Submission Results

Sequence Name: Not Available

GenBank Accession Number: 1160548085

GenInfo (GI) Number: 0000000000

Download Results:

gi|00000000|ref|KY689238.1| Klebsiella pneumoniae strain TP-P16 plasmid pKPC_P16, complete 85874, gc%: 55.97%

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
137.9Kbquestionable703428965-66930 info_outlinePHAGE_Entero_P1_NC_005856(4)56.44%Show info_outline
217.9Kbincomplete501451570-69477 info_outlinePHAGE_Staphy_SPbeta_like_NC_029119(2)59.71%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|KY689238.1| Klebsiella pneumoniae strain TP-P16 plasmid pKPC_P16, complete 85874, gc%: 55.97%

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 38 CDS

#CDS PositionBLAST HitE-ValueSequence
2complement(29527..30231)PROPHAGE_Brucel_1330: transposase, putative; TP_051; phage(gi23502708)1.98e-53Showinfo_outline
4complement(30965..31324)hypothetical protein; TP_0520.0Showinfo_outline
5complement(31386..31709)PHAGE_Rhodob_RcapNL_NC_020489: hypothetical protein; TP_053; phage(gi461475014)1.42e-16Showinfo_outline
6complement(31706..32434)PsiA protein; TP_0540.0Showinfo_outline
7complement(32431..32862)PsiB protein; TP_0550.0Showinfo_outline
8complement(32905..34203)Putative DNA-binding protein; TP_0560.0Showinfo_outline
9complement(34252..34764)Putative DNA-binding protein; TP_0570.0Showinfo_outline
10complement(34966..35196)UPF0401 protein YkfF; TP_0580.0Showinfo_outline
1135370..35783hypothetical protein; TP_0590.0Showinfo_outline
12complement(35822..35947)hypothetical protein; TP_0600.0Showinfo_outline
13complement(35987..36139)hypothetical protein; TP_0610.0Showinfo_outline
14complement(36174..36428)PHAGE_Escher_HK639_NC_016158: DNA pol III theta; TP_062; phage(gi356870660)7.22e-24Showinfo_outline
15complement(36621..36812)hypothetical protein; TP_0630.0Showinfo_outline
16complement(36855..37361)PHAGE_Rhodoc_RGL3_NC_016650: antirestriction protein; TP_064; phage(gi372449791)4.18e-10Showinfo_outline
17complement(37766..38545)YchA; TP_0650.0Showinfo_outline
18complement(38599..39018)Adenine-specific methyltransferase; TP_0660.0Showinfo_outline
19complement(39029..39250)PHAGE_Entero_N15_NC_001901: gp50; TP_067; phage(gi9630517)2.37e-05Showinfo_outline
20complement(39250..39927)PHAGE_Staphy_Stau2_NC_030933: hypothetical protein; TP_068; phage(gi100063)6.14e-28Showinfo_outline
2140057..40182hypothetical protein; TP_0690.0Showinfo_outline
2240286..40957PHAGE_Pseudo_F116_NC_006552: hypothetical protein; TP_070; phage(gi56692976)8.96e-49Showinfo_outline
2341137..41559PHAGE_Cronob_ENT39118_NC_019934: protein umuD; TP_071; phage(gi431811072)5.57e-28Showinfo_outline
2441559..42830PHAGE_Cronob_ENT39118_NC_019934: DNA polymerase; TP_072; phage(gi431811050)0.0Showinfo_outline
25complement(42966..43937)PHAGE_Entero_P1_NC_005856: ParB; TP_073; phage(gi46401681)7.48e-73Showinfo_outline
26complement(43934..45139)PHAGE_Salmon_SJ46_NC_031129: hypothetical protein; TP_074; phage(gi100009)3.47e-173Showinfo_outline
2745502..46113PHAGE_Clostr_phiCD27_NC_011398: putative phage site-specific recombinase; TP_075; phage(gi209901279)1.82e-05Showinfo_outline
2846167..46367hypothetical protein; TP_0760.0Showinfo_outline
2946514..47464PHAGE_Sodali_phiSG1_NC_007902: transposase; TP_077; phage(gi89886005)6.94e-115Showinfo_outline
30complement(47461..48072)hypothetical protein; TP_0780.0Showinfo_outline
31complement(48069..48464)hypothetical protein; TP_0790.0Showinfo_outline
32complement(48517..48924)PHAGE_Vibrio_vB_VpaM_MAR_NC_019722: putative exonuclease; TP_080; phage(gi428782757)3.70e-16Showinfo_outline
3348978..49958PHAGE_Bacill_BMBtpLA_NC_028748: IS5 transposase and trans-activator; TP_081; phage(gi971482498)0.0Showinfo_outline
3449940..50482Aspartate aminotransferase; TP_0820.0Showinfo_outline
3550607..51164hypothetical protein; TP_0830.0Showinfo_outline
3651633..52337PROPHAGE_Brucel_1330: transposase, putative; TP_084; phage(gi23502708)1.98e-53Showinfo_outline

Region 2, total 16 CDS

#CDS PositionBLAST HitE-ValueSequence
2complement(59952..60512)PHAGE_Salmon_SJ46_NC_031129: prohead core protein protease; TP_092; phage(gi100061)3.52e-83Showinfo_outline
360961..61521Replication protein; TP_0930.0Showinfo_outline
461676..62071hypothetical protein; TP_0940.0Showinfo_outline
562055..62333hypothetical protein; TP_0950.0Showinfo_outline
662444..62869PHAGE_Pseudo_YuA_NC_010116: hypothetical protein; TP_096; phage(gi162135127)1.17e-25Showinfo_outline
762997..63152hypothetical protein; TP_0970.0Showinfo_outline
863198..63494hypothetical protein; TP_0980.0Showinfo_outline
963499..64479PHAGE_Staphy_Pvl108_NC_008689: putative transposase; TP_099; phage(gi119443708)1.17e-06Showinfo_outline
10complement(64729..65610)PHAGE_Salmon_SJ46_NC_031129: hypothetical protein; TP_100; phage(gi100066)2.88e-94Showinfo_outline
1165627..65773S-(hydroxymethyl)glutathione dehydrogenase; TP_1010.0Showinfo_outline
12complement(65886..66866)PHAGE_Spirop_SkV1_CR2_3x_NC_009987: hypothetical protein; TP_102; phage(gi160688404)1.73e-09Showinfo_outline
13complement(66989..67384)PHAGE_Sodali_phiSG1_NC_007902: resolvase; TP_103; phage(gi89886020)1.67e-15Showinfo_outline
15complement(67502..68206)PROPHAGE_Brucel_1330: transposase, putative; TP_104; phage(gi23502708)1.98e-53Showinfo_outline
16complement(68218..69477)PROPHAGE_Brucel_1330: transposase, putative; TP_105; phage(gi23501616)2.58e-31Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 85874 bps
Phages: 2
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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