157334_2014 | 234 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2015 | 471 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2016 | 249 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2017 | 390 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2018 | 369 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2019 | 324 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2020 | 786 | NA | NA | NA |
| NC_014364.1|provirus_2119034_2157334_2021 | 1242 | NA | NA | NA |
2.12.2.4 Phage ID: NC_014364.1|provirus_2329685_2350621
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_014364.1|provirus_2329685_2350621_2174 | 1266 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2175 | 516 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2176 | 384 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2177 | 1224 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2178 | 618 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2179 | 1035 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2180 | 1068 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2181 | 342 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2182 | 231 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2183 | 246 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2184 | 204 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2185 | 543 | GENOMAD.112664.VP | PF11195 | NA |
| NC_014364.1|provirus_2329685_2350621_2186 | 255 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2187 | 1116 | GENOMAD.090362.VV | PF13479;TIGR01618;COG2087 | phage nucleotide-binding protein |
| NC_014364.1|provirus_2329685_2350621_2188 | 651 | GENOMAD.025041.VV | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2189 | 639 | GENOMAD.067346.VV | PF06023;TIGR00372;COG4343 | CRISPR-associated protein Cas4 |
| NC_014364.1|provirus_2329685_2350621_2190 | 474 | GENOMAD.111167.VV | PF16784 | Putative HNHc nuclease |
| NC_014364.1|provirus_2329685_2350621_2191 | 234 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2192 | 540 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2193 | 1056 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2194 | 414 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2195 | 219 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2196 | 192 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2197 | 201 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2198 | 1287 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2199 | 981 | NA | NA | NA |
| NC_014364.1|provirus_2329685_2350621_2200 | 507 | GENOMAD.170837.VV | PF05119;COG3747;TIGR01558 | Phage terminase, small subunit |
| NC_014364.1|provirus_2329685_2350621_2201 | 1323 | GENOMAD.194580.VP | PF03354;PF05521;PF20441;COG4626;TIGR01563 | Phage terminase-like protein, large subunit, contains N-terminal HTH domain |
2.12.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_014364.1|provirus_2666253_2703772 | sequence_000000.fasta.fasta | 1_1 | 0.05 | average | ANImf | 1 |
| NC_014364.1|provirus_2976748_3014759 | sequence_000002.fasta.fasta | 1_2 | 0.05 | average | ANImf | 1 |
| NC_014364.1|provirus_2119034_2157334 | sequence_000001.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
| NC_014364.1|provirus_2329685_2350621 | sequence_000003.fasta.fasta | 3_0 | 0.05 | average | ANImf | 3 |
Primary clustering plot
2.12.4 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_014364.1|provirus_2119034_2157334 | RS_GCF_000143985.1 | d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-16054;f__Sediminispirochaetaceae;g__Sediminispirochaeta;s__Sediminispirochaeta smaragdinae | CRISPR | 95.4 | blast;94.80 iPHoP-RF;70.40 |
| NC_014364.1|provirus_2119034_2157334 | RS_GCF_000378205.1 | d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-16054;f__Sediminispirochaetaceae;g__Sediminispirochaeta;s__Sediminispirochaeta bajacaliforniensis | CRISPR | 93.4 | blast;92.00 |
| NC_014364.1|provirus_2329685_2350621 | RS_GCF_000143985.1 | d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-16054;f__Sediminispirochaetaceae;g__Sediminispirochaeta;s__Sediminispirochaeta smaragdinae | blast | 95.7 | iPHoP-RF;65.10 |
| NC_014364.1|provirus_2329685_2350621 | RS_GCF_000378205.1 | d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-16054;f__Sediminispirochaetaceae;g__Sediminispirochaeta;s__Sediminispirochaeta bajacaliforniensis | blast | 92.1 | iPHoP-RF;52.80 |
| NC_014364.1|provirus_2666253_2703772 | RS_GCF_000143985.1 | d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-16054;f__Sediminispirochaetaceae;g__Sediminispirochaeta;s__Sediminispirochaeta smaragdinae | blast | 96.2 | CRISPR;74.20 iPHoP-RF;72.60 |
| NC_014364.1|provirus_2976748_3014759 | RS_GCF_000143985.1 | d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-16054;f__Sediminispirochaetaceae;g__Sediminispirochaeta;s__Sediminispirochaeta smaragdinae | blast | 96.2 | iPHoP-RF;69.80 |
2.12.5 AMG Predictions
Prediction of auxiliary metabolic genes in the prophage contigs.
| protein | scaffold | amg_ko | amg_ko_name | pfam | pfam_name |
|---|---|---|---|---|---|
| NC_014364.1|provirus_2666253_2703772_28 | NC_014364.1|provirus_2666253_2703772 | K00390 | cysH; phosphoadenosine phosphosulfate reductase [EC:1.8.4.8 1.8.4.10] | PF01507.19 | Phosphoadenosine phosphosulfate reductase family |
2.13 NC_015761
2.13.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella bongori |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 4460105 | 100 | 0.14 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_015761.1_PrrC_6 | PrrC | PrrC | NC_015761.1_263 | NC_015761.1_265 | NC_015761.1_263,NC_015761.1_264,NC_015761.1_265 | 3 | PrrC__EcoprrI,PrrC__EcoprrI,RM__Type_I_REases_FAM_0.einsi_trimmed |
| NC_015761.1_DarTG_2 | DarTG | DarTG | NC_015761.1_279 | NC_015761.1_280 | NC_015761.1_279,NC_015761.1_280 | 2 | DarTG__DarG,DarTG__DarT |
| NC_015761.1_RM_Type_III_7 | RM | RM_Type_III | NC_015761.1_310 | NC_015761.1_311 | NC_015761.1_310,NC_015761.1_311 | 2 | RM_Type_III__Type_III_MTases_FAM_0,RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed |
| NC_015761.1_PfiAT_4 | PfiAT | PfiAT | NC_015761.1_932 | NC_015761.1_933 | NC_015761.1_932,NC_015761.1_933 | 2 | PfiAT__PfiA,PfiAT__PfiT |
| NC_015761.1_CAS_Class1-Subtype-I-E_8 | Cas | CAS_Class1-Subtype-I-E | NC_015761.1_2549 | NC_015761.1_2556 | NC_015761.1_2549,NC_015761.1_2550,NC_015761.1_2551,NC_015761.1_2552,NC_015761.1_2553,NC_015761.1_2554,NC_015761.1_2555,NC_015761.1_2556 | 8 | cas1_I-E_1,cas2_I-E_2,cas3_I_5,cas5_I-E_3,cas6e_I_II_III_IV_V_VI_1,cas7_I-E_2,cas8e_I-E_1,cse2gr11_I-E_2 |
| NC_015761.1_dCTPdeaminase_5 | dCTPdeaminase | dCTPdeaminase | NC_015761.1_3620 | NC_015761.1_3620 | NC_015761.1_3620 | 1 | dCTPdeaminase__dCTPdeaminase |
| NC_015761.1_Mokosh_TypeII_3 | Mokosh | Mokosh_TypeII | NC_015761.1_3957 | NC_015761.1_3957 | NC_015761.1_3957 | 1 | Mokosh_TypeII__MkoC |
| NC_015761.1_DS-17_1 | DS-17 | DS-17 | NC_015761.1_3965 | NC_015761.1_3965 | NC_015761.1_3965 | 1 | DS-17__DS-17 |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_015761.1|provirus_3084741_3115735 | 30995 | 41 | 32 | High-quality | High-quality | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 3084741-3115735 |
| NC_015761.1|provirus_847397_862760 | 15364 | 19 | 11 | Low-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 847397-862760 |
| NC_015761.1|provirus_1007223_1043740 | 36518 | 51 | 17 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1007223-1043740 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.13.2 Prophages
Select prophage to show:
2.13.2.1 Phage ID: NC_015761.1|provirus_3084741_3115735
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_015761.1|provirus_3084741_3115735_2808 | 219 | GENOMAD.223866.VP | PF04606;TIGR02098 | Ogr/Delta-like zinc finger |
| NC_015761.1|provirus_3084741_3115735_2809 | 1170 | GENOMAD.209614.VP | PF05954;K06905;COG3500;TIGR03361 | Phage protein D |
| NC_015761.1|provirus_3084741_3115735_2810 | 486 | GENOMAD.125908.VV | PF06995;K06906;COG3499 | Phage P2 GpU |
| NC_015761.1|provirus_3084741_3115735_2811 | 2442 | GENOMAD.130201.VP | COG5283 | Phage-related tail protein |
| NC_015761.1|provirus_3084741_3115735_2812 | 336 | GENOMAD.135969.VP | PF10109 | Phage tail assembly chaperone proteins, E, or 41 or 14 |
| NC_015761.1|provirus_3084741_3115735_2813 | 519 | GENOMAD.222086.VV | PF04985;K06908;TIGR01611;COG3498 | phage contractile tail tube protein, P2 family |
| NC_015761.1|provirus_3084741_3115735_2814 | 1188 | GENOMAD.102019.VV | PF10758;COG3497 | Phage tail sheath protein FI |
| NC_015761.1|provirus_3084741_3115735_2815 | 549 | GENOMAD.209102.VP | NA | NA |
| NC_015761.1|provirus_3084741_3115735_2816 | 1977 | GENOMAD.151930.VP | PF12571;COG5301 | Phage-related tail fibre protein |
| NC_015761.1|provirus_3084741_3115735_2817 | 531 | GENOMAD.114503.VV | PF09684;COG4385;TIGR01634 | Bacteriophage P2-related tail formation protein |
| NC_015761.1|provirus_3084741_3115735_2818 | 909 | GENOMAD.105501.VV | PF03434;COG3948 | Phage-related baseplate assembly protein |
| NC_015761.1|provirus_3084741_3115735_2819 | 348 | GENOMAD.123275.VP | PF04965;K06903;COG3628;TIGR03357 | Phage baseplate assembly protein W |
| NC_015761.1|provirus_3084741_3115735_2820 | 642 | GENOMAD.166314.VP | K22111;TIGR01644;COG4540 | phage baseplate assembly protein V |
| NC_015761.1|provirus_3084741_3115735_2821 | 450 | GENOMAD.140989.VP | PF05069;TIGR01635;COG5005 | phage virion morphogenesis (putative tail completion) protein |
| NC_015761.1|provirus_3084741_3115735_2822 | 468 | GENOMAD.125799.VP | PF06891 | P2 phage tail completion protein R (GpR) |
| NC_015761.1|provirus_3084741_3115735_2823 | 159 | GENOMAD.116277.VV | NA | NA |
| NC_015761.1|provirus_3084741_3115735_2824 | 414 | GENOMAD.191084.VP | PF10828;TIGR03495 | phage lysis regulatory protein, LysB family |
| NC_015761.1|provirus_3084741_3115735_2825 | 498 | NA | NA | NA |
| NC_015761.1|provirus_3084741_3115735_2826 | 297 | GENOMAD.177230.VP | PF04550;TIGR01594 | Phage holin family 2 |
| NC_015761.1|provirus_3084741_3115735_2827 | 189 | GENOMAD.159179.VP | COG5004;K06370 | P2-like prophage tail protein X |
| NC_015761.1|provirus_3084741_3115735_2828 | 507 | GENOMAD.119083.VV | PF05926 | Phage head completion protein (GPL) |
| NC_015761.1|provirus_3084741_3115735_2829 | 750 | GENOMAD.034571.VV | PF05944 | Phage small terminase subunit |
| NC_015761.1|provirus_3084741_3115735_2830 | 1068 | GENOMAD.125799.VP | PF06891 | P2 phage tail completion protein R (GpR) |
| NC_015761.1|provirus_3084741_3115735_2831 | 855 | GENOMAD.042716.VV | COG4388 | Mu-like prophage I protein |
| NC_015761.1|provirus_3084741_3115735_2832 | 1770 | GENOMAD.151636.VP | COG5484 | Uncharacterized protein YjcR, contains N-terminal HTH domain |
| NC_015761.1|provirus_3084741_3115735_2833 | 1047 | NA | NA | NA |
| NC_015761.1|provirus_3084741_3115735_2834 | 1005 | NA | NA | NA |
| NC_015761.1|provirus_3084741_3115735_2835 | 549 | NA | NA | NA |
| NC_015761.1|provirus_3084741_3115735_2836 | 732 | GENOMAD.226160.VP | NA | NA |
| NC_015761.1|provirus_3084741_3115735_2837 | 441 | GENOMAD.137104.VV | NA | NA |
| NC_015761.1|provirus_3084741_3115735_2838 | 2220 | GENOMAD.182861.VP | PF05840 | Bacteriophage replication gene A protein (GPA) |
| NC_015761.1|provirus_3084741_3115735_2839 | 522 | GENOMAD.170058.VV | NA | NA |
| NC_015761.1|provirus_3084741_3115735_2840 | 225 | NA | NA | NA |
| NC_015761.1|provirus_3084741_3115735_2841 | 228 | GENOMAD.071646.VV | PF10809 | NA |
| NC_015761.1|provirus_3084741_3115735_2842 | 201 | GENOMAD.167874.VV | NA | NA |
| NC_015761.1|provirus_3084741_3115735_2843 | 228 | GENOMAD.087231.VV | PF10893 | Bacteriophage 186, Fil |
| NC_015761.1|provirus_3084741_3115735_2844 | 510 | GENOMAD.170830.VP | PF06892 | Phage regulatory protein CII (CP76) |
| NC_015761.1|provirus_3084741_3115735_2845 | 264 | GENOMAD.120542.VV | PF07618;COG3311;TIGR02405 | Putative transcription regulator (DUF1323) |
| NC_015761.1|provirus_3084741_3115735_2846 | 579 | GENOMAD.069724.VV | PF16452 | Bacteriophage CI repressor C-terminal domain |
| NC_015761.1|provirus_3084741_3115735_2847 | 1038 | GENOMAD.212346.VP | PF16452;PF06892;COG1974 | Bacteriophage CI repressor C-terminal domain; Phage regulatory protein CII (CP76) |
| NC_015761.1|provirus_3084741_3115735_2848 | 336 | NA | NA | NA |
2.13.2.2 Phage ID: NC_015761.1|provirus_847397_862760
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_015761.1|provirus_847397_862760_745 | 240 | NA | NA | NA |
| NC_015761.1|provirus_847397_862760_746 | 414 | GENOMAD.138177.VP | PF04717;PF18715;COG4540;TIGR01644 | Phage P2 baseplate assembly protein gpV |
| NC_015761.1|provirus_847397_862760_747 | 360 | GENOMAD.121581.VP | PF04965;COG3628;K06903;TIGR03357 | Phage baseplate assembly protein W |
| NC_015761.1|provirus_847397_862760_748 | 909 | GENOMAD.105501.VV | PF03434;COG3948 | Phage-related baseplate assembly protein |
| NC_015761.1|provirus_847397_862760_749 | 606 | GENOMAD.114503.VV | PF09684;COG4385;TIGR01634 | Bacteriophage P2-related tail formation protein |
| NC_015761.1|provirus_847397_862760_750 | 918 | GENOMAD.118528.VP | PF12571;COG5301 | Phage-related tail fibre protein |
| NC_015761.1|provirus_847397_862760_751 | 1158 | NA | NA | NA |
| NC_015761.1|provirus_847397_862760_752 | 465 | GENOMAD.168001.VP | PF16778 | Phage tail assembly chaperone protein |
| NC_015761.1|provirus_847397_862760_753 | 255 | NA | NA | NA |
| NC_015761.1|provirus_847397_862760_754 | 258 | NA | NA | NA |
| NC_015761.1|provirus_847397_862760_755 | 186 | GENOMAD.120968.VV | COG3497 | Phage tail sheath protein FI |
| NC_015761.1|provirus_847397_862760_756 | 303 | GENOMAD.135969.VP | PF10109 | Phage tail assembly chaperone proteins, E, or 41 or 14 |
| NC_015761.1|provirus_847397_862760_757 | 1149 | GENOMAD.130201.VP | COG5283 | Phage-related tail protein |
| NC_015761.1|provirus_847397_862760_758 | 2025 | GENOMAD.096277.VV | NA | NA |
| NC_015761.1|provirus_847397_862760_759 | 387 | GENOMAD.116424.VV | PF06995;K06906;COG3499 | Phage protein U |
| NC_015761.1|provirus_847397_862760_760 | 1053 | GENOMAD.129122.VP | PF05954;K06905;COG3500;TIGR03361 | Phage protein D |
| NC_015761.1|provirus_847397_862760_761 | 219 | GENOMAD.222803.VP | PF04606;TIGR04165;COG1326 | Ogr/Delta-like zinc finger |
| NC_015761.1|provirus_847397_862760_762 | 1686 | NA | NA | NA |
| NC_015761.1|provirus_847397_862760_763 | 378 | NA | NA | NA |
2.13.2.3 Phage ID: NC_015761.1|provirus_1007223_1043740
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_015761.1|provirus_1007223_1043740_886 | 1020 | GENOMAD.212993.VP | PF14659;K21039 | Phage integrase, N-terminal SAM-like domain |
| NC_015761.1|provirus_1007223_1043740_887 | 225 | GENOMAD.151670.VV | PF13986 | NA |
| NC_015761.1|provirus_1007223_1043740_888 | 141 | GENOMAD.224144.VP | PF10798;K21975 | Biofilm development protein YmgB/AriR |
| NC_015761.1|provirus_1007223_1043740_889 | 807 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_890 | 849 | GENOMAD.212816.VV | PF20613;TIGR03843 | HipA-like kinase |
| NC_015761.1|provirus_1007223_1043740_891 | 468 | GENOMAD.091484.VV | PF13411;COG3415;K22302;TIGR00721 | Transposase |
| NC_015761.1|provirus_1007223_1043740_892 | 228 | GENOMAD.151341.VV | PF11242;TIGR00673;COG5606;K18830 | cyanase |
| NC_015761.1|provirus_1007223_1043740_893 | 321 | GENOMAD.069430.VV | PF18010;TIGR00721;COG4220 | Cry35Ab1 HTH C-terminal domain |
| NC_015761.1|provirus_1007223_1043740_894 | 906 | GENOMAD.208204.VP | PF04492;TIGR01610 | phage replication protein O, N-terminal domain |
| NC_015761.1|provirus_1007223_1043740_895 | 693 | GENOMAD.194512.VV | PF06992 | NA |
| NC_015761.1|provirus_1007223_1043740_896 | 258 | GENOMAD.072808.VV | PF15944 | NA |
| NC_015761.1|provirus_1007223_1043740_897 | 912 | GENOMAD.068933.VV | NA | NA |
| NC_015761.1|provirus_1007223_1043740_898 | 327 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_899 | 108 | GENOMAD.226031.VP | NA | NA |
| NC_015761.1|provirus_1007223_1043740_900 | 432 | GENOMAD.213484.VP | PF05509;COG4877 | Plasmid stability protein |
| NC_015761.1|provirus_1007223_1043740_901 | 168 | GENOMAD.168832.VV | NA | NA |
| NC_015761.1|provirus_1007223_1043740_902 | 915 | GENOMAD.222649.VP | PF10548;PF10547;COG3617 | Prophage antirepressor |
| NC_015761.1|provirus_1007223_1043740_903 | 747 | GENOMAD.167364.VP | NA | NA |
| NC_015761.1|provirus_1007223_1043740_904 | 234 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_905 | 603 | GENOMAD.040195.VV | PF07105 | NA |
| NC_015761.1|provirus_1007223_1043740_906 | 672 | GENOMAD.058019.VV | PF06323 | Phage antitermination protein Q |
| NC_015761.1|provirus_1007223_1043740_907 | 573 | GENOMAD.209828.VP | PF10543;COG3646 | ORF6N domain |
| NC_015761.1|provirus_1007223_1043740_908 | 501 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_909 | 180 | GENOMAD.175300.VV | NA | NA |
| NC_015761.1|provirus_1007223_1043740_910 | 426 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_911 | 744 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_912 | 390 | GENOMAD.222896.VP | PF16931 | Putative phage holin |
| NC_015761.1|provirus_1007223_1043740_913 | 282 | GENOMAD.214895.VP | PF05449 | Putative 3TM holin, Phage_holin_3 |
| NC_015761.1|provirus_1007223_1043740_914 | 615 | GENOMAD.021660.VV | COG3179;K18950 | Predicted chitinase |
| NC_015761.1|provirus_1007223_1043740_915 | 543 | GENOMAD.108518.VV | NA | NA |
| NC_015761.1|provirus_1007223_1043740_916 | 531 | GENOMAD.068419.VV | PF10549 | ORF11CD3 domain |
| NC_015761.1|provirus_1007223_1043740_917 | 360 | GENOMAD.062288.VV | PF10721 | NA |
| NC_015761.1|provirus_1007223_1043740_918 | 411 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_919 | 306 | GENOMAD.210890.VV | NA | NA |
| NC_015761.1|provirus_1007223_1043740_920 | 351 | GENOMAD.179073.VP | NA | NA |
| NC_015761.1|provirus_1007223_1043740_921 | 258 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_922 | 1113 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_923 | 117 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_924 | 579 | GENOMAD.222575.VP | PF06416 | Effector protein NleG |
| NC_015761.1|provirus_1007223_1043740_925 | 2349 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_926 | 1131 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_927 | 198 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_928 | 330 | GENOMAD.182552.PC | PF15781;COG3668;TIGR00053;K06218 | Plasmid stabilization system protein ParE |
| NC_015761.1|provirus_1007223_1043740_929 | 231 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_930 | 294 | GENOMAD.221919.VP | PF00589 | Phage integrase family |
| NC_015761.1|provirus_1007223_1043740_931 | 579 | GENOMAD.222575.VP | PF06416 | Effector protein NleG |
| NC_015761.1|provirus_1007223_1043740_932 | 348 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_933 | 855 | GENOMAD.120636.VV | PF09612;TIGR02192 | protein YibB |
| NC_015761.1|provirus_1007223_1043740_934 | 231 | NA | NA | NA |
| NC_015761.1|provirus_1007223_1043740_935 | 2808 | NA | NA | NA |
2.13.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_015761.1|provirus_3084741_3115735 | sequence_000000.fasta.fasta | 1_0 | 0.05 | average | ANImf | 1 |
| NC_015761.1|provirus_847397_862760 | sequence_000001.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
| NC_015761.1|provirus_1007223_1043740 | sequence_000002.fasta.fasta | 3_0 | 0.05 | average | ANImf | 3 |
Primary clustering plot
2.13.4 Virulence Genes
Screening of virulence genes present in the prophage contigs.
| sequence | start | end | strand | gene | coverage | coverage_map | gaps | percent_coverage | percent_identity | database | accession | product | resistance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NC_015761.1|provirus_1007223_1043740 | 24347 | 26694 |
|
sopA | 1-2348/2349 | =============== | 0/0 | 99.96 | 89.91 | vfdb | NP_461011 | (sopA) type III secretion system effector SopA E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | NA |
2.13.5 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_015761.1|provirus_1007223_1043740 | GB_GCA_900446925.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_B;s__Citrobacter_B koseri | blast | 96.9 | iPHoP-RF;82.80 |
| NC_015761.1|provirus_1007223_1043740 | GB_GCA_900478215.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella houtenae | blast | 96.9 | iPHoP-RF;83.30 |
| NC_015761.1|provirus_1007223_1043740 | RS_GCF_000006945.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella enterica | blast | 96.9 | iPHoP-RF;86.70 |
| NC_015761.1|provirus_1007223_1043740 | RS_GCF_000252995.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella bongori | blast | 96.9 | iPHoP-RF;84.20 |
| NC_015761.1|provirus_1007223_1043740 | RS_GCF_008692785.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella diarizonae | blast | 96.9 | iPHoP-RF;87.60 |
| NC_015761.1|provirus_1007223_1043740 | RS_GCF_008692845.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella arizonae | blast | 96.9 | iPHoP-RF;87.60 |
| NC_015761.1|provirus_1007223_1043740 | RS_GCF_006874705.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia;s__Leclercia adecarboxylata_C | blast | 92.7 | None |
| NC_015761.1|provirus_3084741_3115735 | RS_GCF_000006945.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella enterica | CRISPR | 98.5 | blast;96.80 iPHoP-RF;89.80 |
| NC_015761.1|provirus_3084741_3115735 | RS_GCF_008692785.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella diarizonae | CRISPR | 98.1 | iPHoP-RF;90.80 |
| NC_015761.1|provirus_3084741_3115735 | RS_GCF_000252995.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella bongori | blast | 96.9 | iPHoP-RF;90.10 |
| NC_015761.1|provirus_3084741_3115735 | RS_GCF_002918555.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_C;s__Citrobacter_C amalonaticus_A | blast | 93.2 | None |
| NC_015761.1|provirus_3084741_3115735 | GB_GCA_900446925.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_B;s__Citrobacter_B koseri | iPHoP-RF | 92.1 | CRISPR;67.50 |
| NC_015761.1|provirus_847397_862760 | RS_GCF_003697165.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli | blast | 96.9 | iPHoP-RF;88.90 |
| NC_015761.1|provirus_847397_862760 | RS_GCF_000759775.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia albertii | blast | 96.3 | iPHoP-RF;86.70 |
| NC_015761.1|provirus_847397_862760 | RS_GCF_001729745.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter;s__Enterobacter hormaechei_A | blast | 96.2 | iPHoP-RF;73.00 |
| NC_015761.1|provirus_847397_862760 | RS_GCF_000252995.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella bongori | blast | 93.9 | iPHoP-RF;71.50 |
| NC_015761.1|provirus_847397_862760 | GB_GCA_900478215.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella houtenae | blast | 91.9 | iPHoP-RF;73.70 |
| NC_015761.1|provirus_847397_862760 | RS_GCF_000006945.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella enterica | blast | 91.7 | iPHoP-RF;88.50 |
| NC_015761.1|provirus_847397_862760 | RS_GCF_008692845.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella arizonae | blast | 91.7 | iPHoP-RF;84.50 |
| NC_015761.1|provirus_847397_862760 | RS_GCF_002900365.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia marmotae | blast | 90.0 | iPHoP-RF;87.00 |
2.14 NC_017033
2.14.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria;s__Frateuria aurantia |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 3603458 | 99.99 | 0.04 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_017033.1_PrrC_3 | PrrC | PrrC | NC_017033.1_586 | NC_017033.1_589 | NC_017033.1_586,NC_017033.1_587,NC_017033.1_588,NC_017033.1_589 | 4 | PrrC__EcoprrI,PrrC__PrrC,RM__Type_I_REases_FAM_0.einsi_trimmed,RM__Type_I_S_02 |
| NC_017033.1_DS-6_1 | DS-6 | DS-6 | NC_017033.1_1067 | NC_017033.1_1068 | NC_017033.1_1067,NC_017033.1_1068 | 2 | DS-6__DS-6A,DS-6__DS-6B |
| NC_017033.1_Mokosh_TypeII_2 | Mokosh | Mokosh_TypeII | NC_017033.1_1863 | NC_017033.1_1863 | NC_017033.1_1863 | 1 | Mokosh_TypeII__MkoC |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_017033.1|provirus_1557694_1600481 | 42788 | 71 | 28 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1557694-1600481 |
| NC_017033.1|provirus_1050333_1094910 | 44578 | 68 | 28 | High-quality | High-quality | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1050333-1094910 |
| NC_017033.1|provirus_2089294_2107522 | 18229 | 25 | 3 | Low-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 2089294-2107522 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.14.2 Prophages
Select prophage to show:
2.14.2.1 Phage ID: NC_017033.1|provirus_1557694_1600481
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_017033.1|provirus_1557694_1600481_1419 | 288 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1420 | 189 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1421 | 309 | GENOMAD.060822.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1422 | 369 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1423 | 279 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1424 | 330 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1425 | 1656 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1426 | 333 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1427 | 228 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1428 | 1755 | GENOMAD.151126.VP | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1429 | 741 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1430 | 285 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1431 | 195 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1432 | 216 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1433 | 126 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1434 | 834 | GENOMAD.115107.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1435 | 387 | GENOMAD.094188.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1436 | 237 | GENOMAD.189851.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1437 | 393 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1438 | 753 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1439 | 603 | GENOMAD.205774.CP | PF08000;PF20612 | Bacterial PH domain; SHOCT domain |
| NC_017033.1|provirus_1557694_1600481_1440 | 327 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1441 | 243 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1442 | 294 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1443 | 210 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1444 | 303 | GENOMAD.045996.VV | PF09012;TIGR02702;COG1777 | FeoC like transcriptional regulator |
| NC_017033.1|provirus_1557694_1600481_1445 | 876 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1446 | 492 | GENOMAD.166457.VP | PF06992 | Replication protein P |
| NC_017033.1|provirus_1557694_1600481_1447 | 207 | GENOMAD.063929.VV | PF05810;COG4068 | Predicted nucleic acid-binding protein, contains Zn-ribbon domain |
| NC_017033.1|provirus_1557694_1600481_1448 | 198 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1449 | 195 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1450 | 450 | GENOMAD.061349.VV | PF05772 | NinB protein |
| NC_017033.1|provirus_1557694_1600481_1451 | 348 | GENOMAD.036842.VV | PF07102 | Putative nuclease YbcO |
| NC_017033.1|provirus_1557694_1600481_1452 | 174 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1453 | 336 | GENOMAD.040593.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1454 | 618 | GENOMAD.069895.VV | PF17302;TIGR02642 | Tryptophan RNA-binding attenuator protein inhibitory protein |
| NC_017033.1|provirus_1557694_1600481_1455 | 264 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1456 | 504 | GENOMAD.044304.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1457 | 300 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1458 | 267 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1459 | 342 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1460 | 336 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1461 | 264 | GENOMAD.077615.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1462 | 672 | GENOMAD.076022.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1463 | 1557 | GENOMAD.013124.VV | PF13262;COG5410 | NA |
| NC_017033.1|provirus_1557694_1600481_1464 | 1539 | GENOMAD.003432.VV | PF06381;K09961;TIGR01555;COG3567 | phage-related protein, HI1409 family |
| NC_017033.1|provirus_1557694_1600481_1465 | 654 | GENOMAD.083949.VV | PF04233;COG2369;TIGR01641 | Uncharacterized conserved protein, contains phage Mu gpF-like domain |
| NC_017033.1|provirus_1557694_1600481_1466 | 180 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1467 | 1311 | GENOMAD.099067.VP | PF09979;K09960;COG3566 | NA |
| NC_017033.1|provirus_1557694_1600481_1468 | 495 | GENOMAD.033203.VV | PF23982 | Putative phage cement protein |
| NC_017033.1|provirus_1557694_1600481_1469 | 1008 | GENOMAD.085797.VV | PF09950;COG4834 | Encapsulating protein for peroxidase |
| NC_017033.1|provirus_1557694_1600481_1470 | 225 | GENOMAD.170487.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1471 | 396 | GENOMAD.005453.VV | PF11863;COG4386 | Mu-like prophage tail sheath protein gpL |
| NC_017033.1|provirus_1557694_1600481_1472 | 543 | GENOMAD.008778.VV | PF05069;COG5005;TIGR01635 | NA |
| NC_017033.1|provirus_1557694_1600481_1473 | 384 | GENOMAD.040078.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1474 | 555 | GENOMAD.023692.VV | PF23961 | Phage neck terminator protein |
| NC_017033.1|provirus_1557694_1600481_1475 | 1485 | GENOMAD.005453.VV | PF11863;COG4386 | Mu-like prophage tail sheath protein gpL |
| NC_017033.1|provirus_1557694_1600481_1476 | 441 | GENOMAD.017010.VV | PF11681 | Bacteriophage KPP10, Structural protein ORF10 |
| NC_017033.1|provirus_1557694_1600481_1477 | 390 | GENOMAD.055746.VV | PF10876 | Phage tail assembly chaperone protein, TAC |
| NC_017033.1|provirus_1557694_1600481_1478 | 2253 | GENOMAD.015777.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1479 | 621 | GENOMAD.017318.VV | COG3499 | NA |
| NC_017033.1|provirus_1557694_1600481_1480 | 315 | GENOMAD.105312.VV | PF22479 | Cyanophage baseplate Pam3 plug gp18 |
| NC_017033.1|provirus_1557694_1600481_1481 | 948 | GENOMAD.123309.VP | PF21829 | NA |
| NC_017033.1|provirus_1557694_1600481_1482 | 660 | GENOMAD.006053.VV | PF18352;COG4540;TIGR01644 | Phage protein Gp138 N-terminal domain |
| NC_017033.1|provirus_1557694_1600481_1483 | 348 | GENOMAD.009002.VV | PF10934;COG3628 | Phage baseplate assembly protein W |
| NC_017033.1|provirus_1557694_1600481_1484 | 1179 | GENOMAD.005285.VV | PF03434;COG3299 | Uncharacterized phage protein gp47/JayE |
| NC_017033.1|provirus_1557694_1600481_1485 | 585 | GENOMAD.008482.VV | PF11041;TIGR02242 | Bacteriophage Mu-like, Gp48 |
| NC_017033.1|provirus_1557694_1600481_1486 | 1809 | GENOMAD.051520.VV | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1487 | 486 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1488 | 177 | NA | NA | NA |
| NC_017033.1|provirus_1557694_1600481_1489 | 972 | NA | NA | NA |
2.14.2.2 Phage ID: NC_017033.1|provirus_1050333_1094910
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_017033.1|provirus_1050333_1094910_928 | 1320 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_929 | 546 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_930 | 204 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_931 | 1020 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_932 | 219 | GENOMAD.180717.VC | PF13986 | NA |
| NC_017033.1|provirus_1050333_1094910_933 | 249 | GENOMAD.104567.VV | NA | NA |
| NC_017033.1|provirus_1050333_1094910_934 | 228 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_935 | 282 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_936 | 258 | GENOMAD.178404.VP | NA | NA |
| NC_017033.1|provirus_1050333_1094910_937 | 684 | GENOMAD.171154.VP | PF13986;PF05551 | NA |
| NC_017033.1|provirus_1050333_1094910_938 | 351 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_939 | 252 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_940 | 480 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_941 | 303 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_942 | 276 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_943 | 129 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_944 | 690 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_945 | 279 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_946 | 432 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_947 | 192 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_948 | 294 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_949 | 168 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_950 | 258 | GENOMAD.209492.VC | NA | NA |
| NC_017033.1|provirus_1050333_1094910_951 | 564 | GENOMAD.193207.VC | NA | NA |
| NC_017033.1|provirus_1050333_1094910_952 | 357 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_953 | 696 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_954 | 213 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_955 | 510 | GENOMAD.177794.VC | PF09639 | YjcQ protein |
| NC_017033.1|provirus_1050333_1094910_956 | 627 | GENOMAD.120202.VV | PF06892 | NA |
| NC_017033.1|provirus_1050333_1094910_957 | 990 | GENOMAD.105893.VV | PF07120;COG3756 | Uncharacterized conserved protein YdaU, DUF1376 family |
| NC_017033.1|provirus_1050333_1094910_958 | 663 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_959 | 201 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_960 | 507 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_961 | 390 | GENOMAD.022482.VV | PF16786 | Recombination enhancement, RecA-dependent nuclease |
| NC_017033.1|provirus_1050333_1094910_962 | 498 | GENOMAD.159849.VP | PF07102;PF13264 | Putative nuclease YbcO |
| NC_017033.1|provirus_1050333_1094910_963 | 384 | GENOMAD.099176.VV | NA | NA |
| NC_017033.1|provirus_1050333_1094910_964 | 684 | GENOMAD.069895.VV | PF17302;TIGR02642 | Tryptophan RNA-binding attenuator protein inhibitory protein |
| NC_017033.1|provirus_1050333_1094910_965 | 306 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_966 | 315 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_967 | 507 | GENOMAD.219399.VP | PF10549;COG3646;TIGR02681 | Phage regulatory protein Rha |
| NC_017033.1|provirus_1050333_1094910_968 | 219 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_969 | 477 | GENOMAD.083189.VV | PF00959;COG3772;K01185 | Phage-related lysozyme (muramidase), GH24 family |
| NC_017033.1|provirus_1050333_1094910_970 | 483 | GENOMAD.077452.VV | PF03245;K14744 | Bacteriophage Rz lysis protein |
| NC_017033.1|provirus_1050333_1094910_971 | 342 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_972 | 531 | GENOMAD.161251.VP | PF07471;K22014;COG4220 | Phage DNA packaging protein, Nu1 subunit of terminase |
| NC_017033.1|provirus_1050333_1094910_973 | 1905 | GENOMAD.129396.VP | PF20454 | Terminase large subunit gpA, endonuclease domain |
| NC_017033.1|provirus_1050333_1094910_974 | 237 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_975 | 1602 | GENOMAD.019804.VV | PF05136;TIGR01539;COG5511 | phage portal protein, lambda family |
| NC_017033.1|provirus_1050333_1094910_976 | 1230 | GENOMAD.160855.VP | PF00574;TIGR00706;COG0740 | signal peptide peptidase SppA, 36K type |
| NC_017033.1|provirus_1050333_1094910_977 | 417 | GENOMAD.191487.VP | PF02924 | Bacteriophage lambda head decoration protein D |
| NC_017033.1|provirus_1050333_1094910_978 | 1002 | GENOMAD.124233.VP | PF03864 | Phage major capsid protein E |
| NC_017033.1|provirus_1050333_1094910_979 | 309 | GENOMAD.092349.VV | PF13856 | ATP-binding sugar transporter from pro-phage |
| NC_017033.1|provirus_1050333_1094910_980 | 597 | GENOMAD.066423.VV | PF06763 | Prophage minor tail protein Z (GPZ) |
| NC_017033.1|provirus_1050333_1094910_981 | 582 | GENOMAD.065270.VV | PF09646 | Gp37 protein |
| NC_017033.1|provirus_1050333_1094910_982 | 588 | GENOMAD.162066.VP | PF04717;COG4540;TIGR01644 | Phage P2 baseplate assembly protein gpV |
| NC_017033.1|provirus_1050333_1094910_983 | 357 | GENOMAD.099345.VV | NA | NA |
| NC_017033.1|provirus_1050333_1094910_984 | 330 | GENOMAD.136378.VP | PF05136;PF04965;TIGR01539;K06903;COG5511 | phage portal protein, lambda family |
| NC_017033.1|provirus_1050333_1094910_985 | 885 | GENOMAD.105501.VV | PF03434;COG3948 | Phage-related baseplate assembly protein |
| NC_017033.1|provirus_1050333_1094910_986 | 546 | GENOMAD.114503.VV | PF09684;COG4385;TIGR01634 | Bacteriophage P2-related tail formation protein |
| NC_017033.1|provirus_1050333_1094910_987 | 1968 | GENOMAD.208390.VP | COG5301 | Phage-related tail fibre protein |
| NC_017033.1|provirus_1050333_1094910_988 | 486 | NA | NA | NA |
| NC_017033.1|provirus_1050333_1094910_989 | 1221 | GENOMAD.102019.VV | PF10758;COG3497 | Phage tail sheath protein FI |
| NC_017033.1|provirus_1050333_1094910_990 | 504 | GENOMAD.099825.VV | PF04985;K06908;COG3498;TIGR01611 | Phage tail tube protein FII |
| NC_017033.1|provirus_1050333_1094910_991 | 324 | GENOMAD.073828.VV | PF10109 | Phage tail assembly chaperone proteins, E, or 41 or 14 |
| NC_017033.1|provirus_1050333_1094910_992 | 2319 | GENOMAD.141796.VV | COG3941 | Phage tail tape-measure protein, controls tail length |
| NC_017033.1|provirus_1050333_1094910_993 | 843 | GENOMAD.124222.VP | K06906;COG3499 | Phage protein U |
| NC_017033.1|provirus_1050333_1094910_994 | 207 | GENOMAD.159179.VP | COG5004;K06370 | P2-like prophage tail protein X |
| NC_017033.1|provirus_1050333_1094910_995 | 1053 | GENOMAD.158351.VP | PF05954;K06905;COG3500;TIGR03361 | Phage protein D |
2.14.2.3 Phage ID: NC_017033.1|provirus_2089294_2107522
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_017033.1|provirus_2089294_2107522_1926 | 987 | GENOMAD.147153.VV | PF07120;COG3756 | Uncharacterized conserved protein YdaU, DUF1376 family |
| NC_017033.1|provirus_2089294_2107522_1927 | 447 | GENOMAD.220574.VP | PF06892 | Phage regulatory protein CII (CP76) |
| NC_017033.1|provirus_2089294_2107522_1928 | 504 | GENOMAD.226021.VP | PF14205 | NA |
| NC_017033.1|provirus_2089294_2107522_1929 | 750 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1930 | 900 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1931 | 465 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1932 | 264 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1933 | 888 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1934 | 246 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1935 | 132 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1936 | 321 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1937 | 339 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1938 | 282 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1939 | 822 | GENOMAD.192631.VV | PF03837;TIGR01913 | RecT family |
| NC_017033.1|provirus_2089294_2107522_1940 | 1752 | GENOMAD.151126.VP | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1941 | 228 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1942 | 333 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1943 | 222 | GENOMAD.224342.VP | PF09035;COG3311 | Predicted DNA-binding transcriptional regulator AlpA |
| NC_017033.1|provirus_2089294_2107522_1944 | 927 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1945 | 1797 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1946 | 933 | GENOMAD.166800.VP | COG4643 | Uncharacterized domain associated with phage/plasmid primase |
| NC_017033.1|provirus_2089294_2107522_1947 | 369 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1948 | 348 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1949 | 456 | NA | NA | NA |
| NC_017033.1|provirus_2089294_2107522_1950 | 972 | NA | NA | NA |
2.14.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_017033.1|provirus_1557694_1600481 | sequence_000001.fasta.fasta | 1_0 | 0.05 | average | ANImf | 1 |
| NC_017033.1|provirus_1050333_1094910 | sequence_000002.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
| NC_017033.1|provirus_2089294_2107522 | sequence_000000.fasta.fasta | 3_0 | 0.05 | average | ANImf | 3 |
Primary clustering plot
2.14.4 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_017033.1|provirus_1050333_1094910 | RS_GCF_000242255.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria;s__Frateuria aurantia | blast | 98.2 | None |
| NC_017033.1|provirus_1557694_1600481 | RS_GCF_000242255.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria;s__Frateuria aurantia | blast | 98.4 | iPHoP-RF;64.30 |
| NC_017033.1|provirus_2089294_2107522 | RS_GCF_000242255.2 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria;s__Frateuria aurantia | blast | 95.2 | None |
2.14.5 AMG Predictions
Prediction of auxiliary metabolic genes in the prophage contigs.
| protein | scaffold | amg_ko | amg_ko_name | pfam | pfam_name |
|---|---|---|---|---|---|
| NC_017033.1|provirus_1557694_1600481_7 | NC_017033.1|provirus_1557694_1600481 | K00558 | DNMT1, dcm; DNA (cytosine-5)-methyltransferase 1 [EC:2.1.1.37] | PF00145.17 | C-5 cytosine-specific DNA methylase |
2.15 NC_017095
2.15.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Fervidobacterium;s__Fervidobacterium pennivorans |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 2166381 | 99.95 | 2.67 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_017095.1_RM_Type_I_4 | RM | RM_Type_I | NC_017095.1_540 | NC_017095.1_543 | NC_017095.1_540,NC_017095.1_541,NC_017095.1_542,NC_017095.1_543 | 4 | RM__Type_I_MTases_FAM_0,RM__Type_I_MTases_FAM_0,RM__Type_I_REases_FAM_0.einsi_trimmed,RM__Type_I_S_51 |
| NC_017095.1_CAS_Class1-Subtype-III-B_7 | Cas | CAS_Class1-Subtype-III-B | NC_017095.1_1486 | NC_017095.1_1502 | NC_017095.1_1486,NC_017095.1_1487,NC_017095.1_1488,NC_017095.1_1489,NC_017095.1_1490,NC_017095.1_1491,NC_017095.1_1495,NC_017095.1_1497,NC_017095.1_1499,NC_017095.1_1500,NC_017095.1_1502 | 11 | HTH_III_1,cas10_III_6,cas2_I_II_III_IV_V_VI_3,cas2_I_II_III_IV_V_VI_3,cas6_I_II_III_IV_V_VI_14,cmr1gr7_III-B_1,cmr3gr5_III-B_III-C_6,cmr4gr7_III-B_III-C_1,cmr5gr11_III-B_4,cmr6gr7_III-B_3,csx1_III_9 |
| NC_017095.1_CAS_Class1-Subtype-III-A_6 | Cas | CAS_Class1-Subtype-III-A | NC_017095.1_1495 | NC_017095.1_1512 | NC_017095.1_1495,NC_017095.1_1497,NC_017095.1_1499,NC_017095.1_1500,NC_017095.1_1502,NC_017095.1_1503,NC_017095.1_1504,NC_017095.1_1505,NC_017095.1_1506,NC_017095.1_1507,NC_017095.1_1508,NC_017095.1_1509,NC_017095.1_1512 | 13 | HTH_III_1,cas10_III-A_1,cas1_I_II_III_IV_V_VI_7,cas2_I_II_III_IV_V_VI_3,cas2_I_II_III_IV_V_VI_3,cas6_I_II_III_IV_V_VI_14,cas6_I_II_III_IV_V_VI_19,casR_III_1,csm2gr11_III-A_15,csm3gr7_III-A_1,csm4gr5_III-A_1,csm5gr7_III-A_2,csx1_III_9 |
| NC_017095.1_CAS_Class1-Subtype-III-A_6 | Cas | CAS_Class1-Subtype-III-A | NC_017095.1_1495 | NC_017095.1_1512 | NC_017095.1_1495,NC_017095.1_1497,NC_017095.1_1499,NC_017095.1_1500,NC_017095.1_1502,NC_017095.1_1503,NC_017095.1_1504,NC_017095.1_1505,NC_017095.1_1506,NC_017095.1_1507,NC_017095.1_1508,NC_017095.1_1509,NC_017095.1_1512 | 13 | HTH_III_1,cas10_III-A_1,cas1_I_II_III_IV_V_VI_7,cas2_I_II_III_IV_V_VI_3,cas2_I_II_III_IV_V_VI_3,cas6_I_II_III_IV_V_VI_14,cas6_I_II_III_IV_V_VI_19,casR_III_1,csm2gr11_III-A_15,csm3gr7_III-A_1,csm4gr5_III-A_1,csm5gr7_III-A_2,csx1_III_9 |
| NC_017095.1_Esos_1 | Esos | Esos | NC_017095.1_1541 | NC_017095.1_1541 | NC_017095.1_1541 | 1 | Esos__VCA0450 |
| NC_017095.1_VP1840_2 | VP1840 | VP1840 | NC_017095.1_1651 | NC_017095.1_1651 | NC_017095.1_1651 | 1 | VP1840__VP1840 |
| NC_017095.1_RM_Type_II_5 | RM | RM_Type_II | NC_017095.1_1662 | NC_017095.1_1664 | NC_017095.1_1662,NC_017095.1_1663,NC_017095.1_1664 | 3 | RM_Type_II__Type_II_MTases_FAM_38,RM_Type_II__Type_II_MTases_FAM_4,RM_Type_II__Type_II_REase32 |
2.16 NC_018014
2.16.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Acidobacteriota;c__Terriglobia;o__Terriglobales;f__Acidobacteriaceae;g__Terriglobus;s__Terriglobus roseus |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 5227858 | 99.99 | 9.38 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_018014.1_DS-6_5 | DS-6 | DS-6 | NC_018014.1_132 | NC_018014.1_133 | NC_018014.1_132,NC_018014.1_133 | 2 | DS-6__DS-6A,DS-6__DS-6B |
| NC_018014.1_Pycsar_6 | Pycsar | Pycsar | NC_018014.1_571 | NC_018014.1_573 | NC_018014.1_571,NC_018014.1_572,NC_018014.1_573 | 3 | CBASS__2TM_5,Pycsar__AG_cyclase,Pycsar__AG_cyclase |
| NC_018014.1_DISARM_1_4 | DISARM | DISARM_1 | NC_018014.1_3050 | NC_018014.1_3053 | NC_018014.1_3050,NC_018014.1_3051,NC_018014.1_3052,NC_018014.1_3053 | 4 | DISARM_1__drmMI,DISARM__drmA,DISARM__drmB,DISARM__drmC |
| NC_018014.1_CBASS_III_3 | CBASS | CBASS_III | NC_018014.1_3068 | NC_018014.1_3071 | NC_018014.1_3068,NC_018014.1_3069,NC_018014.1_3070,NC_018014.1_3071 | 4 | CBASS__Cyclase_II,CBASS__Endonuc_big,CBASS__TRIP13,CBASS__bacHORMA_1 |
2.17 NC_018068
2.17.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus acidiphilus |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 4926837 | 99.99 | 0.42 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_018068.1_Hachiman_2 | Hachiman | Hachiman | NC_018068.1_1171 | NC_018068.1_1172 | NC_018068.1_1171,NC_018068.1_1172 | 2 | Hachiman__HamA_1,Hachiman__HamB |
| NC_018068.1_RM_Type_I_10 | RM | RM_Type_I | NC_018068.1_1178 | NC_018068.1_1180 | NC_018068.1_1178,NC_018068.1_1179,NC_018068.1_1180 | 3 | RM__Type_I_MTases_FAM_1,RM__Type_I_REases_FAM_2.einsi_trimmed,RM__Type_I_S_03 |
| NC_018068.1_RM_Type_IV_14 | RM | RM_Type_IV | NC_018068.1_1186 | NC_018068.1_1186 | NC_018068.1_1186 | 1 | RM_Type_IV__Type_IV_03 |
| NC_018068.1_RM_Type_II_11 | RM | RM_Type_II | NC_018068.1_1192 | NC_018068.1_1193 | NC_018068.1_1192,NC_018068.1_1193 | 2 | RM_Type_II__Type_II_MTases_FAM_7,RM_Type_II__Type_II_REase10 |
| NC_018068.1_CAS_Class1-Subtype-I-C_15 | Cas | CAS_Class1-Subtype-I-C | NC_018068.1_1411 | NC_018068.1_1418 | NC_018068.1_1411,NC_018068.1_1412,NC_018068.1_1413,NC_018068.1_1414,NC_018068.1_1415,NC_018068.1_1417,NC_018068.1_1418 | 7 | cas1_I_II_III_IV_V_VI_6,cas2_I_II_III_IV_V_VI_3,cas3_I_5,cas4_I_II_III_IV_V_VI_6,cas5_I-C_11,cas7_I-C_13,cas8c_I-C_4 |
| NC_018068.1_RM_Type_III_13 | RM | RM_Type_III | NC_018068.1_1541 | NC_018068.1_1542 | NC_018068.1_1541,NC_018068.1_1542 | 2 | RM_Type_III__Type_III_MTases_FAM_0,RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed |
| NC_018068.1_Ceres_1 | Ceres | Ceres | NC_018068.1_3152 | NC_018068.1_3152 | NC_018068.1_3152 | 1 | Ceres__CrsA1 |
| NC_018068.1_MazEF_6 | MazEF | MazEF | NC_018068.1_3456 | NC_018068.1_3457 | NC_018068.1_3456,NC_018068.1_3457 | 2 | MazEF__MazE,MazEF__MazF |
| NC_018068.1_Rst_HelicaseDUF2290_7 | Rst_HelicaseDUF2290 | Rst_HelicaseDUF2290 | NC_018068.1_3757 | NC_018068.1_3758 | NC_018068.1_3757,NC_018068.1_3758 | 2 | Rst_HelicaseDUF2290__DUF2290,Rst_HelicaseDUF2290__Helicase |
| NC_018068.1_Hachiman_3 | Hachiman | Hachiman | NC_018068.1_3759 | NC_018068.1_3760 | NC_018068.1_3759,NC_018068.1_3760 | 2 | Hachiman__HamA_1,Hachiman__HamB |
| NC_018068.1_Septu_8 | Septu | Septu | NC_018068.1_4412 | NC_018068.1_4413 | NC_018068.1_4412,NC_018068.1_4413 | 2 | Septu__PtuA,Septu__PtuB |
| NC_018068.1_RM_Type_II_12 | RM | RM_Type_II | NC_018068.1_4429 | NC_018068.1_4430 | NC_018068.1_4429,NC_018068.1_4430 | 2 | RM_Type_II__Type_II_MTases_FAM_25,RM_Type_II__Type_II_REase09 |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_018068.1|provirus_1361108_1399802 | 38695 | 52 | 24 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 1361108-1399802 |
| NC_018068.1|provirus_2072558_2098541 | 25984 | 36 | 4 | High-quality | High-quality | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 2072558-2098541 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.17.2 Prophages
Select prophage to show:
2.17.2.1 Phage ID: NC_018068.1|provirus_1361108_1399802
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_018068.1|provirus_1361108_1399802_1216 | 417 | NA | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1217 | 285 | NA | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1218 | 213 | NA | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1219 | 825 | GENOMAD.133073.VP | PF03374;COG3645 | Phage antirepressor protein YoqD, KilAC domain |
| NC_018068.1|provirus_1361108_1399802_1220 | 1245 | GENOMAD.014802.VV | PF00176;K20093;COG1061;TIGR04095 | Superfamily II DNA or RNA helicase |
| NC_018068.1|provirus_1361108_1399802_1221 | 285 | GENOMAD.062524.VV | PF03838;COG3331;TIGR00648;K03552 | Penicillin-binding protein-related factor A, putative recombinase |
| NC_018068.1|provirus_1361108_1399802_1222 | 1668 | GENOMAD.016341.VV | PF13479;PF12684;TIGR01618;K07465;COG1468 | phage nucleotide-binding protein |
| NC_018068.1|provirus_1361108_1399802_1223 | 450 | GENOMAD.031678.VV | PF05037 | NA |
| NC_018068.1|provirus_1361108_1399802_1224 | 1695 | GENOMAD.102034.VP | TIGR01636 | NA |
| NC_018068.1|provirus_1361108_1399802_1225 | 1875 | GENOMAD.024099.VV | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1226 | 381 | GENOMAD.192072.VP | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1227 | 453 | GENOMAD.076519.VV | PF05263;TIGR01636;COG2739;K01994 | phage transcriptional activator, RinA family |
| NC_018068.1|provirus_1361108_1399802_1228 | 189 | NA | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1229 | 207 | NA | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1230 | 357 | GENOMAD.221055.VP | TIGR02646 | NA |
| NC_018068.1|provirus_1361108_1399802_1231 | 528 | GENOMAD.098194.VV | PF05119;COG3747;TIGR01558 | Phage terminase, small subunit |
| NC_018068.1|provirus_1361108_1399802_1232 | 1254 | GENOMAD.038338.VV | COG3392 | NA |
| NC_018068.1|provirus_1361108_1399802_1233 | 525 | GENOMAD.133508.VP | PF13392 | HNH endonuclease |
| NC_018068.1|provirus_1361108_1399802_1234 | 186 | GENOMAD.209016.VC | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1235 | 816 | GENOMAD.105515.VV | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1236 | 240 | GENOMAD.225559.VP | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1237 | 252 | NA | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1238 | 210 | NA | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1239 | 1548 | GENOMAD.190509.VP | PF03354;COG4626 | Phage terminase-like protein, large subunit, contains N-terminal HTH domain |
| NC_018068.1|provirus_1361108_1399802_1240 | 1164 | GENOMAD.179073.VP | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1241 | 1068 | GENOMAD.158277.VP | PF00574;PF19602;K01358;TIGR00493;COG3904 | ATP-dependent Clp endopeptidase, proteolytic subunit ClpP |
| NC_018068.1|provirus_1361108_1399802_1242 | 1275 | GENOMAD.092606.VV | PF05065;COG4653;TIGR01554 | Predicted phage phi-C31 gp36 major capsid-like protein |
| NC_018068.1|provirus_1361108_1399802_1243 | 477 | GENOMAD.077304.VV | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1244 | 594 | GENOMAD.067701.VV | PF05135;TIGR02215 | phage conserved hypothetical protein, phiE125 gp8 family |
| NC_018068.1|provirus_1361108_1399802_1245 | 330 | GENOMAD.027939.VV | PF05521;COG5614;TIGR01563 | Bacteriophage head-tail adaptor |
| NC_018068.1|provirus_1361108_1399802_1246 | 414 | GENOMAD.018908.VV | PF04883;TIGR01725;COG5005 | Bacteriophage HK97-gp10, putative tail-component |
| NC_018068.1|provirus_1361108_1399802_1247 | 435 | GENOMAD.029331.VV | PF20765 | Phage tail terminator protein |
| NC_018068.1|provirus_1361108_1399802_1248 | 1068 | GENOMAD.014203.VV | PF04984;PF17482;COG4386 | Mu-like prophage tail sheath protein gpL |
| NC_018068.1|provirus_1361108_1399802_1249 | 429 | GENOMAD.008035.VV | PF09393 | Phage tail tube protein |
| NC_018068.1|provirus_1361108_1399802_1250 | 402 | GENOMAD.020710.VV | PF08890 | Phage XkdN-like tail assembly chaperone protein, TAC |
| NC_018068.1|provirus_1361108_1399802_1251 | 2172 | GENOMAD.117212.VP | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1252 | 405 | GENOMAD.025221.VV | PF06995;COG1652 | Nucleoid-associated protein YgaU, contains BON and LysM domains |
| NC_018068.1|provirus_1361108_1399802_1253 | 993 | GENOMAD.020668.VV | PF05954;COG4379;K06905;TIGR03361 | Mu-like prophage tail protein gpP |
| NC_018068.1|provirus_1361108_1399802_1254 | 369 | GENOMAD.046601.VV | PF10844 | NA |
| NC_018068.1|provirus_1361108_1399802_1255 | 432 | GENOMAD.015505.VV | PF10934;COG4381 | Mu-like prophage protein gp46 |
| NC_018068.1|provirus_1361108_1399802_1256 | 1074 | GENOMAD.110264.VV | PF04865;COG3948 | Phage-related baseplate assembly protein |
| NC_018068.1|provirus_1361108_1399802_1257 | 522 | GENOMAD.018612.VV | PF10076;COG3778;TIGR02242 | Uncharacterized protein YmfQ in lambdoid prophage, DUF2313 family |
| NC_018068.1|provirus_1361108_1399802_1258 | 567 | GENOMAD.069954.VV | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1259 | 336 | NA | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1260 | 1644 | GENOMAD.014429.VV | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1261 | 339 | GENOMAD.213587.VP | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1262 | 138 | GENOMAD.041649.VV | PF09693;TIGR01669 | phage uncharacterized protein, XkdX family |
| NC_018068.1|provirus_1361108_1399802_1263 | 240 | NA | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1264 | 321 | GENOMAD.130222.VV | COG3105 | NA |
| NC_018068.1|provirus_1361108_1399802_1265 | 486 | GENOMAD.151608.VV | PF19988 | NA |
| NC_018068.1|provirus_1361108_1399802_1266 | 774 | NA | NA | NA |
| NC_018068.1|provirus_1361108_1399802_1267 | 414 | NA | NA | NA |
2.17.2.2 Phage ID: NC_018068.1|provirus_2072558_2098541
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_018068.1|provirus_2072558_2098541_1928 | 177 | GENOMAD.171344.VV | PF07278;K22014;COG4220;TIGR01764 | Phage DNA packaging protein, Nu1 subunit of terminase |
| NC_018068.1|provirus_2072558_2098541_1929 | 189 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1930 | 204 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1931 | 147 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1932 | 867 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1933 | 2490 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1934 | 264 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1935 | 213 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1936 | 189 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1937 | 309 | GENOMAD.037442.VV | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1938 | 135 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1939 | 144 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1940 | 204 | GENOMAD.220824.VP | PF18903 | NA |
| NC_018068.1|provirus_2072558_2098541_1941 | 129 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1942 | 207 | GENOMAD.207723.VP | PF10960 | BhlA holin family |
| NC_018068.1|provirus_2072558_2098541_1943 | 417 | GENOMAD.126365.VV | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1944 | 888 | GENOMAD.136497.VV | PF17236 | Phage capsid-like protein |
| NC_018068.1|provirus_2072558_2098541_1945 | 192 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1946 | 813 | GENOMAD.225339.VP | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1947 | 1497 | GENOMAD.225126.VP | PF06862;TIGR01587;COG4098;K17677 | CRISPR-associated helicase Cas3 |
| NC_018068.1|provirus_2072558_2098541_1948 | 393 | GENOMAD.142024.VV | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1949 | 1572 | GENOMAD.180947.VP | PF04466;COG5323;TIGR01547;K21523 | Large terminase phage packaging protein |
| NC_018068.1|provirus_2072558_2098541_1950 | 1461 | GENOMAD.003260.VV | PF05133;TIGR01538;COG3567 | phage portal protein, SPP1 family |
| NC_018068.1|provirus_2072558_2098541_1951 | 294 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1952 | 351 | GENOMAD.223401.VP | PF09851 | NA |
| NC_018068.1|provirus_2072558_2098541_1953 | 1242 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1954 | 867 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1955 | 219 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1956 | 261 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1957 | 348 | GENOMAD.220167.VP | PF20449 | NA |
| NC_018068.1|provirus_2072558_2098541_1958 | 1119 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1959 | 213 | NA | NA | NA |
| NC_018068.1|provirus_2072558_2098541_1960 | 987 | NA | NA | NA |
2.17.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_018068.1|provirus_1361108_1399802 | sequence_000000.fasta.fasta | 1_0 | 0.05 | average | ANImf | 1 |
| NC_018068.1|provirus_2072558_2098541 | sequence_000001.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
Primary clustering plot
2.17.4 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_018068.1|provirus_1361108_1399802 | RS_GCF_000255115.2 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus acidiphilus | blast | 96.4 | iPHoP-RF;53.60 |
| NC_018068.1|provirus_1361108_1399802 | RS_GCF_001707885.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp001707885 | iPHoP-RF | 95.4 | None |
| NC_018068.1|provirus_1361108_1399802 | RS_GCF_001936615.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus metallidurans | iPHoP-RF | 95.4 | None |
| NC_018068.1|provirus_1361108_1399802 | RS_GCF_000224515.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp000224515 | iPHoP-RF | 95.1 | None |
| NC_018068.1|provirus_1361108_1399802 | RS_GCF_000960765.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp000960765 | iPHoP-RF | 93.4 | None |
| NC_018068.1|provirus_1361108_1399802 | RS_GCF_004766055.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp004766055 | iPHoP-RF | 93.1 | None |
| NC_018068.1|provirus_1361108_1399802 | 3300011997_21 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;gDesulfosporosinus;s | iPHoP-RF | 92.1 | None |
| NC_018068.1|provirus_1361108_1399802 | GB_GCA_002404215.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp002404215 | iPHoP-RF | 91.8 | None |
| NC_018068.1|provirus_1361108_1399802 | RS_GCF_001029285.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus acididurans | blast | 91.8 | None |
| NC_018068.1|provirus_1361108_1399802 | RS_GCF_002196705.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp002196705 | blast | 91.2 | iPHoP-RF;78.30 |
| NC_018068.1|provirus_1361108_1399802 | GB_GCA_900290375.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus infrequens | blast | 90.3 | iPHoP-RF;73.50 |
| NC_018068.1|provirus_2072558_2098541 | RS_GCF_000255115.2 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus acidiphilus | blast | 93.6 | iPHoP-RF;69.50 |
2.18 NC_018515
2.18.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus meridiei |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 4873567 | 100 | 1.83 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_018515.1_AbiAlpha_1 | AbiAlpha | AbiAlpha | NC_018515.1_121 | NC_018515.1_121 | NC_018515.1_121 | 1 | AbiAlpha__AbiAlpha |
| NC_018515.1_VP1839_11 | VP1839 | VP1839 | NC_018515.1_122 | NC_018515.1_122 | NC_018515.1_122 | 1 | VP1839__VP1839 |
| NC_018515.1_CBASS_IV_7 | CBASS | CBASS_IV | NC_018515.1_324 | NC_018515.1_328 | NC_018515.1_324,NC_018515.1_325,NC_018515.1_326,NC_018515.1_327,NC_018515.1_328 | 5 | CBASS__2TM_type_IV,CBASS__Cyclase_SMODS,CBASS__OGG,CBASS__QueC,CBASS__TGT |
| NC_018515.1_BREX_I_4 | BREX | BREX_I | NC_018515.1_329 | NC_018515.1_335 | NC_018515.1_329,NC_018515.1_330,NC_018515.1_331,NC_018515.1_332,NC_018515.1_334,NC_018515.1_335 | 6 | BREX__brxA_DUF1819,BREX__brxB_DUF1788,BREX__brxC,BREX__brxL,BREX__pglX1,BREX__pglZA |
| NC_018515.1_Prometheus_9 | Prometheus | Prometheus | NC_018515.1_337 | NC_018515.1_337 | NC_018515.1_337 | 1 | Prometheus__ProA |
| NC_018515.1_Azaca_2 | Azaca | Azaca | NC_018515.1_349 | NC_018515.1_351 | NC_018515.1_349,NC_018515.1_350,NC_018515.1_351 | 3 | Azaca__ZacA,Azaca__ZacB,Azaca__ZacC |
| NC_018515.1_Wadjet_III_13 | Wadjet | Wadjet_III | NC_018515.1_1811 | NC_018515.1_1814 | NC_018515.1_1811,NC_018515.1_1812,NC_018515.1_1813,NC_018515.1_1814 | 4 | Wadjet__JetA_III,Wadjet__JetB_III,Wadjet__JetC_III,Wadjet__JetD_III |
| NC_018515.1_SpbK_10 | SpbK | SpbK | NC_018515.1_2272 | NC_018515.1_2272 | NC_018515.1_2272 | 1 | SpbK__SpbK |
| NC_018515.1_Kiwa_8 | Kiwa | Kiwa | NC_018515.1_3261 | NC_018515.1_3262 | NC_018515.1_3261,NC_018515.1_3262 | 2 | Kiwa__KwaA,Kiwa__KwaB_2 |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_018515.1|provirus_3418112_3436097 | 17986 | 25 | 18 | Low-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 3418112-3436097 |
| NC_018515.1|provirus_4659544_4693604 | 34061 | 46 | 20 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 4659544-4693604 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.18.2 Prophages
Select prophage to show:
2.18.2.1 Phage ID: NC_018515.1|provirus_3418112_3436097
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_018515.1|provirus_3418112_3436097_3127 | 576 | NA | NA | NA |
| NC_018515.1|provirus_3418112_3436097_3128 | 345 | GENOMAD.178485.VV | NA | NA |
| NC_018515.1|provirus_3418112_3436097_3129 | 756 | NA | NA | NA |
| NC_018515.1|provirus_3418112_3436097_3130 | 249 | GENOMAD.042597.VV | PF10779 | Haemolysin XhlA |
| NC_018515.1|provirus_3418112_3436097_3131 | 171 | GENOMAD.019319.VV | PF09693;TIGR01669 | phage uncharacterized protein, XkdX family |
| NC_018515.1|provirus_3418112_3436097_3132 | 300 | NA | NA | NA |
| NC_018515.1|provirus_3418112_3436097_3133 | 1080 | GENOMAD.010477.VV | NA | NA |
| NC_018515.1|provirus_3418112_3436097_3134 | 612 | GENOMAD.018612.VV | PF10076;COG3778;TIGR02242 | Uncharacterized protein YmfQ in lambdoid prophage, DUF2313 family |
| NC_018515.1|provirus_3418112_3436097_3135 | 717 | GENOMAD.072355.VV | PF18454 | Major tropism determinant N-terminal domain |
| NC_018515.1|provirus_3418112_3436097_3136 | 1023 | GENOMAD.037496.VV | PF18454 | Major tropism determinant N-terminal domain |
| NC_018515.1|provirus_3418112_3436097_3137 | 414 | GENOMAD.105081.VV | NA | NA |
| NC_018515.1|provirus_3418112_3436097_3138 | 1038 | GENOMAD.004833.VV | PF04865;COG3299 | Baseplate J-like protein |
| NC_018515.1|provirus_3418112_3436097_3139 | 402 | GENOMAD.016318.VV | PF10934;COG4381;TIGR03357 | Mu-like prophage protein gp46 |
| NC_018515.1|provirus_3418112_3436097_3140 | 357 | GENOMAD.020599.VV | PF10844 | NA |
| NC_018515.1|provirus_3418112_3436097_3141 | 987 | GENOMAD.018966.VV | PF14594;COG4379;TIGR03361;K06905 | Mu-like prophage tail protein gpP |
| NC_018515.1|provirus_3418112_3436097_3142 | 663 | GENOMAD.015578.VV | PF06995;COG1652 | Nucleoid-associated protein YgaU, contains BON and LysM domains |
| NC_018515.1|provirus_3418112_3436097_3143 | 1689 | GENOMAD.032671.VV | NA | NA |
| NC_018515.1|provirus_3418112_3436097_3144 | 423 | GENOMAD.001212.VV | PF08890 | Phage XkdN-like tail assembly chaperone protein, TAC |
| NC_018515.1|provirus_3418112_3436097_3145 | 468 | GENOMAD.011307.VV | PF09393 | Phage tail tube protein |
| NC_018515.1|provirus_3418112_3436097_3146 | 1317 | GENOMAD.013578.VV | PF17481;PF04984;PF17482;COG4386 | Mu-like prophage tail sheath protein gpL |
| NC_018515.1|provirus_3418112_3436097_3147 | 183 | NA | NA | NA |
| NC_018515.1|provirus_3418112_3436097_3148 | 420 | GENOMAD.023771.VV | PF20765 | Phage tail terminator protein |
| NC_018515.1|provirus_3418112_3436097_3149 | 471 | NA | NA | NA |
| NC_018515.1|provirus_3418112_3436097_3150 | 597 | GENOMAD.220722.VV | COG3655 | DNA-binding transcriptional regulator, XRE family |
| NC_018515.1|provirus_3418112_3436097_3151 | 480 | GENOMAD.123021.VV | PF06114;COG2856 | IrrE N-terminal-like domain |
2.18.2.2 Phage ID: NC_018515.1|provirus_4659544_4693604
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_018515.1|provirus_4659544_4693604_4266 | 246 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4267 | 783 | GENOMAD.053051.VV | PF10772;PF02086;TIGR00571;COG0338 | Bacteriophage HP1, Orf24; D12 class N6 adenine-specific DNA methyltransferase |
| NC_018515.1|provirus_4659544_4693604_4268 | 726 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4269 | 1290 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4270 | 831 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4271 | 501 | GENOMAD.220913.VP | PF09682;TIGR01673 | Bacteriophage holin of superfamily 6 (Holin_LLH) |
| NC_018515.1|provirus_4659544_4693604_4272 | 846 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4273 | 366 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4274 | 255 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4275 | 177 | GENOMAD.202651.VV | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4276 | 279 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4277 | 1095 | GENOMAD.135924.VV | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4278 | 1377 | GENOMAD.007293.VV | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4279 | 1092 | GENOMAD.006687.VV | PF14594;COG4926;TIGR01665 | Siphovirus ReqiPepy6 Gp37-like protein |
| NC_018515.1|provirus_4659544_4693604_4280 | 864 | GENOMAD.009232.VV | PF16774;COG4722;TIGR01633 | Phage-related protein |
| NC_018515.1|provirus_4659544_4693604_4281 | 2739 | GENOMAD.110013.VP | COG5280 | Phage-related minor tail protein |
| NC_018515.1|provirus_4659544_4693604_4282 | 228 | GENOMAD.095592.VV | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4283 | 327 | GENOMAD.044337.VV | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4284 | 564 | GENOMAD.009652.VV | TIGR01537 | NA |
| NC_018515.1|provirus_4659544_4693604_4285 | 360 | GENOMAD.058243.VV | PF11367 | NA |
| NC_018515.1|provirus_4659544_4693604_4286 | 426 | GENOMAD.072075.VV | PF11114;TIGR01725;COG5005 | phage protein, HK97 gp10 family |
| NC_018515.1|provirus_4659544_4693604_4287 | 312 | GENOMAD.008635.VV | PF05521;TIGR01563;COG5614 | phage head-tail adaptor, putative, SPP1 family |
| NC_018515.1|provirus_4659544_4693604_4288 | 270 | GENOMAD.053459.VV | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4289 | 198 | GENOMAD.188189.VV | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4290 | 1224 | GENOMAD.088359.VV | PF05065;PF18316;PF17078;TIGR01554;COG4653 | phage major capsid protein, HK97 family |
| NC_018515.1|provirus_4659544_4693604_4291 | 621 | GENOMAD.116539.VV | PF04586;PF05065;K06904;COG3740;TIGR01543 | Phage head maturation protease |
| NC_018515.1|provirus_4659544_4693604_4292 | 1230 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4293 | 1755 | GENOMAD.194580.VP | PF03354;PF05521;PF20441;COG4626;TIGR01563 | Phage terminase-like protein, large subunit, contains N-terminal HTH domain |
| NC_018515.1|provirus_4659544_4693604_4294 | 384 | GENOMAD.092852.VV | TIGR01558 | NA |
| NC_018515.1|provirus_4659544_4693604_4295 | 363 | GENOMAD.080571.VV | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4296 | 786 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4297 | 849 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4298 | 513 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4299 | 363 | GENOMAD.151656.VP | PF17288;K06909;TIGR01547;COG1783 | phage terminase, large subunit, PBSX family |
| NC_018515.1|provirus_4659544_4693604_4300 | 522 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4301 | 975 | GENOMAD.017981.VV | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4302 | 168 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4303 | 744 | GENOMAD.129273.VC | PF12706;TIGR02651;COG1234;K06167 | ribonuclease Z |
| NC_018515.1|provirus_4659544_4693604_4304 | 828 | GENOMAD.121864.VP | PF03837;COG3723;K07455;TIGR00616 | Recombinational DNA repair protein RecT |
| NC_018515.1|provirus_4659544_4693604_4305 | 108 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4306 | 1965 | GENOMAD.062081.VV | PF04423;COG1579 | Predicted nucleic acid-binding protein, contains Zn-ribbon domain |
| NC_018515.1|provirus_4659544_4693604_4307 | 387 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4308 | 273 | GENOMAD.199250.VV | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4309 | 264 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4310 | 267 | NA | NA | NA |
| NC_018515.1|provirus_4659544_4693604_4311 | 114 | NA | NA | NA |
2.18.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_018515.1|provirus_3418112_3436097 | sequence_000000.fasta.fasta | 1_0 | 0.05 | average | ANImf | 1 |
| NC_018515.1|provirus_4659544_4693604 | sequence_000001.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
Primary clustering plot
2.18.4 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_018515.1|provirus_3418112_3436097 | RS_GCF_000231385.2 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus meridiei | blast | 95.9 | iPHoP-RF;79.80 |
| NC_018515.1|provirus_3418112_3436097 | RS_GCF_004766055.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp004766055 | iPHoP-RF | 95.7 | None |
| NC_018515.1|provirus_3418112_3436097 | GB_GCA_002404215.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp002404215 | iPHoP-RF | 95.1 | None |
| NC_018515.1|provirus_3418112_3436097 | 3300011997_21 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;gDesulfosporosinus;s | iPHoP-RF | 94.7 | None |
| NC_018515.1|provirus_3418112_3436097 | GB_GCA_021779415.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp021779415 | iPHoP-RF | 92.8 | None |
| NC_018515.1|provirus_3418112_3436097 | RS_GCF_023897015.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus nitroreducens | blast | 91.8 | iPHoP-RF;73.20 |
| NC_018515.1|provirus_3418112_3436097 | GB_GCA_003132105.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp003132105 | iPHoP-RF | 91.4 | None |
| NC_018515.1|provirus_3418112_3436097 | RS_GCF_020595055.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp020595055 | blast | 91.4 | iPHoP-RF;74.10 |
| NC_018515.1|provirus_3418112_3436097 | RS_GCF_000235605.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus orientis | blast | 90.7 | iPHoP-RF;73.00 |
| NC_018515.1|provirus_3418112_3436097 | RS_GCF_900100785.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus hippei | blast | 90.3 | iPHoP-RF;71.70 |
| NC_018515.1|provirus_4659544_4693604 | RS_GCF_000231385.2 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus meridiei | blast | 96.5 | iPHoP-RF;74.60 |
| NC_018515.1|provirus_4659544_4693604 | RS_GCF_023897015.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus nitroreducens | blast | 95.6 | iPHoP-RF;78.00 |
| NC_018515.1|provirus_4659544_4693604 | RS_GCF_900100785.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus hippei | blast | 92.3 | iPHoP-RF;69.50 |
| NC_018515.1|provirus_4659544_4693604 | 3300011997_21 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;gDesulfosporosinus;s | iPHoP-RF | 91.4 | None |
| NC_018515.1|provirus_4659544_4693604 | GB_GCA_002404215.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp002404215 | iPHoP-RF | 91.1 | None |
| NC_018515.1|provirus_4659544_4693604 | RS_GCF_000244895.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus youngiae | blast | 90.6 | iPHoP-RF;82.50 |
| NC_018515.1|provirus_4659544_4693604 | GB_GCA_021779415.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus sp021779415 | iPHoP-RF | 90.1 | None |
| NC_018515.1|provirus_4659544_4693604 | GB_GCA_900290375.1 | d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus;s__Desulfosporosinus infrequens | iPHoP-RF | 90.1 | None |
2.18.5 AMG Predictions
Prediction of auxiliary metabolic genes in the prophage contigs.
| protein | scaffold | amg_ko | amg_ko_name | pfam | pfam_name |
|---|---|---|---|---|---|
| NC_018515.1|provirus_3418112_3436097_1 | NC_018515.1|provirus_3418112_3436097 | K00106 | XDH; xanthine dehydrogenase/oxidase [EC:1.17.1.4 1.17.3.2] | PF02738.18 | Molybdopterin-binding domain of aldehyde dehydrogenase |
| NC_018515.1|provirus_4659544_4693604_38 | NC_018515.1|provirus_4659544_4693604 | K06167 | phnP; phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [EC:3.1.4.55] | PF00753.27 | Metallo-beta-lactamase superfamily |
2.19 NC_019897
2.19.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Bacillota;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus;s__Thermobacillus xylanilyticus |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 4206343 | 99.95 | 0.34 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_019897.1_RM_Type_III_11 | RM | RM_Type_III | NC_019897.1_86 | NC_019897.1_87 | NC_019897.1_86,NC_019897.1_87 | 2 | RM_Type_III__Type_III_MTases_FAM_0,RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed |
| NC_019897.1_MazEF_3 | MazEF | MazEF | NC_019897.1_128 | NC_019897.1_129 | NC_019897.1_128,NC_019897.1_129 | 2 | MazEF__MazE,MazEF__MazF |
| NC_019897.1_RM_Type_II_9 | RM | RM_Type_II | NC_019897.1_789 | NC_019897.1_790 | NC_019897.1_789,NC_019897.1_790 | 2 | RM_Type_II__Type_II_MTases_FAM_2,RM_Type_II__Type_II_REase27 |
| NC_019897.1_Mokosh_TypeII_4 | Mokosh | Mokosh_TypeII | NC_019897.1_913 | NC_019897.1_913 | NC_019897.1_913 | 1 | Mokosh_TypeII__MkoC |
| NC_019897.1_Druantia_I_2 | Druantia | Druantia_I | NC_019897.1_2741 | NC_019897.1_2744 | NC_019897.1_2741,NC_019897.1_2742,NC_019897.1_2743,NC_019897.1_2744 | 4 | Druantia_I__DruB,Druantia_I__DruC,Druantia_I__DruD,Druantia__DruE_1 |
| NC_019897.1_CAS_Class1-Subtype-III-D_14 | Cas | CAS_Class1-Subtype-III-D | NC_019897.1_3030 | NC_019897.1_3035 | NC_019897.1_3030,NC_019897.1_3031,NC_019897.1_3032,NC_019897.1_3033,NC_019897.1_3034,NC_019897.1_3035 | 6 | cas10_III-D_3,csm3gr7_III-D_2,csm3gr7_III-D_3,csm3gr7_III_1,csx19_III-D_17,csx1_III_11 |
| NC_019897.1_CAS_Class1-Subtype-I-B_12 | Cas | CAS_Class1-Subtype-I-B | NC_019897.1_3046 | NC_019897.1_3053 | NC_019897.1_3046,NC_019897.1_3047,NC_019897.1_3048,NC_019897.1_3049,NC_019897.1_3050,NC_019897.1_3051,NC_019897.1_3052,NC_019897.1_3053 | 8 | cas1_I_II_III_IV_V_VI_7,cas2_I_II_III_IV_V_VI_3,cas3_I_2,cas4_I_II_III_IV_V_VI_6,cas5_I-B_17,cas6_I_II_III_IV_V_VI_20,cas7b_I-B_I-C_2,cas8b1_I-B_8 |
| NC_019897.1_CAS_Class1-Subtype-I-C_13 | Cas | CAS_Class1-Subtype-I-C | NC_019897.1_3155 | NC_019897.1_3158 | NC_019897.1_3155,NC_019897.1_3156,NC_019897.1_3157,NC_019897.1_3158 | 4 | cas3_I_5,cas5_I-C_5,cas7_I-C_7,cas8c_I-C_4 |
| NC_019897.1_Wadjet_II_6 | Wadjet | Wadjet_II | NC_019897.1_3286 | NC_019897.1_3289 | NC_019897.1_3286,NC_019897.1_3287,NC_019897.1_3288,NC_019897.1_3289 | 4 | Wadjet__JetA_II,Wadjet__JetB_II,Wadjet__JetC_II,Wadjet__JetD_II |
| NC_019897.1_RM_Type_I_8 | RM | RM_Type_I | NC_019897.1_3326 | NC_019897.1_3328 | NC_019897.1_3326,NC_019897.1_3327,NC_019897.1_3328 | 3 | RM__Type_I_MTases_FAM_1,RM__Type_I_REases_FAM_2.einsi_trimmed,RM__Type_I_S_51 |
| NC_019897.1_RM_Type_II_10 | RM | RM_Type_II | NC_019897.1_3527 | NC_019897.1_3528 | NC_019897.1_3527,NC_019897.1_3528 | 2 | RM_Type_II__Type_II_MTases_FAM_16,RM_Type_II__Type_II_REase01 |
| NC_019897.1_Ceres_1 | Ceres | Ceres | NC_019897.1_3704 | NC_019897.1_3704 | NC_019897.1_3704 | 1 | Ceres__CrsA1 |
2.20 NC_019904
2.20.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola;s__Echinicola vietnamensis |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 5608040 | 100 | 0.23 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_019904.1_HEC-05_12 | HEC-05 | HEC-05 | NC_019904.1_318 | NC_019904.1_318 | NC_019904.1_318 | 1 | HEC-05__HEC-05 |
| NC_019904.1_RM_Type_I_19 | RM | RM_Type_I | NC_019904.1_371 | NC_019904.1_374 | NC_019904.1_371,NC_019904.1_372,NC_019904.1_374 | 3 | RM__Type_I_MTases_FAM_1,RM__Type_I_REases_FAM_2.einsi_trimmed,RM__Type_I_S_01 |
| NC_019904.1_dCTPdeaminase_15 | dCTPdeaminase | dCTPdeaminase | NC_019904.1_408 | NC_019904.1_408 | NC_019904.1_408 | 1 | dCTPdeaminase__dCTPdeaminase |
| NC_019904.1_RM_Type_I_20 | RM | RM_Type_I | NC_019904.1_411 | NC_019904.1_413 | NC_019904.1_411,NC_019904.1_412,NC_019904.1_413 | 3 | RM__Type_I_MTases_FAM_1,RM__Type_I_REases_FAM_2.einsi_trimmed,RM__Type_I_S_03 |
| NC_019904.1_Gabija_8 | Gabija | Gabija | NC_019904.1_430 | NC_019904.1_431 | NC_019904.1_430,NC_019904.1_431 | 2 | Gabija__GajA,Gabija__GajB_2 |
| NC_019904.1_Gao_Qat_11 | Gao_Qat | Gao_Qat | NC_019904.1_1323 | NC_019904.1_1326 | NC_019904.1_1323,NC_019904.1_1324,NC_019904.1_1325,NC_019904.1_1326 | 4 | Gao_Qat__QatA,Gao_Qat__QatB,Gao_Qat__QatC,Gao_Qat__QatD |
| NC_019904.1_SoFic_14 | SoFIC | SoFic | NC_019904.1_1676 | NC_019904.1_1676 | NC_019904.1_1676 | 1 | SoFic__SoFic |
| NC_019904.1_Gabija_9 | Gabija | Gabija | NC_019904.1_1900 | NC_019904.1_1901 | NC_019904.1_1900,NC_019904.1_1901 | 2 | Gabija__GajA,Gabija__GajB_3 |
| NC_019904.1_RM_Type_II_22 | RM | RM_Type_II | NC_019904.1_1947 | NC_019904.1_1949 | NC_019904.1_1947,NC_019904.1_1948,NC_019904.1_1949 | 3 | RM_Type_II__Type_II_MTases_FAM_2,RM_Type_II__Type_II_REase06,RM_Type_II__Type_II_REase38 |
| NC_019904.1_Sirona_13 | Sirona | Sirona | NC_019904.1_1950 | NC_019904.1_1950 | NC_019904.1_1950 | 1 | Sirona__VCA0356 |
| NC_019904.1_CBASS_II_5 | CBASS | CBASS_II | NC_019904.1_3143 | NC_019904.1_3145 | NC_019904.1_3143,NC_019904.1_3144,NC_019904.1_3145 | 3 | CBASS__Cyclase_II,CBASS__E2,CBASS__Effector_2TM_Sa_NUDIX |
| NC_019904.1_AbiE_2 | AbiE | AbiE | NC_019904.1_3195 | NC_019904.1_3196 | NC_019904.1_3195,NC_019904.1_3196 | 2 | AbiEii__AbiEi_3,AbiEii__AbiEii |
| NC_019904.1_RM_Type_I_21 | RM | RM_Type_I | NC_019904.1_4383 | NC_019904.1_4389 | NC_019904.1_4383,NC_019904.1_4387,NC_019904.1_4388,NC_019904.1_4389 | 4 | RM__Type_I_MTases_FAM_0,RM__Type_I_REases_FAM_0.einsi_trimmed,RM__Type_I_S_01,RM__Type_I_S_51 |
| NC_019904.1_AbiD_1 | AbiD | AbiD | NC_019904.1_4385 | NC_019904.1_4385 | NC_019904.1_4385 | 1 | AbiD__AbiD |
| NC_019904.1_Cernunnos_7 | Cernunnos | Cernunnos | NC_019904.1_4390 | NC_019904.1_4390 | NC_019904.1_4390 | 1 | Cernunnos__VCA0410 |
| NC_019904.1_Gabija_10 | Gabija | Gabija | NC_019904.1_4391 | NC_019904.1_4392 | NC_019904.1_4391,NC_019904.1_4392 | 2 | Gabija__GajA,Gabija__GajB_1 |
| NC_019904.1_Ceres_6 | Ceres | Ceres | NC_019904.1_4414 | NC_019904.1_4414 | NC_019904.1_4414 | 1 | Ceres__CrsA1 |
2.21 NC_019936
2.21.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_AE |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 4575057 | 100 | 0.13 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_019936.1_Gabija_5 | Gabija | Gabija | NC_019936.1_617 | NC_019936.1_618 | NC_019936.1_617,NC_019936.1_618 | 2 | Gabija__GajA,Gabija__GajB_3 |
| NC_019936.1_RM_Type_I_12 | RM | RM_Type_I | NC_019936.1_860 | NC_019936.1_862 | NC_019936.1_860,NC_019936.1_861,NC_019936.1_862 | 3 | RM__Type_I_MTases_FAM_3,RM__Type_I_REases_FAM_1.einsi_trimmed,RM__Type_I_S_52 |
| NC_019936.1_Shango_6 | Shango | Shango | NC_019936.1_896 | NC_019936.1_898 | NC_019936.1_896,NC_019936.1_897,NC_019936.1_898 | 3 | Shango__SngA,Shango__SngB,Shango__SngC |
| NC_019936.1_RM_Type_I_13 | RM | RM_Type_I | NC_019936.1_1070 | NC_019936.1_1072 | NC_019936.1_1070,NC_019936.1_1071,NC_019936.1_1072 | 3 | RM__Type_I_MTases_FAM_1,RM__Type_I_REases_FAM_2.einsi_trimmed,RM__Type_I_S_03 |
| NC_019936.1_RM_Type_IV_16 | RM | RM_Type_IV | NC_019936.1_1377 | NC_019936.1_1377 | NC_019936.1_1377 | 1 | RM_Type_IV__FAM_0 |
| NC_019936.1_AbiC_1 | AbiC | AbiC | NC_019936.1_2817 | NC_019936.1_2817 | NC_019936.1_2817 | 1 | AbiC__AbiC |
| NC_019936.1_RM_Type_I_14 | RM | RM_Type_I | NC_019936.1_3312 | NC_019936.1_3317 | NC_019936.1_3312,NC_019936.1_3313,NC_019936.1_3314,NC_019936.1_3317 | 4 | RM__Type_I_MTases_FAM_3,RM__Type_I_REases_FAM_1.einsi_trimmed,RM__Type_I_REases_FAM_2.einsi_trimmed,RM__Type_I_S_52 |
| NC_019936.1_CBASS_III_4 | CBASS | CBASS_III | NC_019936.1_3322 | NC_019936.1_3325 | NC_019936.1_3322,NC_019936.1_3323,NC_019936.1_3324,NC_019936.1_3325 | 4 | CBASS__Cyclase_II,CBASS__Endonuc_big,CBASS__TRIP13,CBASS__bacHORMA_1 |
| NC_019936.1_RM_Type_I_15 | RM | RM_Type_I | NC_019936.1_3936 | NC_019936.1_3940 | NC_019936.1_3936,NC_019936.1_3939,NC_019936.1_3940 | 3 | RM__Type_I_MTases_FAM_0,RM__Type_I_REases_FAM_0.einsi_trimmed,RM__Type_I_S_06 |
| NC_019936.1_dCTPdeaminase_7 | dCTPdeaminase | dCTPdeaminase | NC_019936.1_4004 | NC_019936.1_4004 | NC_019936.1_4004 | 1 | dCTPdeaminase__dCTPdeaminase |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_019936.1|provirus_4296137_4304306 | 8170 | 12 | 2 | High-quality | High-quality | Viruses;Monodnaviria;Loebvirae;Hofneiviricota;Faserviricetes;Tubulavirales;Inoviridae | Provirus | 4296137-4304306 |
| NC_019936.1|provirus_3233292_3241441 | 8150 | 14 | 3 | Medium-quality | Genome-fragment | Viruses;Monodnaviria;Loebvirae;Hofneiviricota;Faserviricetes;Tubulavirales;Inoviridae | Provirus | 3233292-3241441 |
| NC_019936.1|provirus_2346826_2361929 | 15104 | 25 | 2 | High-quality | High-quality | Viruses;Monodnaviria;Loebvirae;Hofneiviricota;Faserviricetes;Tubulavirales;Inoviridae | Provirus | 2346826-2361929 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.21.2 Prophages
Select prophage to show:
2.21.2.1 Phage ID: NC_019936.1|provirus_4296137_4304306
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_019936.1|provirus_4296137_4304306_3987 | 216 | NA | NA | NA |
| NC_019936.1|provirus_4296137_4304306_3988 | 582 | NA | NA | NA |
| NC_019936.1|provirus_4296137_4304306_3989 | 372 | GENOMAD.225482.VP | NA | NA |
| NC_019936.1|provirus_4296137_4304306_3990 | 180 | GENOMAD.226094.VP | NA | NA |
| NC_019936.1|provirus_4296137_4304306_3991 | 216 | GENOMAD.225528.VP | NA | NA |
| NC_019936.1|provirus_4296137_4304306_3992 | 210 | GENOMAD.224287.VP | PF05356 | Inovirus Coat protein B |
| NC_019936.1|provirus_4296137_4304306_3993 | 1494 | GENOMAD.222416.VP | NA | NA |
| NC_019936.1|provirus_4296137_4304306_3994 | 327 | GENOMAD.224290.VP | PF10734 | NA |
| NC_019936.1|provirus_4296137_4304306_3995 | 1185 | GENOMAD.090645.VV | NA | NA |
| NC_019936.1|provirus_4296137_4304306_3996 | 1281 | GENOMAD.226808.VP | PF02486 | Replication initiation factor |
| NC_019936.1|provirus_4296137_4304306_3997 | 1059 | GENOMAD.212346.VP | PF16452;PF06892;COG1974 | Bacteriophage CI repressor C-terminal domain; Phage regulatory protein CII (CP76) |
| NC_019936.1|provirus_4296137_4304306_3998 | 318 | GENOMAD.200462.VV | NA | NA |
2.21.2.2 Phage ID: NC_019936.1|provirus_3233292_3241441
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_019936.1|provirus_3233292_3241441_2952 | 1008 | GENOMAD.212346.VP | PF16452;PF06892;COG1974 | Bacteriophage CI repressor C-terminal domain; Phage regulatory protein CII (CP76) |
| NC_019936.1|provirus_3233292_3241441_2953 | 1278 | GENOMAD.226808.VP | PF02486 | Replication initiation factor |
| NC_019936.1|provirus_3233292_3241441_2954 | 1185 | GENOMAD.090645.VV | NA | NA |
| NC_019936.1|provirus_3233292_3241441_2955 | 327 | GENOMAD.224290.VP | PF10734 | NA |
| NC_019936.1|provirus_3233292_3241441_2956 | 1494 | GENOMAD.222416.VP | NA | NA |
| NC_019936.1|provirus_3233292_3241441_2957 | 129 | NA | NA | NA |
| NC_019936.1|provirus_3233292_3241441_2958 | 210 | GENOMAD.224287.VP | PF05356 | Inovirus Coat protein B |
| NC_019936.1|provirus_3233292_3241441_2959 | 216 | GENOMAD.225528.VP | NA | NA |
| NC_019936.1|provirus_3233292_3241441_2960 | 180 | GENOMAD.226094.VP | NA | NA |
| NC_019936.1|provirus_3233292_3241441_2961 | 360 | GENOMAD.225482.VP | NA | NA |
| NC_019936.1|provirus_3233292_3241441_2962 | 771 | NA | NA | NA |
| NC_019936.1|provirus_3233292_3241441_2963 | 144 | GENOMAD.213484.VP | PF05509;COG4877 | Plasmid stability protein |
| NC_019936.1|provirus_3233292_3241441_2964 | 144 | NA | NA | NA |
| NC_019936.1|provirus_3233292_3241441_2965 | 216 | NA | NA | NA |
2.21.2.3 Phage ID: NC_019936.1|provirus_2346826_2361929
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_019936.1|provirus_2346826_2361929_2121 | 288 | NA | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2122 | 213 | GENOMAD.221461.VP | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2123 | 1263 | GENOMAD.223897.VP | PF05155 | Phage X family |
| NC_019936.1|provirus_2346826_2361929_2124 | 147 | NA | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2125 | 345 | GENOMAD.228002.VV | PF17426 | Putative Gamma DNA binding protein G5P |
| NC_019936.1|provirus_2346826_2361929_2126 | 147 | NA | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2127 | 1512 | GENOMAD.222416.VP | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2128 | 267 | GENOMAD.197598.VP | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2129 | 1194 | NA | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2130 | 288 | NA | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2131 | 213 | GENOMAD.221461.VP | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2132 | 1263 | GENOMAD.223897.VP | PF05155 | Phage X family |
| NC_019936.1|provirus_2346826_2361929_2133 | 147 | NA | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2134 | 345 | GENOMAD.228002.VV | PF17426 | Putative Gamma DNA binding protein G5P |
| NC_019936.1|provirus_2346826_2361929_2135 | 147 | NA | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2136 | 1512 | GENOMAD.222416.VP | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2137 | 267 | GENOMAD.197598.VP | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2138 | 1194 | NA | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2139 | 288 | NA | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2140 | 360 | NA | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2141 | 285 | NA | NA | NA |
| NC_019936.1|provirus_2346826_2361929_2142 | 288 | NA | NA | NA |
2.21.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_019936.1|provirus_4296137_4304306 | sequence_000001.fasta.fasta | 1_1 | 0.05 | average | ANImf | 1 |
| NC_019936.1|provirus_3233292_3241441 | sequence_000002.fasta.fasta | 1_2 | 0.05 | average | ANImf | 1 |
| NC_019936.1|provirus_2346826_2361929 | sequence_000000.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
Primary clustering plot
2.21.4 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_019936.1|provirus_2346826_2361929 | RS_GCF_015291885.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_AC | CRISPR | 97.4 | blast;95.20 iPHoP-RF;85.40 |
| NC_019936.1|provirus_2346826_2361929 | RS_GCF_003640395.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas urumqiensis | CRISPR | 96.9 | iPHoP-RF;52.20 |
| NC_019936.1|provirus_2346826_2361929 | RS_GCF_000219605.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri | blast | 96.2 | CRISPR;90.50 iPHoP-RF;82.80 |
| NC_019936.1|provirus_2346826_2361929 | RS_GCF_000327065.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_AE | blast | 95.9 | iPHoP-RF;64.00 |
| NC_019936.1|provirus_2346826_2361929 | RS_GCF_002929225.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_U | blast | 94.1 | iPHoP-RF;87.60 |
| NC_019936.1|provirus_2346826_2361929 | RS_GCF_003935375.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas xanthomarina_A | blast | 94.0 | iPHoP-RF;87.90 CRISPR;82.70 |
| NC_019936.1|provirus_2346826_2361929 | GB_GCA_007713455.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas sp007713455 | blast | 93.1 | iPHoP-RF;76.60 |
| NC_019936.1|provirus_2346826_2361929 | RS_GCF_021432085.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas kunmingensis_A | blast | 93.1 | iPHoP-RF;89.80 |
| NC_019936.1|provirus_2346826_2361929 | RS_GCF_000341615.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_G | blast | 91.8 | iPHoP-RF;74.80 |
| NC_019936.1|provirus_2346826_2361929 | RS_GCF_003696285.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas nitrititolerans | blast | 90.6 | iPHoP-RF;52.20 |
| NC_019936.1|provirus_2346826_2361929 | RS_GCF_015070855.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas lopnurensis | blast | 90.6 | iPHoP-RF;79.80 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_000219605.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri | blast | 96.9 | iPHoP-RF;86.70 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_002929225.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_U | blast | 96.9 | iPHoP-RF;86.30 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_003696285.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas nitrititolerans | blast | 96.9 | None |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_000495915.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas chloritidismutans | blast | 96.8 | iPHoP-RF;88.90 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_003935375.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas xanthomarina_A | blast | 96.8 | iPHoP-RF;81.10 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_015291885.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_AC | blast | 96.8 | iPHoP-RF;83.10 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_021432085.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas kunmingensis_A | blast | 96.8 | iPHoP-RF;82.50 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_900114065.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas kunmingensis | blast | 96.8 | iPHoP-RF;88.20 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_000818015.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas balearica | blast | 96.7 | None |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_003696315.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas songnenensis | blast | 96.5 | iPHoP-RF;93.40 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_000327065.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_AE | blast | 96.4 | iPHoP-RF;92.40 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_002909485.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_AH | blast | 96.3 | iPHoP-RF;75.90 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_000661915.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_A | blast | 94.0 | iPHoP-RF;91.40 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_002890795.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_AA | blast | 92.7 | iPHoP-RF;77.10 |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_000341615.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_G | iPHoP-RF | 90.8 | None |
| NC_019936.1|provirus_3233292_3241441 | RS_GCF_024448505.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas degradans | blast | 90.6 | iPHoP-RF;75.20 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_003696285.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas nitrititolerans | blast | 96.9 | iPHoP-RF;77.80 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_000219605.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri | blast | 96.8 | iPHoP-RF;90.50 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_015291885.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_AC | blast | 96.7 | iPHoP-RF;88.20 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_000818015.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas balearica | blast | 96.2 | iPHoP-RF;70.40 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_003696315.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas songnenensis | blast | 93.9 | iPHoP-RF;80.30 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_000327065.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_AE | blast | 93.6 | iPHoP-RF;74.10 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_002909485.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_AH | blast | 92.5 | iPHoP-RF;85.40 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_000661915.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_A | blast | 91.7 | iPHoP-RF;68.90 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_003935375.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas xanthomarina_A | iPHoP-RF | 91.4 | blast;90.20 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_002929225.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_U | blast | 91.0 | iPHoP-RF;90.10 |
| NC_019936.1|provirus_4296137_4304306 | GB_GCA_003488145.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas sp003488145 | iPHoP-RF | 90.8 | None |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_000495915.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas chloritidismutans | blast | 90.7 | iPHoP-RF;89.80 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_000935215.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas stutzeri_AD | blast | 90.2 | iPHoP-RF;87.30 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_021432085.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas kunmingensis_A | blast | 90.2 | iPHoP-RF;86.00 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_900114065.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas kunmingensis | blast | 90.2 | iPHoP-RF;90.10 |
| NC_019936.1|provirus_4296137_4304306 | RS_GCF_014764705.1 | d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Stutzerimonas;s__Stutzerimonas sp002692525 | iPHoP-RF | 90.1 | None |
2.22 NC_021184
2.22.1 Host Genome
GTDB-Tk taxonomy:
| classification |
|---|
| d__Bacteria;p__Bacillota_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum;s__Sporotomaculum gibsoniae |
CheckM2 Summary:
| total_contigs | contig_n50 | completeness | contamination |
|---|---|---|---|
| 1 | 4855529 | 100 | 3.04 |
Defense-Finder Systems:
| sys_id | type | subtype | sys_beg | sys_end | protein_in_syst | genes_count | name_of_profiles_in_sys |
|---|---|---|---|---|---|---|---|
| NC_021184.1_SoFic_11 | SoFIC | SoFic | NC_021184.1_113 | NC_021184.1_113 | NC_021184.1_113 | 1 | SoFic__SoFic |
| NC_021184.1_RM_Type_I_21 | RM | RM_Type_I | NC_021184.1_221 | NC_021184.1_224 | NC_021184.1_221,NC_021184.1_223,NC_021184.1_224 | 3 | RM__Type_I_MTases_FAM_0,RM__Type_I_REases_FAM_0.einsi_trimmed,RM__Type_I_S_51 |
| NC_021184.1_RM_Type_I_22 | RM | RM_Type_I | NC_021184.1_242 | NC_021184.1_244 | NC_021184.1_242,NC_021184.1_243,NC_021184.1_244 | 3 | RM__Type_I_MTases_FAM_2,RM__Type_I_REases_FAM_2.einsi_trimmed,RM__Type_I_S_52 |
| NC_021184.1_MazEF_8 | MazEF | MazEF | NC_021184.1_395 | NC_021184.1_396 | NC_021184.1_395,NC_021184.1_396 | 2 | MazEF__MazE,MazEF__MazF |
| NC_021184.1_CAS_Class1-Subtype-I-B_29 | Cas | CAS_Class1-Subtype-I-B | NC_021184.1_509 | NC_021184.1_516 | NC_021184.1_509,NC_021184.1_510,NC_021184.1_511,NC_021184.1_512,NC_021184.1_513,NC_021184.1_514,NC_021184.1_515,NC_021184.1_516 | 8 | cas1_I_II_III_IV_V_VI_7,cas2_I_II_III_IV_V_VI_3,cas3_I_2,cas4_I_II_III_IV_V_VI_6,cas5_I-B_17,cas6_I-B_III_1,cas7b_I-B_I-C_2,cas8b1_I-B_9 |
| NC_021184.1_CAS_Class1-Subtype-I-B_30 | Cas | CAS_Class1-Subtype-I-B | NC_021184.1_770 | NC_021184.1_779 | NC_021184.1_770,NC_021184.1_773,NC_021184.1_774,NC_021184.1_775,NC_021184.1_776,NC_021184.1_777,NC_021184.1_778,NC_021184.1_779 | 8 | cas1_I_II_III_IV_V_VI_7,cas2_I_II_III_IV_V_VI_3,cas3_I_5,cas4_I_II_III_IV_V_VI_6,cas5_I-B_17,cas6_I_II_III_IV_V_VI_20,cas7_I-B_8,cas8b1_I-B_14 |
| NC_021184.1_Wadjet_II_17 | Wadjet | Wadjet_II | NC_021184.1_925 | NC_021184.1_928 | NC_021184.1_925,NC_021184.1_926,NC_021184.1_927,NC_021184.1_928 | 4 | Wadjet__JetA_II,Wadjet__JetB_II,Wadjet__JetC_II,Wadjet__JetD_II |
| NC_021184.1_RM_Type_I_23 | RM | RM_Type_I | NC_021184.1_963 | NC_021184.1_967 | NC_021184.1_963,NC_021184.1_965,NC_021184.1_967 | 3 | RM__Type_I_MTases_FAM_0,RM__Type_I_REases_FAM_0.einsi_trimmed,RM__Type_I_S_06 |
| NC_021184.1_Kiwa_6 | Kiwa | Kiwa | NC_021184.1_1016 | NC_021184.1_1017 | NC_021184.1_1016,NC_021184.1_1017 | 2 | Kiwa__KwaA,Kiwa__KwaB |
| NC_021184.1_PfiAT_10 | PfiAT | PfiAT | NC_021184.1_1033 | NC_021184.1_1034 | NC_021184.1_1033,NC_021184.1_1034 | 2 | PfiAT__PfiA,PfiAT__PfiT |
| NC_021184.1_BREX_I_4 | BREX | BREX_I | NC_021184.1_1159 | NC_021184.1_1165 | NC_021184.1_1159,NC_021184.1_1160,NC_021184.1_1161,NC_021184.1_1162,NC_021184.1_1165 | 5 | BREX__brxA_DUF1819,BREX__brxB_DUF1788,BREX__brxC,BREX__pglX1,BREX__pglZA |
| NC_021184.1_AbiE_1 | AbiE | AbiE | NC_021184.1_1208 | NC_021184.1_1209 | NC_021184.1_1208,NC_021184.1_1209 | 2 | AbiEii__AbiEi_4,AbiEii__AbiEii |
| NC_021184.1_RM_Type_III_26 | RM | RM_Type_III | NC_021184.1_1419 | NC_021184.1_1420 | NC_021184.1_1419,NC_021184.1_1420 | 2 | RM_Type_III__Type_III_MTases_FAM_0,RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed |
| NC_021184.1_Gabija_5 | Gabija | Gabija | NC_021184.1_1422 | NC_021184.1_1423 | NC_021184.1_1422,NC_021184.1_1423 | 2 | Gabija__GajA,Gabija__GajB_2 |
| NC_021184.1_PD-T7-2_9 | PD-T7-2 | PD-T7-2 | NC_021184.1_1424 | NC_021184.1_1428 | NC_021184.1_1424,NC_021184.1_1428 | 2 | PD-T7-2__PD-T7-2_A,PD-T7-2__PD-T7-2_B |
| NC_021184.1_RM_Type_IV_28 | RM | RM_Type_IV | NC_021184.1_1656 | NC_021184.1_1656 | NC_021184.1_1656 | 1 | RM_Type_IV__Type_IV_05 |
| NC_021184.1_RM_Type_II_24 | RM | RM_Type_II | NC_021184.1_3394 | NC_021184.1_3396 | NC_021184.1_3394,NC_021184.1_3395,NC_021184.1_3396 | 3 | RM_Type_II__Type_II_MTases_FAM_16,RM_Type_II__Type_II_REase01,RM_Type_II__Type_II_REase17 |
| NC_021184.1_Wadjet_I_15 | Wadjet | Wadjet_I | NC_021184.1_3691 | NC_021184.1_3693 | NC_021184.1_3691,NC_021184.1_3692,NC_021184.1_3693 | 3 | Wadjet__JetA_I,Wadjet__JetB_I,Wadjet__JetC_I |
| NC_021184.1_Wadjet_I_16 | Wadjet | Wadjet_I | NC_021184.1_3803 | NC_021184.1_3806 | NC_021184.1_3803,NC_021184.1_3804,NC_021184.1_3805,NC_021184.1_3806 | 4 | Wadjet__JetA_I,Wadjet__JetB_I,Wadjet__JetC_I,Wadjet__JetD_I |
| NC_021184.1_CAS_Class1-Subtype-I-C_31 | Cas | CAS_Class1-Subtype-I-C | NC_021184.1_4025 | NC_021184.1_4031 | NC_021184.1_4025,NC_021184.1_4026,NC_021184.1_4027,NC_021184.1_4028,NC_021184.1_4029,NC_021184.1_4030,NC_021184.1_4031 | 7 | cas1_I_II_III_IV_V_VI_6,cas2_I_II_III_IV_V_VI_3,cas3_I_5,cas4_I_II_III_IV_V_VI_6,cas5_I-C_11,cas7_I-C_7,cas8c_I-C_2 |
| NC_021184.1_RM_Type_III_27 | RM | RM_Type_III | NC_021184.1_4091 | NC_021184.1_4092 | NC_021184.1_4091,NC_021184.1_4092 | 2 | RM_Type_III__Type_III_MTases_FAM_0,RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed |
| NC_021184.1_Lamassu-Hypothetical_7 | Lamassu-Fam | Lamassu-Hypothetical | NC_021184.1_4235 | NC_021184.1_4237 | NC_021184.1_4235,NC_021184.1_4236,NC_021184.1_4237 | 3 | Lamassu-Fam__LmuA_effector_hypothetical,Lamassu-Fam__LmuB_SMC_hypothetical,Lamassu-Fam__LmuC_acc_hypothetical |
| NC_021184.1_AbiH_2 | AbiH | AbiH | NC_021184.1_4301 | NC_021184.1_4301 | NC_021184.1_4301 | 1 | AbiH__AbiH |
| NC_021184.1_RM_Type_II_25 | RM | RM_Type_II | NC_021184.1_4531 | NC_021184.1_4532 | NC_021184.1_4531,NC_021184.1_4532 | 2 | RM_Type_II__Type_II_MTases_FAM_27,RM_Type_II__Type_II_REase01 |
Genomad and CheckV Summary:
| seq_name | length | gene_count | viral_genes | checkv_quality | miuvig_quality | taxonomy | topology | coordinates |
|---|---|---|---|---|---|---|---|---|
| NC_021184.1|provirus_4565036_4615358 | 50323 | 58 | 23 | Medium-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 4565036-4615358 |
| NC_021184.1|provirus_4471243_4518329 | 47087 | 58 | 22 | High-quality | High-quality | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 4471243-4518329 |
| NC_021184.1|provirus_19778_35564 | 15787 | 22 | 5 | Low-quality | Genome-fragment | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; | Provirus | 19778-35564 |
Host Genome Ideogram with Phages:
In
this circular plot, “c” indicates the contig, and the
number that follows (e.g., c1) represents the contig
number. If multiple contigs are present in the genome, each will be
shown with a distinct label (e.g., c1,
c2, etc.).
2.22.2 Prophages
Select prophage to show:
2.22.2.1 Phage ID: NC_021184.1|provirus_4565036_4615358
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_021184.1|provirus_4565036_4615358_4320 | 594 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4321 | 2580 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4322 | 240 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4323 | 267 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4324 | 759 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4325 | 1011 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4326 | 657 | GENOMAD.055867.VV | COG5632 | N-acetylmuramoyl-L-alanine amidase CwlA |
| NC_021184.1|provirus_4565036_4615358_4327 | 423 | GENOMAD.083633.VV | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4328 | 1098 | GENOMAD.006687.VV | PF14594;COG4926;TIGR01665 | Siphovirus ReqiPepy6 Gp37-like protein |
| NC_021184.1|provirus_4565036_4615358_4329 | 141 | GENOMAD.166984.VP | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4330 | 279 | GENOMAD.169028.VV | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4331 | 1863 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4332 | 798 | GENOMAD.078804.VV | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4333 | 1077 | GENOMAD.007754.VV | PF08931 | Receptor-binding protein of phage tail base-plate Siphoviridae, head |
| NC_021184.1|provirus_4565036_4615358_4334 | 852 | GENOMAD.008827.VV | PF20195;COG4722;TIGR01633 | Phage-related protein |
| NC_021184.1|provirus_4565036_4615358_4335 | 3420 | GENOMAD.207179.VP | PF05521;COG5283;TIGR01563 | Phage-related tail protein |
| NC_021184.1|provirus_4565036_4615358_4336 | 156 | GENOMAD.108553.VV | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4337 | 294 | GENOMAD.063000.VV | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4338 | 807 | GENOMAD.003250.VV | PF04630;TIGR01603 | phage major tail protein, phi13 family |
| NC_021184.1|provirus_4565036_4615358_4339 | 327 | GENOMAD.018077.VV | PF05657 | NA |
| NC_021184.1|provirus_4565036_4615358_4340 | 372 | GENOMAD.137411.VP | PF11114;TIGR01725;COG5005 | phage protein, HK97 gp10 family |
| NC_021184.1|provirus_4565036_4615358_4341 | 333 | GENOMAD.142742.VP | PF05521;COG5614;TIGR01563 | Bacteriophage head-tail adaptor |
| NC_021184.1|provirus_4565036_4615358_4342 | 303 | GENOMAD.041843.VV | PF05135;TIGR01560 | Phage gp6-like head-tail connector protein |
| NC_021184.1|provirus_4565036_4615358_4343 | 687 | GENOMAD.111513.VV | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4344 | 1185 | GENOMAD.168658.VV | PF05065;PF04586;PF12518;COG4653;TIGR01554;K06904 | Predicted phage phi-C31 gp36 major capsid-like protein |
| NC_021184.1|provirus_4565036_4615358_4345 | 699 | GENOMAD.028909.VV | PF05135;TIGR01560 | Phage gp6-like head-tail connector protein |
| NC_021184.1|provirus_4565036_4615358_4346 | 1293 | GENOMAD.179073.VP | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4347 | 327 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4348 | 312 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4349 | 1557 | GENOMAD.181434.VP | PF20441 | Terminase large subunit, endonuclease domain |
| NC_021184.1|provirus_4565036_4615358_4350 | 474 | GENOMAD.168120.VP | PF05119;COG3747;TIGR01558 | Phage terminase, small subunit |
| NC_021184.1|provirus_4565036_4615358_4351 | 207 | GENOMAD.225559.VP | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4352 | 453 | GENOMAD.191984.VP | PF07128 | NA |
| NC_021184.1|provirus_4565036_4615358_4353 | 339 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4354 | 909 | GENOMAD.105515.VV | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4355 | 189 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4356 | 765 | GENOMAD.105515.VV | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4357 | 1224 | GENOMAD.038338.VV | COG3392 | NA |
| NC_021184.1|provirus_4565036_4615358_4358 | 1395 | GENOMAD.005053.VV | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4359 | 321 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4360 | 957 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4361 | 759 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4362 | 432 | GENOMAD.159035.VP | PF07374;TIGR01636;COG2739 | phage transcriptional activator, RinA family |
| NC_021184.1|provirus_4565036_4615358_4363 | 198 | GENOMAD.212426.VP | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4364 | 1353 | GENOMAD.116250.VP | PF00270;COG1111;TIGR04095;K17677 | ERCC4-related helicase |
| NC_021184.1|provirus_4565036_4615358_4365 | 282 | GENOMAD.004000.VV | COG1591 | NA |
| NC_021184.1|provirus_4565036_4615358_4366 | 2247 | GENOMAD.016441.VV | TIGR01613 | phage/plasmid primase, P4 family, C-terminal domain |
| NC_021184.1|provirus_4565036_4615358_4367 | 648 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4368 | 408 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4369 | 258 | GENOMAD.159187.VV | PF14205;TIGR02098;COG1996 | MJ0042 family finger-like domain |
| NC_021184.1|provirus_4565036_4615358_4370 | 2301 | GENOMAD.038590.VV | PF00476;PF13482;K02334;COG0749;TIGR01388 | DNA polymerase I - 3’-5’ exonuclease and polymerase domains |
| NC_021184.1|provirus_4565036_4615358_4371 | 558 | GENOMAD.039702.VV | PF10991 | NA |
| NC_021184.1|provirus_4565036_4615358_4372 | 1122 | GENOMAD.136786.VV | PF10926;TIGR01896;COG2887;K07465 | CRISPR-associated exonuclease Csa1 |
| NC_021184.1|provirus_4565036_4615358_4373 | 318 | GENOMAD.222352.VV | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4374 | 162 | GENOMAD.116519.VV | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4375 | 498 | GENOMAD.204246.VV | PF03333;K01994;TIGR03879 | Adhesin biosynthesis transcription regulatory protein |
| NC_021184.1|provirus_4565036_4615358_4376 | 1863 | NA | NA | NA |
| NC_021184.1|provirus_4565036_4615358_4377 | 204 | NA | NA | NA |
2.22.2.2 Phage ID: NC_021184.1|provirus_4471243_4518329
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_021184.1|provirus_4471243_4518329_4220 | 1776 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4221 | 456 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4222 | 1011 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4223 | 267 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4224 | 546 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4225 | 276 | GENOMAD.222700.VP | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4226 | 1197 | GENOMAD.014802.VV | PF00176;K20093;COG1061;TIGR04095 | Superfamily II DNA or RNA helicase |
| NC_021184.1|provirus_4471243_4518329_4227 | 1701 | GENOMAD.016341.VV | PF13479;PF12684;TIGR01618;K07465;COG1468 | phage nucleotide-binding protein |
| NC_021184.1|provirus_4471243_4518329_4228 | 453 | GENOMAD.031678.VV | PF05037 | NA |
| NC_021184.1|provirus_4471243_4518329_4229 | 1695 | GENOMAD.102034.VP | TIGR01636 | NA |
| NC_021184.1|provirus_4471243_4518329_4230 | 654 | GENOMAD.171549.VP | COG3617 | Prophage antirepressor |
| NC_021184.1|provirus_4471243_4518329_4231 | 1911 | GENOMAD.024099.VV | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4232 | 345 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4233 | 225 | GENOMAD.212426.VP | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4234 | 369 | GENOMAD.159035.VP | PF07374;TIGR01636;COG2739 | phage transcriptional activator, RinA family |
| NC_021184.1|provirus_4471243_4518329_4235 | 207 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4236 | 399 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4237 | 273 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4238 | 276 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4239 | 1395 | GENOMAD.038338.VV | COG3392 | NA |
| NC_021184.1|provirus_4471243_4518329_4240 | 1224 | GENOMAD.038338.VV | COG3392 | NA |
| NC_021184.1|provirus_4471243_4518329_4241 | 765 | GENOMAD.105515.VV | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4242 | 189 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4243 | 909 | GENOMAD.105515.VV | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4244 | 339 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4245 | 432 | GENOMAD.191984.VP | PF07128 | NA |
| NC_021184.1|provirus_4471243_4518329_4246 | 207 | GENOMAD.225559.VP | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4247 | 474 | GENOMAD.168120.VP | PF05119;COG3747;TIGR01558 | Phage terminase, small subunit |
| NC_021184.1|provirus_4471243_4518329_4248 | 1557 | GENOMAD.181434.VP | PF20441 | Terminase large subunit, endonuclease domain |
| NC_021184.1|provirus_4471243_4518329_4249 | 312 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4250 | 330 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4251 | 1236 | GENOMAD.179073.VP | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4252 | 714 | GENOMAD.028909.VV | PF05135;TIGR01560 | Phage gp6-like head-tail connector protein |
| NC_021184.1|provirus_4471243_4518329_4253 | 936 | GENOMAD.168658.VV | PF05065;PF04586;PF12518;COG4653;TIGR01554;K06904 | Predicted phage phi-C31 gp36 major capsid-like protein |
| NC_021184.1|provirus_4471243_4518329_4254 | 1821 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4255 | 342 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4256 | 687 | GENOMAD.111513.VV | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4257 | 303 | GENOMAD.041843.VV | PF05135;TIGR01560 | Phage gp6-like head-tail connector protein |
| NC_021184.1|provirus_4471243_4518329_4258 | 333 | GENOMAD.142742.VP | PF05521;COG5614;TIGR01563 | Bacteriophage head-tail adaptor |
| NC_021184.1|provirus_4471243_4518329_4259 | 372 | GENOMAD.137411.VP | PF11114;TIGR01725;COG5005 | phage protein, HK97 gp10 family |
| NC_021184.1|provirus_4471243_4518329_4260 | 327 | GENOMAD.018077.VV | PF05657 | NA |
| NC_021184.1|provirus_4471243_4518329_4261 | 567 | GENOMAD.003250.VV | PF04630;TIGR01603 | phage major tail protein, phi13 family |
| NC_021184.1|provirus_4471243_4518329_4262 | 300 | GENOMAD.063000.VV | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4263 | 156 | GENOMAD.108553.VV | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4264 | 267 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4265 | 321 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4266 | 3429 | GENOMAD.181727.VP | COG5280 | Phage-related minor tail protein |
| NC_021184.1|provirus_4471243_4518329_4267 | 852 | GENOMAD.008827.VV | PF20195;COG4722;TIGR01633 | Phage-related protein |
| NC_021184.1|provirus_4471243_4518329_4268 | 1071 | GENOMAD.007754.VV | PF08931 | Receptor-binding protein of phage tail base-plate Siphoviridae, head |
| NC_021184.1|provirus_4471243_4518329_4269 | 798 | GENOMAD.078804.VV | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4270 | 1863 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4271 | 279 | GENOMAD.169028.VV | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4272 | 141 | GENOMAD.166984.VP | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4273 | 711 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4274 | 1098 | GENOMAD.006687.VV | PF14594;COG4926;TIGR01665 | Siphovirus ReqiPepy6 Gp37-like protein |
| NC_021184.1|provirus_4471243_4518329_4275 | 411 | GENOMAD.083633.VV | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4276 | 687 | NA | NA | NA |
| NC_021184.1|provirus_4471243_4518329_4277 | 858 | NA | NA | NA |
2.22.2.3 Phage ID: NC_021184.1|provirus_19778_35564
Phage-Host Genome Ideogram:
Genes Annotation (geNomad):
| gene | length | marker | annotation_accessions | annotation_description |
|---|---|---|---|---|
| NC_021184.1|provirus_19778_35564_13 | 1269 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_14 | 1185 | GENOMAD.016861.VV | PF13671;COG2019;TIGR01359;K13829 | AAA domain |
| NC_021184.1|provirus_19778_35564_15 | 456 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_16 | 264 | GENOMAD.221988.VV | PF06806;COG3311;TIGR01764 | Predicted DNA-binding transcriptional regulator AlpA |
| NC_021184.1|provirus_19778_35564_17 | 621 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_18 | 1278 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_19 | 240 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_20 | 171 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_21 | 207 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_22 | 357 | GENOMAD.096257.VV | NA | NA |
| NC_021184.1|provirus_19778_35564_23 | 189 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_24 | 573 | GENOMAD.103011.VV | PF04586;COG3740;K06904;TIGR01543 | Phage head maturation protease |
| NC_021184.1|provirus_19778_35564_25 | 1245 | GENOMAD.113164.VP | PF05521;COG5614;TIGR01563 | Bacteriophage head-tail adaptor |
| NC_021184.1|provirus_19778_35564_26 | 2025 | GENOMAD.110013.VP | COG5280 | Phage-related minor tail protein |
| NC_021184.1|provirus_19778_35564_27 | 1161 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_28 | 465 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_29 | 291 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_30 | 282 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_31 | 231 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_32 | 141 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_33 | 123 | NA | NA | NA |
| NC_021184.1|provirus_19778_35564_34 | 171 | NA | NA | NA |
2.22.3 vOTUs
When more than 1 phage is detected in the host genome, we perform a clustering step using the tool dRep.
A threshold of 0.95 was applied to the ANI similarity index to define clusters of virus operational taxonomic units (vOTUs).
Final cluster designations
| genomad_summary$seq_name | genome | secondary_cluster | threshold | cluster_method | comparison_algorithm | primary_cluster |
|---|---|---|---|---|---|---|
| NC_021184.1|provirus_4565036_4615358 | sequence_000001.fasta.fasta | 1_1 | 0.05 | average | ANImf | 1 |
| NC_021184.1|provirus_4471243_4518329 | sequence_000002.fasta.fasta | 1_2 | 0.05 | average | ANImf | 1 |
| NC_021184.1|provirus_19778_35564 | sequence_000000.fasta.fasta | 2_0 | 0.05 | average | ANImf | 2 |
Primary clustering plot
2.22.4 Prophage-Host Prediction
Prediction of potential hosts for the prophage contigs.
| virus | host_genome | host_taxonomy | main_method | confidence_score | additional_methods |
|---|---|---|---|---|---|
| NC_021184.1|provirus_19778_35564 | RS_GCF_000233715.2 | d__Bacteria;p__Bacillota_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum;s__Sporotomaculum gibsoniae | blast | 95.5 | iPHoP-RF;84.20 |
| NC_021184.1|provirus_19778_35564 | RS_GCF_008124625.1 | d__Bacteria;p__Bacillota_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum;s__Sporotomaculum thermosapovorans | iPHoP-RF | 93.4 | blast;90.30 |
| NC_021184.1|provirus_19778_35564 | GB_GCA_016841645.1 | d__Bacteria;p__Bacillota_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum;s__Sporotomaculum geothermicum_B | blast | 90.9 | iPHoP-RF;74.80 |
| NC_021184.1|provirus_19778_35564 | GB_GCA_016841205.1 | d__Bacteria;p__Bacillota_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum;s__Sporotomaculum geothermicum_A | blast | 90.6 | iPHoP-RF;70.90 |
| NC_021184.1|provirus_19778_35564 | GB_GCA_016841905.1 | d__Bacteria;p__Bacillota_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum;s__Sporotomaculum geothermicum_C | blast | 90.4 | iPHoP-RF;51.20 |
| NC_021184.1|provirus_19778_35564 | RS_GCF_009932395.1 | d__Bacteria;p__Bacillota_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum;s__Sporotomaculum syntrophicum | blast | 90.3 | iPHoP-RF;83.30 |
| NC_021184.1|provirus_4471243_4518329 | RS_GCF_000233715.2 | d__Bacteria;p__Bacillota_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum;s__Sporotomaculum gibsoniae | blast | 98.1 | iPHoP-RF;73.20 |
| NC_021184.1|provirus_4565036_4615358 | RS_GCF_000233715.2 | d__Bacteria;p__Bacillota_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum;s__Sporotomaculum gibsoniae | blast | 98.2 | iPHoP-RF;77.30 |