Submission Results

Sequence Name: Not Available

GenBank Accession Number: 1163046337

GenInfo (GI) Number: 0000000000

Download Results:

gi|00000000|ref|CP020062.1| Klebsiella pneumoniae strain AR_0117 plasmid unitig_1, complete 152697, gc%: 50.47%

Download summary as .txt file: summary.txt file_download

Total: 3 prophage regions have been identified, of which 0 regions are intact, 2 regions are incomplete, and 1 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
13.2Kbincomplete60611436-14664 info_outlinePHAGE_Entero_P1_NC_005856(2)53.08%Show info_outline
29.7Kbquestionable701739951-49655 info_outlinePHAGE_Entero_P1_NC_005856(2)54.65%Show info_outline
310.5Kbincomplete2013139463-150039 info_outlinePHAGE_Entero_P1_NC_005856(3)54.18%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|CP020062.1| Klebsiella pneumoniae strain AR_0117 plasmid unitig_1, complete 152697, gc%: 50.47%

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 6 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(11436..11939)PHAGE_Shigel_SfIV_NC_022749: IS1 transposase B; AM364_27430; phage(gi557307573)1.43e-110Showinfo_outline
2complement(11858..12133)PHAGE_Entero_P1_NC_005856: InsA; AM364_27435; phage(gi46401643)6.23e-60Showinfo_outline
3complement(12324..13160)PROPHAGE_Escher_CFT073: insertion element IS2 transposase InsD; AM364_27440; phage(gi26249446)1.36e-120Showinfo_outline
4complement(13163..13558)PROPHAGE_Escher_CFT073: transposase insC; AM364_27445; phage(gi26251004)4.17e-56Showinfo_outline
513561..14106PHAGE_Shigel_SfIV_NC_022749: IS1 transposase B; AM364_27450; phage(gi557307573)1.99e-109Showinfo_outline
614116..14664PHAGE_Ralsto_RSA1_NC_009382: transposase IRSO15-like; AM364_27455; phage(gi145708108)2.15e-05Showinfo_outline

Region 2, total 17 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(39951..40655)PROPHAGE_Brucel_1330: transposase, putative; AM364_27570; phage(gi23502708)1.98e-53Showinfo_outline
2complement(40731..41231)N-acetyltransferase; AM364_275750.0Showinfo_outline
341250..41429hypothetical protein; AM364_275800.0Showinfo_outline
4complement(41359..42198)sulfonamide-resistant dihydropteroate synthase Sul1; AM364_275850.0Showinfo_outline
5complement(42192..42539)PHAGE_Acinet_Acj61_NC_014661: putative quaternary ammonium compound-resistance protein qacE; AM364_27590; phage(gi311992758)9.11e-09Showinfo_outline
6complement(42696..43328)type B-3 chloramphenicol O-acetyltransferase CatB3; AM364_275950.0Showinfo_outline
7complement(43411..43944)aminoglycoside nucleotidyltransferase ANT(2'')-Ia; AM364_276000.0Showinfo_outline
844090..45103PHAGE_Mycoba_Butters_NC_021061: integrase; AM364_27605; phage(gi479336499)2.26e-12Showinfo_outline
9complement(45062..45241)transcriptional regulator; AM364_276100.0Showinfo_outline
10complement(45706..46275)PHAGE_Vibrio_PWH3a_P1_NC_020863: dihydrofolate reductase; AM364_27615; phage(gi472342455)7.50e-14Showinfo_outline
11complement(46275..46775)PHAGE_Bacill_AR9_NC_031039: hypothetical protein; AM364_27620; phage(gi100094)2.88e-06Showinfo_outline
12complement(47041..47880)IS91 family transposase; AM364_276250.0Showinfo_outline
1347907..48005glycosyl transferase; AM364_276300.0Showinfo_outline
1447962..48237PHAGE_Entero_P1_NC_005856: InsA; AM364_27635; phage(gi46401643)7.08e-63Showinfo_outline
1548156..48659PHAGE_Shigel_SfIV_NC_022749: IS1 transposase B; AM364_27640; phage(gi557307573)1.15e-118Showinfo_outline
16complement(48861..49028)integrase; AM364_276450.0Showinfo_outline
1749170..49655PHAGE_Entero_fiAA91_ss_NC_022750: IS21 transposase; AM364_27650; phage(gi557307612)1.88e-101Showinfo_outline

Region 3, total 13 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(139463..139717)PHAGE_Escher_HK639_NC_016158: DNA pol III theta; AM364_28190; phage(gi356870660)3.30e-22Showinfo_outline
2complement(139954..140379)PHAGE_Pseudo_YuA_NC_010116: hypothetical protein; AM364_28195; phage(gi162135127)1.98e-14Showinfo_outline
3complement(140900..141130)hypothetical protein; AM364_282000.0Showinfo_outline
4complement(141364..142848)PHAGE_Pseudo_phi3_NC_030940: hypothetical protein; AM364_28205; phage(gi100001)1.95e-36Showinfo_outline
5complement(142848..143099)hypothetical protein; AM364_282100.0Showinfo_outline
6143254..143679PHAGE_Cronob_ENT39118_NC_019934: protein umuD; AM364_28215; phage(gi431811072)6.78e-32Showinfo_outline
7143679..144950PHAGE_Cronob_ENT39118_NC_019934: DNA polymerase; AM364_28220; phage(gi431811050)0.0Showinfo_outline
8145029..145244plasmid stabilization protein; AM364_282250.0Showinfo_outline
9complement(145267..146465)PROPHAGE_Escher_Sakai: putative transposase; AM364_28230; phage(gi38704244)7.61e-64Showinfo_outline
10146679..146913hypothetical protein; AM364_282350.0Showinfo_outline
11complement(146940..147902)hypothetical protein; AM364_282400.0Showinfo_outline
12complement(147902..148873)PHAGE_Yersin_PY54_NC_005069: partitioning protein SpyB; AM364_28245; phage(gi33770536)9.74e-114Showinfo_outline
13complement(148873..150039)PHAGE_Klebsi_phiKO2_NC_005857: plasmid partition protein SopA; AM364_28250; phage(gi46402111)0.0Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

Viewer Options
Length: 152697 bps
Phages: 3
Click on a region in the genome above to show details here.
Viewer Options
Click on a sequence to see details.
Viewer Options
Click on a sequence to see details.
Viewer Options
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