Submission Results

Sequence Name: Not Available

GenBank Accession Number: RRZQ01000002.1

GenInfo (GI) Number: 0000000000

Download Results: RRZQ01000002.1.PHASTER.zip

gi|00000000|ref|RRZQ01000002.1| Streptococcus suis strain IMT40201 Contig_2, whole genome shotgun 199627, gc%: 41.01%

Download summary as .txt file: summary.txt file_download

Total: 2 prophage regions have been identified, of which 0 regions are intact, 1 regions are incomplete, and 1 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
133.2Kbquestionable9034136535-169772 info_outlinePHAGE_Strept_phiARI0131_2_NC_031941(8)40.94%Show info_outline
213.8Kbincomplete4010185778-199627 info_outlinePHAGE_Strept_phiARI0131_2_NC_031941(4)41.35%Show info_outline
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)
Region: The number assigned to the region.
Region Length: The length of the sequence of that region (in bp).
Completeness: A prediction of whether the region contains a intact or incomplete prophage based on the above criteria.
Score: The score of the region based on the above criteria.
# Total Proteins: The number of ORFs present in the region.
Region Position: The start and end positions of the region on the bacterial chromosome.
Most Common Phage: The phage(s) with the highest number of proteins most similar to those in the region.
GC %: The percentage of GC nucleotides of the region.

Criteria for scoring prophage regions (as intact, questionable, or incomplete):
Method 1:

  1. If the number of certain phage organism in this table is more than or equal to 100% of the total number of CDS of the region, the region is marked with total score 150. If less than 100%, method 2 and 3 will be used.
Method 2:
  1. If the number of certain phage organism in this table is more than 50% of the total number of CDS of the region, that phage organism is considered as the major potential phage for that region; the percentage of the total number of that phage organism in this table in the total number of proteins of the region is calculated and then multipled by 100; the percentage of the length of that phage organism in this table in the length of the region is calculated and then multipled by 50 (phage head's encapsulation capability is considered).
Method 3:
  1. If any of the specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin') are present, the score will be increased by 10 for each keyword found.
  2. If the size of the region is greater than 30 Kb, the score will be increased by 10.
  3. If there are at least 40 proteins in the region, the score will be increased by 10.
  4. If all of the phage-related proteins and hypothetical proteins constitute more than 70% of the total number of proteins in the region, the score will be increased by 10.
Compared the total score of method 2 with the total score of method 3, the bigger one is chosen as the total score of the region.
If the region's total score is less than 70, it is marked as incomplete; if between 70 to 90, it is marked as questionable; if greater than 90, it is marked as intact.

gi|00000000|ref|RRZQ01000002.1| Streptococcus suis strain IMT40201 Contig_2, whole genome shotgun 199627, gc%: 41.01%

Download details as .txt file: detail.txt file_download

Hits against Virus and Prophage Database
Hits against Bacterial Database or GenBank File

Region 1, total 36 CDS

#CDS PositionBLAST HitE-ValueSequence
1136535..136546attL0.0Showinfo_outline
2complement(136912..138474)PHAGE_Bacill_Gamma_NC_007458: site-specific recombinase; EI219_00695; phage(gi77020163)2.37e-25Showinfo_outline
3complement(138474..139709)PHAGE_Clostr_phiCTC2B_NC_030951: protector from prophage-induced early lysis; EI219_00700; phage(gi100001)2.56e-21Showinfo_outline
4complement(140035..141504)PHAGE_Strept_Str_PAP_1_NC_028666: endolysin; EI219_00705; phage(gi966198635)2.96e-48Showinfo_outline
5complement(141511..141906)PHAGE_Paenib_PG1_NC_021558: holin; EI219_00710; phage(gi514231208)5.69e-23Showinfo_outline
6complement(141884..142252)PHAGE_Strept_phiARI0462_NC_031942: DNA topoisomerase medium subunit; EI219_00715; phage(gi100004)1.14e-42Showinfo_outline
7complement(142270..142464)PHAGE_Strept_phiARI0131_1_NC_031901: hypothetical protein; EI219_00720; phage(gi100009)9.56e-10Showinfo_outline
8complement(142477..146958)PHAGE_Strept_phiARI0131_2_NC_031941: DNA topoisomerase II large subunit; EI219_00725; phage(gi100005)8.98e-130Showinfo_outline
9complement(146958..147680)PHAGE_Strept_phiARI0131_2_NC_031941: hypothetical protein; EI219_00730; phage(gi100006)7.59e-104Showinfo_outline
10complement(147677..150535)PHAGE_Strept_phiARI0131_2_NC_031941: hypothetical protein; EI219_00735; phage(gi100007)0.0Showinfo_outline
11complement(150718..151137)PHAGE_Strept_phiARI0131_2_NC_031941: hypothetical protein; EI219_00740; phage(gi100008)6.57e-63Showinfo_outline
12complement(151148..151717)PHAGE_Strept_phiARI0131_2_NC_031941: hypothetical protein; EI219_00745; phage(gi100009)3.86e-67Showinfo_outline
13complement(151719..152045)PHAGE_Strept_phiARI0131_2_NC_031941: hypothetical protein; EI219_00750; phage(gi100010)4.14e-12Showinfo_outline
14complement(152052..152420)PHAGE_Strept_phiARI0131_2_NC_031941: hypothetical protein; EI219_00755; phage(gi100011)5.11e-19Showinfo_outline
15complement(152413..152751)PHAGE_Geobac_E2_NC_009552: putative head-tail adaptor; EI219_00760; phage(gi148747735)1.32e-05Showinfo_outline
16complement(152751..153008)phage gp6-like head-tail connector protein; EI219_007650.0Showinfo_outline
17complement(153011..154216)PHAGE_Burkho_KS9_NC_013055: major capsid protein gp5; EI219_00770; phage(gi255033737)4.82e-41Showinfo_outline
18complement(154235..154930)PHAGE_Geobac_E2_NC_009552: putative Clp peptidase; EI219_00775; phage(gi148747731)2.20e-53Showinfo_outline
19complement(154923..156206)PHAGE_Burkho_phi6442_NC_009235: gp4, phage portal protein, HK97 family; EI219_00780; phage(gi134288632)2.56e-87Showinfo_outline
20complement(156347..156718)PHAGE_Gordon_Bantam_NC_031074: hypothetical protein; EI219_00785; phage(gi100132)2.74e-14Showinfo_outline
21complement(156715..156972)type II toxin-antitoxin system Phd/YefM family antitoxin; EI219_007900.0Showinfo_outline
22complement(157043..157222)PHAGE_Gordon_Zirinka_NC_031097: hypothetical protein; EI219_00795; phage(gi100002)7.57e-10Showinfo_outline
23complement(157218..157937)PHAGE_Entero_phiEf11_NC_013696: ParB-like nuclease domain protein; EI219_00800; phage(gi282598764)2.52e-33Showinfo_outline
24complement(157909..158370)helix-turn-helix domain-containing protein; EI219_008050.0Showinfo_outline
25complement(158669..159034)PHAGE_Bacill_phi105_NC_004167: hypothetical protein; EI219_00810; phage(gi22855043)5.85e-31Showinfo_outline
26complement(159036..160073)methionine adenosyltransferase; EI219_008150.0Showinfo_outline
27complement(160121..160303)PHAGE_Agroba_Atu_ph07_NC_042013: hypothetical protein; EI219_00820; phage(gi100594)4.16e-06Showinfo_outline
28complement(160498..160974)hypothetical protein; EI219_008250.0Showinfo_outline
29complement(160967..162343)PHAGE_Entero_phiFL4A_NC_013644: DNA helicase; EI219_00830; phage(gi281416462)1.83e-159Showinfo_outline
30complement(162324..162605)PHAGE_Bacter_APSE_2_NC_011551: hypothetical protein; EI219_00835; phage(gi212499740)2.26e-17Showinfo_outline
31complement(162890..165175)PHAGE_Lactob_A2_NC_004112: putative primase; EI219_00840; phage(gi22296557)6.27e-57Showinfo_outline
32163868..163879attR0.0Showinfo_outline
33165592..165915hypothetical protein; EI219_008450.0Showinfo_outline
34165908..167029PHAGE_Clostr_phiCT453A_NC_028991: hypothetical protein; EI219_00850; phage(gi100016)3.68e-114Showinfo_outline
35167034..167582PHAGE_Clostr_phiCT453A_NC_028991: hypothetical protein; EI219_00855; phage(gi100017)1.41e-68Showinfo_outline
36167817..169772PHAGE_Clostr_phiCT453A_NC_028991: exonuclease A; EI219_00860; phage(gi100018)0.0Showinfo_outline

Region 2, total 10 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(185778..186317)PHAGE_Bacill_SPbeta_NC_001884: hypothetical protein; EI219_00940; phage(gi9630137)6.08e-09Showinfo_outline
2complement(186491..187807)PHAGE_Bacill_WBeta_NC_007734: putative site-specific recombinase; EI219_00945; phage(gi85701406)1.35e-33Showinfo_outline
3complement(187746..188987)PHAGE_Clostr_phiCTC2B_NC_030951: protector from prophage-induced early lysis; EI219_00950; phage(gi100001)1.96e-29Showinfo_outline
4complement(189211..190680)PHAGE_Strept_Str_PAP_1_NC_028666: endolysin; EI219_00955; phage(gi966198635)1.35e-48Showinfo_outline
5complement(190687..191082)PHAGE_Paenib_PG1_NC_021558: holin; EI219_00960; phage(gi514231208)4.15e-23Showinfo_outline
6complement(191060..191428)PHAGE_Strept_phiARI0462_NC_031942: DNA topoisomerase medium subunit; EI219_00965; phage(gi100004)2.35e-42Showinfo_outline
7complement(191434..191640)PHAGE_Strept_phiARI0131_1_NC_031901: hypothetical protein; EI219_00970; phage(gi100009)1.20e-10Showinfo_outline
8complement(191653..196200)PHAGE_Strept_phiARI0131_2_NC_031941: DNA topoisomerase II large subunit; EI219_00975; phage(gi100005)1.43e-126Showinfo_outline
9complement(196200..196922)PHAGE_Strept_phiARI0131_2_NC_031941: hypothetical protein; EI219_00980; phage(gi100006)1.87e-103Showinfo_outline
10complement(196919..199627)PHAGE_Strept_phiARI0131_2_NC_031941: hypothetical protein; EI219_00985; phage(gi100007)0.0Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 199627 bps
Phages: 2
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Lysis
Terminase
Portal Protein
Protease
Coat Protein
Tail Shaft
Attachment Site
Integrase
Phage-like Protein
Hypotheical Protein
Other
Transposase
Fiber Protein
Plate Protein
tRNA

Download data as .txt file: png_input file_download