Submission Results

Sequence Name: Not Available

GenBank Accession Number: 1163063310

GenInfo (GI) Number: 0000000000

Download Results: 1163063310.PHASTER.zip

gi|00000000|ref|CP020072.1| Klebsiella pneumoniae strain AR_0115 plasmid tig00000002, complete 209424, gc%: 52.88%

Download summary as .txt file: summary.txt file_download

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

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
137.1Kbintact1403043596-80758 info_outlinePHAGE_Stx2_c_1717_NC_011357(3)55.33%Show info_outline
234.1Kbincomplete3031138556-172667 info_outlinePHAGE_Entero_P1_NC_005856(4)52.35%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|CP020072.1| Klebsiella pneumoniae strain AR_0115 plasmid tig00000002, complete 209424, gc%: 52.88%

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 34 CDS

#CDS PositionBLAST HitE-ValueSequence
143596..43608attL0.0Showinfo_outline
2complement(46497..46994)PHAGE_Bacill_Bp8p_C_NC_029121: putative dihydrofolate reductase; AM362_28585; phage(gi985761486)1.16e-33Showinfo_outline
347139..48152PHAGE_Mycoba_Butters_NC_021061: integrase; AM362_28590; phage(gi479336499)2.26e-12Showinfo_outline
4complement(48111..48290)transcriptional regulator; AM362_285950.0Showinfo_outline
548355..48705transposase; AM362_286000.0Showinfo_outline
648831..49391PHAGE_Salmon_SJ46_NC_031129: prohead core protein protease; AM362_28605; phage(gi100061)7.62e-69Showinfo_outline
749394..52360PROPHAGE_Xantho_33913: Tn5041 transposase; AM362_28610; phage(gi21231545)8.67e-46Showinfo_outline
852427..52804N-acetyltransferase; AM362_286150.0Showinfo_outline
9complement(53005..53664)PHAGE_Stx2_vB_EcoP_24B_NC_027984: Cat; AM362_28620; phage(gi937456276)3.11e-167Showinfo_outline
1053718..53909hypothetical protein; AM362_286250.0Showinfo_outline
1153888..53986glycosyl transferase; AM362_286300.0Showinfo_outline
1253943..54218PHAGE_Entero_P1_NC_005856: InsA; AM362_28635; phage(gi46401643)7.08e-63Showinfo_outline
1354137..54640PHAGE_Shigel_SfIV_NC_022749: IS1 transposase B; AM362_28640; phage(gi557307573)1.15e-118Showinfo_outline
14complement(54655..54804)PROPHAGE_Escher_CFT073: transposase insC; AM362_28645; phage(gi26250372)1.30e-28Showinfo_outline
1554764..54924nitrite extrusion protein 2; AM362_286500.0Showinfo_outline
1655281..55553His-Xaa-Ser system protein HxsD; AM362_286550.0Showinfo_outline
1755553..56941PHAGE_Erwini_vB_EamM_Asesino_NC_031107: chaperone for long tail fiber formation; AM362_28660; phage(gi100168)9.30e-05Showinfo_outline
1856934..58046PHAGE_Campyl_CP21_NC_019507: radical SAM domain-containing protein; AM362_28665; phage(gi422935302)3.17e-07Showinfo_outline
1958043..58678His-Xaa-Ser repeat protein HxsA; AM362_286700.0Showinfo_outline
2059235..59612PHAGE_Stx2_c_1717_NC_011357: truncated transposase; AM362_28675; phage(gi209447151)2.21e-76Showinfo_outline
2159609..59956PHAGE_Stx2_c_1717_NC_011357: transposase; AM362_28680; phage(gi209447152)8.81e-76Showinfo_outline
2260006..61543PHAGE_Stx2_c_1717_NC_011357: transposase; AM362_28685; phage(gi209447153)0.0Showinfo_outline
2361611..61958PHAGE_Stx2_c_1717_NC_011357: transposase; AM362_28690; phage(gi209447153)2.73e-67Showinfo_outline
2461986..61998attR0.0Showinfo_outline
2563438..63449attL0.0Showinfo_outline
26complement(63779..65512)PHAGE_Plankt_PaV_LD_NC_016564: ABC transporter; AM362_28695; phage(gi371496158)1.53e-19Showinfo_outline
27complement(65520..66467)acetamidase; AM362_287000.0Showinfo_outline
28complement(66512..68116)peptide ABC transporter substrate-binding protein; AM362_287050.0Showinfo_outline
29complement(68129..69049)glutathione ABC transporter permease GsiC; AM362_287100.0Showinfo_outline
30complement(69049..69897)peptide ABC transporter permease; AM362_287150.0Showinfo_outline
31complement(69894..70487)response regulator; AM362_287200.0Showinfo_outline
32complement(70484..71611)regulator; AM362_287250.0Showinfo_outline
33complement(71896..72063)integrase; AM362_287300.0Showinfo_outline
3480758..80769attR0.0Showinfo_outline

Region 2, total 33 CDS

#CDS PositionBLAST HitE-ValueSequence
1138556..138570attL0.0Showinfo_outline
2147353..148432PHAGE_Spirop_SkV1_CR2_3x_NC_009987: hypothetical protein; AM362_29200; phage(gi160688404)1.08e-08Showinfo_outline
3148439..148621hypothetical protein; AM362_292050.0Showinfo_outline
4complement(148610..148984)hypothetical protein; AM362_292100.0Showinfo_outline
5complement(149040..149366)PHAGE_Rhodob_RcapNL_NC_020489: hypothetical protein; AM362_29215; phage(gi461475014)4.42e-17Showinfo_outline
6complement(149363..150091)plasmid SOS inhibition protein A; AM362_292200.0Showinfo_outline
7complement(150088..150519)conjugation system SOS inhibitor PsiB; AM362_292250.0Showinfo_outline
8complement(150564..152622)PHAGE_Gordon_Hedwig_NC_031099: RNA polymerase binding protein; AM362_29230; phage(gi100054)4.77e-07Showinfo_outline
9complement(152692..152940)transcriptional regulator; AM362_292350.0Showinfo_outline
10complement(152989..153531)PHAGE_Salmon_SJ46_NC_031129: hypothetical protein; AM362_29240; phage(gi100049)6.19e-64Showinfo_outline
11complement(153556..153651)single-stranded DNA-binding protein; AM362_292450.0Showinfo_outline
12complement(153787..153963)hypothetical protein; AM362_292500.0Showinfo_outline
13154201..154296hypothetical protein; AM362_292550.0Showinfo_outline
14complement(154307..154870)PHAGE_Thalas_BA3_NC_009990: hypothetical protein; AM362_29260; phage(gi160700596)2.33e-22Showinfo_outline
15complement(154918..156273)hydrolase; AM362_292650.0Showinfo_outline
16complement(156325..156555)hypothetical protein; AM362_292700.0Showinfo_outline
17complement(156647..156874)hypothetical protein; AM362_292750.0Showinfo_outline
18complement(156978..157319)hypothetical protein; AM362_292800.0Showinfo_outline
19complement(157656..157973)hypothetical protein; AM362_292850.0Showinfo_outline
20complement(158008..158262)PHAGE_Escher_HK639_NC_016158: DNA pol III theta; AM362_29290; phage(gi356870660)3.30e-22Showinfo_outline
21complement(158499..158924)PHAGE_Pseudo_YuA_NC_010116: hypothetical protein; AM362_29295; phage(gi162135127)1.98e-14Showinfo_outline
22complement(159445..159675)hypothetical protein; AM362_293000.0Showinfo_outline
23complement(159909..161393)PHAGE_Pseudo_phi3_NC_030940: hypothetical protein; AM362_29305; phage(gi100001)1.95e-36Showinfo_outline
24complement(161393..161644)hypothetical protein; AM362_293100.0Showinfo_outline
25161799..162224PHAGE_Cronob_ENT39118_NC_019934: protein umuD; AM362_29315; phage(gi431811072)6.78e-32Showinfo_outline
26162224..163495PHAGE_Cronob_ENT39118_NC_019934: DNA polymerase; AM362_29320; phage(gi431811050)0.0Showinfo_outline
27163574..163789plasmid stabilization protein; AM362_293250.0Showinfo_outline
28complement(163812..165010)PROPHAGE_Escher_Sakai: putative transposase; AM362_29330; phage(gi38704244)7.61e-64Showinfo_outline
29165224..165458hypothetical protein; AM362_293350.0Showinfo_outline
30complement(165485..166447)hypothetical protein; AM362_293400.0Showinfo_outline
31complement(166447..167418)PHAGE_Yersin_PY54_NC_005069: partitioning protein SpyB; AM362_29345; phage(gi33770536)9.74e-114Showinfo_outline
32complement(167418..168584)PHAGE_Klebsi_phiKO2_NC_005857: plasmid partition protein SopA; AM362_29350; phage(gi46402111)0.0Showinfo_outline
33172667..172681attR0.0Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 209424 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