Submission Results

Sequence Name: Not Available

GenBank Accession Number: RRMP01000003.1

GenInfo (GI) Number: 0000000000

Download Results: RRMP01000003.1.PHASTER.zip

gi|00000000|ref|RRMP01000003.1| Escherichia coli strain FWSEC0365 FWSEC0365_contig00003, whole 256551, gc%: 48.53%

Download summary as .txt file: summary.txt file_download

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

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
127.1Kbincomplete402916293-43461 info_outlinePHAGE_Vibrio_12B8_NC_021073(3)43.13%Show info_outline
232.3Kbincomplete5033224168-256551 info_outlinePHAGE_Entero_Min27_NC_010237(4)48.79%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|RRMP01000003.1| Escherichia coli strain FWSEC0365 FWSEC0365_contig00003, whole 256551, gc%: 48.53%

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 31 CDS

#CDS PositionBLAST HitE-ValueSequence
116293..16305attL0.0Showinfo_outline
219438..22968PHAGE_Entero_RB49_NC_005066: large distal tail fiber subunit; C9141_03045; phage(gi33620684)0.0Showinfo_outline
323008..23304hypothetical protein; C9141_030500.0Showinfo_outline
423307..23612hypothetical protein; C9141_030550.0Showinfo_outline
523612..23914hypothetical protein; C9141_030600.0Showinfo_outline
623969..24442PHAGE_Vibrio_12B8_NC_021073: hypothetical protein; C9141_03065; phage(gi481019752)1.72e-07Showinfo_outline
724525..24833cytochrome; C9141_030700.0Showinfo_outline
824863..25204hypothetical protein; C9141_030750.0Showinfo_outline
925216..27645PHAGE_Pantoe_vB_PagS_Vid5_NC_042120: exonuclease A; C9141_03080; phage(gi100018)2.49e-24Showinfo_outline
1027696..28256PHAGE_Vibrio_12B8_NC_021073: hypothetical protein; C9141_03085; phage(gi481019747)2.54e-06Showinfo_outline
1128340..28909PHAGE_Vibrio_12B8_NC_021073: hypothetical protein; C9141_03090; phage(gi481019746)2.26e-10Showinfo_outline
1228984..29757PHAGE_Pseudo_pf16_NC_041881: baseplate hub subunit; C9141_03095; phage(gi100101)9.84e-17Showinfo_outline
1329789..30223PHAGE_Salmon_(in:Nonagvirus)_NC_042025: hypothetical protein; C9141_03100; phage(gi100003)8.96e-06Showinfo_outline
1430223..33999PHAGE_Entero_YYZ_2008_NC_011356: phage-related tail protein; C9141_03105; phage(gi209427791)9.72e-45Showinfo_outline
1534105..34383hypothetical protein; C9141_031100.0Showinfo_outline
1634574..35257hypothetical protein; C9141_031150.0Showinfo_outline
1735296..35643hypothetical protein; C9141_031200.0Showinfo_outline
1835653..36006PHAGE_Salmon_BP12B_NC_031271: ssDNA binding protein; C9141_03125; phage(gi100044)3.38e-48Showinfo_outline
1936035..36047attR0.0Showinfo_outline
20complement(36159..37838)PHAGE_Strept_phiARI0031_NC_031910: hypothetical protein; C9141_03130; phage(gi100051)1.35e-09Showinfo_outline
21complement(37904..38149)hypothetical protein; C9141_031350.0Showinfo_outline
22complement(38179..38520)hypothetical protein; C9141_031400.0Showinfo_outline
23complement(38829..39215)PHAGE_Entero_Phi1_NC_009821: hypothetical protein; C9141_03145; phage(gi157311495)4.44e-17Showinfo_outline
24complement(39228..39500)PHAGE_Escher_SRT8_NC_042043: hypothetical protein; C9141_03150; phage(gi100058)5.62e-20Showinfo_outline
2539531..39881phosphotransferase; C9141_031550.0Showinfo_outline
2639905..40459PHAGE_Escher_RCS47_NC_042128: RI membrane protein; C9141_03160; phage(gi100135)4.26e-08Showinfo_outline
2740561..41052DUF1097 domain-containing protein; C9141_031650.0Showinfo_outline
28complement(41116..41949)PHAGE_Pelagi_HTVC008M_NC_020484: curli production assembly/transport component; C9141_03170; phage(gi460042451)5.19e-52Showinfo_outline
29complement(41976..42392)curli production assembly/transport component CsgF; C9141_031750.0Showinfo_outline
30complement(42417..42806)curli production assembly/transport component CsgE; C9141_031800.0Showinfo_outline
31complement(42811..43461)PHAGE_Altero_vB_AmaP_AD45_P1_NC_021532: hypothetical protein; C9141_03185; phage(gi514051613)1.42e-05Showinfo_outline

Region 2, total 38 CDS

#CDS PositionBLAST HitE-ValueSequence
1224168..224180attL0.0Showinfo_outline
2complement(236165..237295)PHAGE_Entero_HK022_NC_002166: integrase; C9141_04175; phage(gi9634144)1.48e-67Showinfo_outline
3complement(237273..237521)excisionase; C9141_041800.0Showinfo_outline
4complement(237586..240057)PHAGE_Salmon_118970_sal3_NC_031940: baseplate hub subunit; C9141_04185; phage(gi100107)1.07e-61Showinfo_outline
5complement(240153..240341)DUF1482 family protein; C9141_041900.0Showinfo_outline
6complement(240338..240526)cell division inhibitor; C9141_041950.0Showinfo_outline
7240823..241065hypothetical protein; C9141_042000.0Showinfo_outline
8241055..241570PHAGE_Salmon_HK620_NC_002730: hypothetical protein; C9141_04205; phage(gi13559839)1.39e-15Showinfo_outline
9complement(241684..241836)PHAGE_Salico_CGphi29_NC_020844: hypothetical protein; C9141_04210; phage(gi472340166)6.26e-11Showinfo_outline
10complement(241874..242057)hypothetical protein; C9141_042150.0Showinfo_outline
11complement(242134..242553)PHAGE_Escher_HK75_NC_016160: cI repressor; C9141_04220; phage(gi356870714)5.19e-25Showinfo_outline
12242633..242899PHAGE_Escher_HK75_NC_016160: regulatory protein cro; C9141_04225; phage(gi356870715)2.48e-24Showinfo_outline
13242883..243434hypothetical protein; C9141_042300.0Showinfo_outline
14243406..244443PHAGE_Escher_TL_2011b_NC_019445: hypothetical protein; C9141_04235; phage(gi418487646)2.35e-50Showinfo_outline
15244475..244897PHAGE_Escher_HK639_NC_016158: replication protein 14; C9141_04240; phage(gi356870655)3.44e-34Showinfo_outline
16244931..245647PHAGE_Shigel_Stx_NC_029120: hypothetical protein; C9141_04245; phage(gi985761264)4.08e-52Showinfo_outline
17245680..245961DNA-binding protein; C9141_042500.0Showinfo_outline
18245958..246254PHAGE_Klebsi_phiKO2_NC_005857: Gp58; C9141_04255; phage(gi46402144)5.03e-35Showinfo_outline
19246251..246712PHAGE_Escher_RCS47_NC_042128: baseplate hub assembly protein; C9141_04260; phage(gi100106)4.14e-18Showinfo_outline
20246690..247045hypothetical protein; C9141_042650.0Showinfo_outline
21247096..247308hypothetical protein; C9141_042700.0Showinfo_outline
22247341..247559PHAGE_Escher_PA28_NC_041935: hypothetical protein; C9141_04275; phage(gi100012)8.91e-39Showinfo_outline
23247561..247926PHAGE_Entero_HK225_NC_019717: HNH endonuclease; C9141_04280; phage(gi428782431)9.36e-45Showinfo_outline
24247923..248187hypothetical protein; C9141_042850.0Showinfo_outline
25248422..248634PHAGE_Entero_933W_NC_000924: protein MokW; C9141_04290; phage(gi9632542)8.79e-37Showinfo_outline
26248801..249073PHAGE_Cronob_phiES15_NC_018454: hypothetical protein; C9141_04295; phage(gi401817580)1.95e-15Showinfo_outline
27249075..250124PHAGE_Entero_mEp460_NC_019716: hypothetical protein; C9141_04300; phage(gi428782365)5.03e-136Showinfo_outline
28250137..250499PHAGE_Escher_HK75_NC_016160: RusA-like protein; C9141_04305; phage(gi356870726)9.79e-45Showinfo_outline
29250492..251181PHAGE_Phage_Gifsy_1_NC_010392: bacteriophage antiterminator protein Q; C9141_04310; phage(gi169257244)2.63e-89Showinfo_outline
30251394..251591PHAGE_Entero_phiP27_NC_003356: hypothetical protein; C9141_04315; phage(gi18249887)1.34e-39Showinfo_outline
31251742..252800PHAGE_Entero_phiP27_NC_003356: putative DNA methylase; C9141_04320; phage(gi18249888)0.0Showinfo_outline
32252841..252916tRNA0.0Showinfo_outline
33252924..253000tRNA0.0Showinfo_outline
34253014..253090tRNA0.0Showinfo_outline
35253176..254111PHAGE_Mannhe_vB_MhS_587AP2_NC_028743: hypothetical protein; C9141_04340; phage(gi970580043)2.96e-52Showinfo_outline
36254323..254589hypothetical protein; C9141_043450.0Showinfo_outline
37255135..256551PHAGE_Entero_BP_4795_NC_004813: hypothetical protein YjhS; C9141_04350; phage(gi157166028)0.0Showinfo_outline
38255363..255375attR0.0Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 256551 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