Submission Results

Sequence Name: Streptococcus pyogenes M49 591, whole genome shotgun sequencing

GenBank Accession Number: AAFV00000000.1

GenInfo (GI) Number: 56791245

Download Results:

gi|56791245|ref|AAFV00000000| Streptococcus pyogenes M49 591 sp001.351.7585, whole genome shotgun .1327684, gc%: 38.33%

Download summary as .txt file: summary.txt file_download

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

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
130.8Kbquestionable84431590-32389 info_outlinePHAGE_Strept_539.14%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|56791245|ref|AAFV00000000| Streptococcus pyogenes M49 591 sp001.351.7585, whole genome shotgun [asmbl_id: NC_000000].1327684, gc%: 38.33%

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 43 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(1590..2945)PHAGE_Acanth_mimivirus: putative RNA methyltransferase; PP_00002; phage(gi311977789)4e-23Showinfo_outline
2complement(3136..3318)PHAGE_Strept_5: hypothetical protein SpyM3_1300; PP_00003; phage(gi28876382)6e-28Showinfo_outline
33539..4294PHAGE_Strept_5: exotoxin type A precursor; PP_00004; phage(gi28876383)1e-145Showinfo_outline
4complement(4416..5075)PHAGE_Strept_5: hypothetical protein SpyM3_1302; PP_00005; phage(gi28876384)1e-125Showinfo_outline
5complement(5075..5296)PHAGE_Strept_5: hypothetical protein SpyM3_1303; PP_00006; phage(gi28876385)5e-36Showinfo_outline
6complement(5306..6079)PHAGE_Strept_5: hypothetical protein SpyM3_1304; PP_00007; phage(gi28876386)2e-134Showinfo_outline
7complement(6090..6692)PHAGE_Strept_5: hypothetical protein SpyM3_1305; PP_00008; phage(gi28876387)1e-108Showinfo_outline
8complement(6704..7459)PHAGE_Strept_5: putative cell wall hydrolase, lysin; PP_00009; phage(gi28876388)9e-146Showinfo_outline
9complement(7461..7793)PHAGE_Strept_5: putative holin; PP_00010; phage(gi28876389)6e-54Showinfo_outline
10complement(7793..8116)PHAGE_Temper_1: hypothetical protein phiNIH1.1_48; PP_00011; phage(gi16271824)2e-08Showinfo_outline
11complement(8130..8252)PHAGE_Strept_5: hypothetical protein SpyM3_1308; PP_00012; phage(gi28876390)2e-17Showinfo_outline
12complement(8266..8613)PHAGE_Strept_5: hypothetical protein SpyM3_1309; PP_00013; phage(gi28876391)5e-62Showinfo_outline
13complement(8624..10486)PHAGE_Strept_5: putative minor structural protein; PP_00014; phage(gi28876392)0.0Showinfo_outline
14complement(10491..13580)PHAGE_Strept_5: putative tail protein; PP_00015; phage(gi28876393)0.0Showinfo_outline
15complement(13932..15416)PHAGE_Strept_5: putative minor structural protein; PP_00016; phage(gi28876394)0.0Showinfo_outline
16complement(15417..15680)PHAGE_Strept_5: putative platlet-binding protein, minor tail fiber protein; PP_00017; phage(gi28876395)8e-44Showinfo_outline
17complement(15790..17223)PHAGE_Strept_5: putative platlet-binding protein, minor tail fiber protein; PP_00018; phage(gi28876395)0.0Showinfo_outline
18complement(17216..17674)PHAGE_Strept_5: hypothetical protein SpyM3_1314; PP_00019; phage(gi28876396)1e-84Showinfo_outline
19complement(17647..17964)PHAGE_Strept_5: hypothetical protein SpyM3_1315; PP_00020; phage(gi28876397)1e-54Showinfo_outline
20complement(17977..18483)PHAGE_Strept_5: hypothetical protein SpyM3_1316; PP_00021; phage(gi28876398)2e-92Showinfo_outline
21complement(18495..18905)PHAGE_Strept_5: hypothetical protein SpyM3_1317; PP_00022; phage(gi28876399)8e-74Showinfo_outline
22complement(18907..19290)PHAGE_Strept_5: hypothetical protein SpyM3_1318; PP_00023; phage(gi28876400)2e-70Showinfo_outline
23complement(19299..19610)PHAGE_Strept_5: hypothetical protein SpyM3_1319; PP_00024; phage(gi28876401)3e-53Showinfo_outline
24complement(19607..19951)PHAGE_Strept_5: hypothetical protein SpyM3_1320; PP_00025; phage(gi28876402)9e-58Showinfo_outline
25complement(19965..20258)PHAGE_Strept_5: hypothetical protein SpyM3_1321; PP_00026; phage(gi28876403)9e-50Showinfo_outline
26complement(20270..21160)PHAGE_Strept_5: hypothetical protein SpyM3_1322; PP_00027; phage(gi28876404)3e-166Showinfo_outline
27complement(21178..21747)PHAGE_Strept_5: hypothetical protein SpyM3_1323; PP_00028; phage(gi28876405)7e-98Showinfo_outline
28complement(21897..22163)PHAGE_Strept_5: hypothetical protein SpyM3_1324; PP_00029; phage(gi28876406)2e-42Showinfo_outline
29complement(22170..23078)PHAGE_Strept_5: hypothetical protein SpyM3_1325; PP_00030; phage(gi28876407)1e-174Showinfo_outline
30complement(23047..24372)PHAGE_Strept_5: hypothetical protein SpyM3_1326; PP_00031; phage(gi28876408)0.0Showinfo_outline
31complement(24372..25646)PHAGE_Brocho_NF5: gp2; PP_00032; phage(gi327197586)0.0Showinfo_outline
32complement(25636..26016)PHAGE_Strept_5: hypothetical protein SpyM3_1329; PP_00033; phage(gi28876411)4e-62Showinfo_outline
33complement(26360..26794)PHAGE_Strept_5: hypothetical protein SpyM3_1330; PP_00034; phage(gi28876412)1e-77Showinfo_outline
34complement(27453..27866)PHAGE_Strept_5: hypothetical protein SpyM3_1335; PP_00035; phage(gi28876417)1e-72Showinfo_outline
35complement(27876..28145)PHAGE_Temper_1: hypothetical protein phiNIH1.1_18; PP_00036; phage(gi16271794)8e-49Showinfo_outline
36complement(28142..28321)PHAGE_Strept_5: hypothetical protein SpyM3_1336; PP_00037; phage(gi28876418)2e-29Showinfo_outline
37complement(28421..28618)PHAGE_Strept_phi3396: hypothetical protein phi3396_17; PP_00038; phage(gi126011079)2e-14Showinfo_outline
38complement(28605..29003)PHAGE_Strept_MM1: hypothetical protein MM1p20; PP_00039; phage(gi15088762)1e-29Showinfo_outline
39complement(29176..29343)PHAGE_Strept_MM1: hypothetical protein MM1p12; PP_00040; phage(gi26553444)7e-10Showinfo_outline
40complement(29353..30150)PHAGE_Strept_3: hypothetical protein SpyM3_1132; PP_00041; phage(gi28876302)1e-145Showinfo_outline
41complement(30326..31075)PHAGE_Strept_3: putative recombinase; PP_00042; phage(gi28876304)5e-133Showinfo_outline
42complement(31078..31407)PHAGE_Strept_3: hypothetical protein SpyM3_1136; PP_00043; phage(gi28876306)6e-25Showinfo_outline
4331733..32389PHAGE_Amsact_: putative ATP-binding cassette transporter; PP_00044; phage(gi9964444)5e-08Showinfo_outline
Streptococcus pyogenes M49 591 sp001.351.7585, whole genome shotgun
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 1327684 bps
Phages: 1
Click on a region in the genome above to show details here.
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Click on a sequence to see details.
Portal Protein
Coat Protein
Tail Shaft
Attachment Site
Phage-like Protein
Hypotheical Protein
Fiber Protein
Plate Protein

Download data as .txt file: png_input file_download