Submission Results

Sequence Name: Not Available

GenBank Accession Number: 1062719365

GenInfo (GI) Number: 0000000000

Download Results: 1062719365.PHASTER.zip

gi|00000000|ref|CP012571.1| Klebsiella pneumoniae strain UCLAOXA232KP plasmid pUCLAOXA232-5.X, 126863, gc%: 52.92%

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
110.4Kbincomplete20141721-12122 info_outlinePHAGE_Entero_P1_NC_005856(3)54.68%Show info_outline
28.2Kbincomplete301218241-26442 info_outlinePHAGE_Entero_N15_NC_001901(2)53.29%Show info_outline
314.5Kbquestionable701279700-94283 info_outlinePHAGE_Staphy_SPbeta_like_NC_029119(2)52.69%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|CP012571.1| Klebsiella pneumoniae strain UCLAOXA232KP plasmid pUCLAOXA232-5.X, 126863, gc%: 52.92%

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 14 CDS

#CDS PositionBLAST HitE-ValueSequence
11721..2926PHAGE_Salmon_SJ46_NC_031129: hypothetical protein; AM278_27550; phage(gi100009)0.0Showinfo_outline
22926..3900PHAGE_Entero_P1_NC_005856: ParB; AM278_27555; phage(gi46401681)3.13e-114Showinfo_outline
3complement(3982..5253)PHAGE_Cronob_ENT39118_NC_019934: DNA polymerase; AM278_27560; phage(gi431811050)0.0Showinfo_outline
4complement(5253..5684)PHAGE_Cronob_ENT39118_NC_019934: protein umuD; AM278_27565; phage(gi431811072)5.10e-34Showinfo_outline
55918..6889PHAGE_Entero_P88_NC_026014: recombinase; AM278_27570; phage(gi744692717)3.15e-77Showinfo_outline
66892..7563Mediator of plasmid stability; AM278_275750.0Showinfo_outline
77626..7856hypothetical protein; AM278_275800.0Showinfo_outline
88293..8994PHAGE_Staphy_Stau2_NC_030933: hypothetical protein; AM278_27585; phage(gi100063)7.28e-28Showinfo_outline
98994..9215PHAGE_Entero_N15_NC_001901: gp50; AM278_27590; phage(gi9630517)6.40e-06Showinfo_outline
109225..9644adenine-specific methyltransferase; AM278_275950.0Showinfo_outline
119698..10465hypothetical protein; AM278_276000.0Showinfo_outline
1210537..10893hypothetical protein; AM278_276050.0Showinfo_outline
1311145..11573PHAGE_Pseudo_YuA_NC_010116: hypothetical protein; AM278_27610; phage(gi162135127)1.34e-12Showinfo_outline
1411616..12122PHAGE_Rhodoc_CosmicSans_NC_028677: ArdA; AM278_27615; phage(gi966199624)2.20e-12Showinfo_outline

Region 2, total 12 CDS

#CDS PositionBLAST HitE-ValueSequence
118241..20298PHAGE_Gordon_Hedwig_NC_031099: RNA polymerase binding protein; AM278_27670; phage(gi100054)1.07e-06Showinfo_outline
220343..20774plasmid SOS inhibition protein B; AM278_276750.0Showinfo_outline
320771..21499recombinase; AM278_276800.0Showinfo_outline
421496..21822PHAGE_Rhodob_RcapNL_NC_020489: hypothetical protein; AM278_27685; phage(gi461475014)4.51e-17Showinfo_outline
5complement(22188..23168)PHAGE_Bacill_BMBtpLA_NC_028748: IS5 transposase and trans-activator; AM278_27695; phage(gi971482498)0.0Showinfo_outline
623261..23473hypothetical protein; AM278_277000.0Showinfo_outline
723484..23708hypothetical protein; AM278_277050.0Showinfo_outline
823789..24109PHAGE_Entero_N15_NC_001901: gp49; AM278_27710; phage(gi9630516)7.77e-23Showinfo_outline
924099..24377PHAGE_Entero_N15_NC_001901: gp48; AM278_27715; phage(gi9630515)7.11e-14Showinfo_outline
1024378..24791XRE family transcriptional regulator; AM278_277200.0Showinfo_outline
11complement(24687..24902)hypothetical protein; AM278_277250.0Showinfo_outline
1225621..26442PHAGE_Cronob_vB_CsaM_GAP32_NC_019401: hypothetical protein; AM278_27730; phage(gi414086954)3.67e-58Showinfo_outline

Region 3, total 14 CDS

#CDS PositionBLAST HitE-ValueSequence
179700..79711attL0.0Showinfo_outline
2complement(83873..84637)PROPHAGE_Brucel_1330: transposase, putative; AM278_28040; phage(gi23502708)3.18e-55Showinfo_outline
3complement(85144..85644)acetyltransferase; AM278_280450.0Showinfo_outline
4complement(85772..86611)dihydropteroate synthase; AM278_280500.0Showinfo_outline
5complement(86605..86952)PHAGE_Acinet_Acj61_NC_014661: putative quaternary ammonium compound-resistance protein qacE; AM278_28055; phage(gi311992758)9.11e-09Showinfo_outline
6complement(87656..88129)PHAGE_Bacill_Blue_NC_031056: hypothetical protein; AM278_28060; phage(gi100007)3.20e-25Showinfo_outline
7complement(88264..88716)rifampin ADP-ribosylating transferase ARR-2; AM278_280650.0Showinfo_outline
888889..89902PHAGE_Mycoba_Butters_NC_021061: integrase; AM278_28070; phage(gi479336499)2.05e-12Showinfo_outline
9complement(90139..90843)PROPHAGE_Brucel_1330: transposase, putative; AM278_28075; phage(gi23502708)1.98e-53Showinfo_outline
1090834..91319PROPHAGE_Xantho_33913: Tn5041 transposase; AM278_28080; phage(gi21231545)4.47e-13Showinfo_outline
1191398..92402PROPHAGE_Shewan_MR-1: IS110 family transposase; AM278_28085; phage(gi24375433)1.70e-59Showinfo_outline
12complement(92817..93017)glycogen synthesis protein GlgS; AM278_280900.0Showinfo_outline
13complement(93318..94241)PHAGE_Entero_HK022_NC_002166: IS903 transposase; AM278_28095; phage(gi9634149)0.0Showinfo_outline
1494283..94294attR0.0Showinfo_outline
Klebsiella pneumoniae strain UCLAOXA232KP plasmid pUCLAOXA232-5.X
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 126863 bps
Phages: 3
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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