Submission Results

Sequence Name: Not Available

GenBank Accession Number: 1035427607

GenInfo (GI) Number: 0000000000

Download Results:

gi|00000000|ref|LT009688.1| Klebsiella pneumoniae plasmid pIT-06C07, strain O6CO7, complete 166484, gc%: 52.83%

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
111.3Kbincomplete60175372-16709 info_outlinePHAGE_Prochl_P_SSM3_NC_021559(1)59.34%Show info_outline
213.7Kbincomplete301871903-85655 info_outlinePHAGE_Entero_P1_NC_005856(4)53.44%Show info_outline
314.7Kbquestionable8013149079-163850 info_outlinePHAGE_Salmon_SJ46_NC_031129(3)56.64%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|LT009688.1| Klebsiella pneumoniae plasmid pIT-06C07, strain O6CO7, complete 166484, gc%: 52.83%

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 17 CDS

#CDS PositionBLAST HitE-ValueSequence
15372..6007PROPHAGE_Xantho_33913: IS1479 transposase; -; phage(gi21229605)6.68e-45Showinfo_outline
2complement(5970..6491)FIG00854731: hypothetical protein; -0.0Showinfo_outline
3complement(6473..7453)PHAGE_Bacill_BMBtpLA_NC_028748: IS5 transposase and trans-activator; -; phage(gi971482498)0.0Showinfo_outline
4complement(7531..7692)hypothetical protein; -0.0Showinfo_outline
5complement(7712..8215)PHAGE_Shigel_SfIV_NC_022749: IS1 transposase B; -; phage(gi557307573)2.64e-114Showinfo_outline
68339..8467hypothetical protein; -0.0Showinfo_outline
78512..8628hypothetical protein; -0.0Showinfo_outline
88679..8933hypothetical protein; -0.0Showinfo_outline
98933..9181phospholipase D/Transphosphatidylase; -0.0Showinfo_outline
109439..9720PHAGE_Bacill_SPP1_NC_004166: hypothetical protein; -; phage(gi22855124)2.71e-06Showinfo_outline
119755..10324PHAGE_Cyanop_P_RSM1_NC_021071: heat shock protein; -; phage(gi481019345)7.81e-08Showinfo_outline
1210439..13234PROPHAGE_Escher_EDL933: ATP-dependent Clp protease ATP-binding subunit; -; phage(gi15800640)1.10e-161Showinfo_outline
1313234..13431hypothetical protein; -0.0Showinfo_outline
1413669..14418conserved hypothetical protein; -0.0Showinfo_outline
1514405..15367Peptidase, M48 family; -0.0Showinfo_outline
1615481..15987Mobile element protein; -0.0Showinfo_outline
1715990..16709PROPHAGE_Ralsto_GMI1000: isrso11-transposase orfb protein; -; phage(gi17546155)2.89e-59Showinfo_outline

Region 2, total 18 CDS

#CDS PositionBLAST HitE-ValueSequence
171903..72643PHAGE_Brevib_Jenst_NC_028805: putative recombinase XerD; -; phage(gi971744895)8.40e-06Showinfo_outline
272742..73023hypothetical protein; -0.0Showinfo_outline
3complement(73360..74370)PHAGE_Salmon_SSU5_NC_018843: putative replication protein RepA; -; phage(gi410491479)2.05e-115Showinfo_outline
475122..76288PHAGE_Klebsi_phiKO2_NC_005857: plasmid partition protein SopA; -; phage(gi46402111)0.0Showinfo_outline
576288..77259PHAGE_Yersin_PY54_NC_005069: partitioning protein SpyB; -; phage(gi33770536)9.74e-114Showinfo_outline
677259..77990hypothetical protein; -0.0Showinfo_outline
778032..78178hypothetical protein; -0.0Showinfo_outline
878713..78997PROPHAGE_Escher_Sakai: putative transposase; -; phage(gi38704244)4.51e-52Showinfo_outline
978994..79851PHAGE_Entero_If1_NC_001954: hypothetical protein; -; phage(gi9630756)6.62e-157Showinfo_outline
10complement(79874..80029)RelB/StbD replicon stabilization protein (antitoxin to RelE/StbE); -0.0Showinfo_outline
11complement(80168..81439)PHAGE_Cronob_ENT39118_NC_019934: DNA polymerase; -; phage(gi431811050)0.0Showinfo_outline
12complement(81439..81864)PHAGE_Cronob_ENT39118_NC_019934: protein umuD; -; phage(gi431811072)6.78e-32Showinfo_outline
1382267..83754PHAGE_Pseudo_phi3_NC_030940: hypothetical protein; -; phage(gi100001)2.31e-36Showinfo_outline
1483871..84218FIG00732883: hypothetical protein; -0.0Showinfo_outline
15complement(84283..84441)hypothetical protein; -0.0Showinfo_outline
16complement(84480..84701)hypothetical protein; -0.0Showinfo_outline
1784739..85164PHAGE_Pseudo_YuA_NC_010116: hypothetical protein; -; phage(gi162135127)1.98e-14Showinfo_outline
1885401..85655PHAGE_Escher_HK639_NC_016158: DNA pol III theta; -; phage(gi356870660)3.30e-22Showinfo_outline

Region 3, total 15 CDS

#CDS PositionBLAST HitE-ValueSequence
1149079..152108PROPHAGE_Xantho_306: Tn5044 transposase; -; phage(gi21243163)0.0Showinfo_outline
3152215..153240PHAGE_Entero_fiAA91_ss_NC_022750: IS21 transposase; -; phage(gi557307612)2.30e-44Showinfo_outline
4153237..154016PHAGE_Entero_fiAA91_ss_NC_022750: IS21 transposition protein; -; phage(gi557307613)8.13e-78Showinfo_outline
5154013..154252Mobile element protein; -0.0Showinfo_outline
6154304..155185PHAGE_Salmon_SJ46_NC_031129: hypothetical protein; -; phage(gi100066)2.88e-94Showinfo_outline
7complement(155435..156754)PHAGE_Staphy_phiPV83_NC_002486: transposase; -; phage(gi9635722)7.29e-29Showinfo_outline
8complement(157031..158215)PROPHAGE_Shewan_MR-1: transposase, putative; -; phage(gi24373689)2.31e-142Showinfo_outline
9158335..158547PHAGE_Entero_HK022_NC_002166: IS903 transposase; -; phage(gi9634149)2.33e-15Showinfo_outline
10158719..159078putative exported protein; -0.0Showinfo_outline
11complement(159205..159321)hypothetical protein; -0.0Showinfo_outline
12complement(159735..160118)hypothetical protein; -0.0Showinfo_outline
14complement(160244..160864)PHAGE_Clostr_phiCD27_NC_011398: putative phage site-specific recombinase; -; phage(gi209901279)3.94e-07Showinfo_outline
15complement(160953..163850)PROPHAGE_Xantho_33913: Tn5041 transposase; -; phage(gi21231545)3.56e-34Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 166484 bps
Phages: 3
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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