Submission Results

Sequence Name: Not Available

GenBank Accession Number: 1036430138

GenInfo (GI) Number: 0000000000

Download Results:

gi|00000000|ref|CP014763.1| Klebsiella pneumoniae strain KPNIH39 plasmid pKPN-332, complete 284894, gc%: 50.90%

Download summary as .txt file: summary.txt file_download

Total: 5 prophage regions have been identified, of which 0 regions are intact, 2 regions are incomplete, and 3 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
126.7Kbquestionable9010626-27398 info_outlinePHAGE_Staphy_SPbeta_like_NC_029119(2)56.50%Show info_outline
219.2Kbquestionable701338138-57427 info_outlinePHAGE_Entero_P1_NC_005856(2)52.20%Show info_outline
36.5Kbincomplete50680422-86964 info_outlinePHAGE_Entero_N15_NC_001901(2)50.92%Show info_outline
45.8Kbincomplete107126062-131941 info_outlinePHAGE_Bacill_JL_NC_028982(2)49.98%Show info_outline
56.7Kbquestionable809225618-232320 info_outlinePHAGE_Stx2_c_1717_NC_011357(3)53.24%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|CP014763.1| Klebsiella pneumoniae strain KPNIH39 plasmid pKPN-332, complete 284894, gc%: 50.90%

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 12 CDS

#CDS PositionBLAST HitE-ValueSequence
213923..14918PHAGE_Bacill_250_NC_029024: transposase IS116/IS110/IS902; WM47_26775; phage(gi971766660)5.41e-06Showinfo_outline
315052..17190ATP-dependent endonuclease; WM47_267800.0Showinfo_outline
417187..18971PHAGE_Bacill_0305phi8_36_NC_009760: PcrA helicase; WM47_26785; phage(gi156564011)2.34e-22Showinfo_outline
5complement(19502..20470)PROPHAGE_Escher_CFT073: transposase; WM47_26790; phage(gi26248352)6.82e-10Showinfo_outline
620713..20850PROPHAGE_Escher_CFT073: transposase insC; WM47_26795; phage(gi26251004)1.43e-17Showinfo_outline
7complement(21088..21912)PROPHAGE_Xantho_33913: IS1477 transposase; WM47_26800; phage(gi77747809)8.38e-103Showinfo_outline
8complement(21945..22208)PROPHAGE_Xantho_33913: IS1404 transposase; WM47_26805; phage(gi21232568)7.34e-33Showinfo_outline
922279..22911PROPHAGE_Escher_MG1655: IS2 transposase TnpB; WM47_26810; phage(gi16132094)2.67e-139Showinfo_outline
10complement(23047..23241)PROPHAGE_Brucel_1330: transposase, putative; WM47_26815; phage(gi23502708)2.49e-05Showinfo_outline
11complement(23373..23750)PROPHAGE_Brucel_1330: transposase, putative; WM47_26820; phage(gi23502708)7.67e-38Showinfo_outline

Region 2, total 15 CDS

#CDS PositionBLAST HitE-ValueSequence
238142..39065PHAGE_Entero_HK022_NC_002166: IS903 transposase; WM47_26900; phage(gi9634149)0.0Showinfo_outline
3complement(39261..39926)RNA polymerase subunit sigma-70; WM47_269050.0Showinfo_outline
4complement(40084..40587)PHAGE_Shigel_SfIV_NC_022749: IS1 transposase B; WM47_26910; phage(gi557307573)1.14e-119Showinfo_outline
5complement(40506..40781)PHAGE_Entero_P1_NC_005856: InsA; WM47_26915; phage(gi46401643)3.18e-61Showinfo_outline
6complement(41015..41263)PHAGE_Acinet_YMC11/12/R2315_NC_028855: hypothetical protein; WM47_26925; phage(gi971749826)6.68e-06Showinfo_outline
741617..41919PROPHAGE_Shewan_MR-1: ISSod1, transposase OrfA; WM47_26930; phage(gi24373865)4.00e-10Showinfo_outline
8complement(42039..42332)hypothetical protein; WM47_269350.0Showinfo_outline
942978..44486PHAGE_Pseudo_phi3_NC_030940: hypothetical protein; WM47_26940; phage(gi100001)2.19e-48Showinfo_outline
1045028..46104transposase; WM47_269450.0Showinfo_outline
1146172..46384PHAGE_Shigel_SfIV_NC_022749: ISEhe3 orfB; WM47_26950; phage(gi557307549)4.84e-23Showinfo_outline
1246545..47696sodium:proton antiporter; WM47_269550.0Showinfo_outline
1347889..48236PROPHAGE_Brucel_1330: transposase, putative; WM47_26960; phage(gi23502708)7.13e-33Showinfo_outline
1448273..48977PROPHAGE_Brucel_1330: transposase, putative; WM47_26965; phage(gi23502708)1.98e-53Showinfo_outline

Region 3, total 6 CDS

#CDS PositionBLAST HitE-ValueSequence
180422..81588PHAGE_Entero_N15_NC_001901: plasmid partition protein SopA; WM47_27105; phage(gi9630492)0.0Showinfo_outline
281588..82559PHAGE_Entero_N15_NC_001901: ParB; WM47_27110; phage(gi9630491)4.19e-106Showinfo_outline
3complement(84081..84779)PROPHAGE_Ralsto_GMI1000: ISRSO12-transposase ORFB protein; WM47_27125; phage(gi17546158)1.37e-92Showinfo_outline
485075..86091PROPHAGE_Shewan_MR-1: IS110 family transposase; WM47_27130; phage(gi24375433)1.11e-74Showinfo_outline
5complement(86220..86432)PROPHAGE_Ralsto_GMI1000: isrso12-transposase orfa protein; WM47_27135; phage(gi17546157)2.38e-14Showinfo_outline
6complement(86680..86964)PROPHAGE_Xantho_33913: ISxac3 transposase; WM47_27140; phage(gi21231087)7.19e-23Showinfo_outline

Region 4, total 7 CDS

#CDS PositionBLAST HitE-ValueSequence
1126062..126646PHAGE_Cronob_vB_CsaP_GAP52_NC_019402: hypothetical protein; WM47_27345; phage(gi414087555)6.44e-12Showinfo_outline
2126643..127794tellurium resistance protein TerA; WM47_273500.0Showinfo_outline
3127817..128272PHAGE_Erwini_vB_EamM_ChrisDB_NC_031126: hypothetical protein; WM47_27355; phage(gi100004)8.11e-08Showinfo_outline
4128296..129336PHAGE_Cronob_vB_CsaP_GAP52_NC_019402: hypothetical protein; WM47_27360; phage(gi414087559)1.75e-74Showinfo_outline
5129375..129953PHAGE_Caulob_CcrColossus_NC_019406: putative TerD-like bacterial stress protein; WM47_27365; phage(gi414088275)2.35e-43Showinfo_outline
6130040..130615PHAGE_Caulob_CcrColossus_NC_019406: putative TerD-like bacterial stress protein; WM47_27370; phage(gi414088275)3.82e-40Showinfo_outline
7130700..131941PHAGE_Gordon_Cucurbita_NC_031029: hypothetical protein; WM47_27375; phage(gi100110)9.91e-24Showinfo_outline

Region 5, total 9 CDS

#CDS PositionBLAST HitE-ValueSequence
1225618..226541PHAGE_Entero_HK022_NC_002166: IS903 transposase; WM47_27800; phage(gi9634149)0.0Showinfo_outline
2complement(226590..227648)PHAGE_Stx2_c_1717_NC_011357: transposase; WM47_27805; phage(gi209447153)0.0Showinfo_outline
3complement(227697..228044)PHAGE_Stx2_c_1717_NC_011357: transposase; WM47_27810; phage(gi209447152)9.82e-76Showinfo_outline
4complement(228041..228379)PHAGE_Stx2_c_1717_NC_011357: truncated transposase; WM47_27815; phage(gi209447151)5.02e-63Showinfo_outline
5228430..228930PROPHAGE_Escher_CFT073: insertion element IS2 transposase InsD; WM47_27820; phage(gi26249446)1.79e-92Showinfo_outline
6229135..229446PHAGE_Riemer_RAP44_NC_019490: DUF2136 superfamily protein; WM47_27825; phage(gi418489860)1.08e-11Showinfo_outline
7229443..229862PHAGE_Entero_BP_4795_NC_004813: hypothetical protein; WM47_27830; phage(gi157166006)5.98e-05Showinfo_outline
8230054..230977PHAGE_Entero_HK022_NC_002166: IS903 transposase; WM47_27835; phage(gi9634149)0.0Showinfo_outline
9complement(231295..232320)PROPHAGE_Shewan_MR-1: IS110 family transposase; WM47_27840; phage(gi24375433)6.80e-80Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 284894 bps
Phages: 5
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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