Submission Results

Sequence Name: Not Available

GenBank Accession Number: CP129187.1

Download Results: CP129187.1.PHASTEST.zip

gi|00000000|ref|NC_000000| Klebsiella pneumoniae strain YZE1-3D plasmid pYZE1-3D-2, complete 135702, gc%: 50.41%

Download summary as .txt file:summary.txt file_download

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

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
152.3Kbquestionable90431550-53924 info_outlinePHAGE_Salmon_SSU5_NC_018843(19)52.26%Show info_outline
256.3Kbintact1505646860-103245 info_outlinePHAGE_Salmon_SSU5_NC_018843(45)51.31%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|CP129187.1| Klebsiella pneumoniae strain YZE1-3D plasmid pYZE1-3D-2, complete 135702, gc%: 50.41%

Download details as .txt file:detail.txt file_download

Phage-like protein
Hypothetical protein
Endonuclease
Integrase
DNA Helicase
Transposase
Holin
Fiber protein
Tail protein
Head protein
Portal protein
Terminase
Repressor

questionable

Region 1, total 41 CDS

#CDS PositionBLAST HitE-ValueSequence
11550..1762PP_00001;putative Cre-associated protein;phage;PHAGE_Salmon_SSU5_NC_0188431.92e-36Show info_outline
21762..2097PP_00002;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188433.68e-46Show info_outline
32460..2636PP_00003;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.24e-16Show info_outline
42807..5149PP_00004;putative RecA-like recombinase;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
55152..5418PP_00005;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188433.33e-49Show info_outline
65418..6362PP_00006;DNA polymerase I;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
76423..7430PP_00007;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
87550..7981PP_00008;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188436.09e-92Show info_outline
98503..8922PP_00010;hypothetical protein;phage;PHAGE_Entero_mEp460_NC_0197165.89e-63Show info_outline
109123..9548PP_00011;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188436.12e-82Show info_outline
119563..10699PP_00012;DNA polymerase III alpha subunit;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
1210754..11449PP_00013;HNH endonuclease;phage;PHAGE_Gordon_Wizard_NC_0309131.08e-27Show info_outline
1311488..13815PP_00014;DNA polymerase III alpha subunit;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
1413996..15228PP_00015;putative porphyrin biosynthetic protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
1515325..17604PP_00016;putative porphyrin biosynthetic protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
1618207..18587PP_00017;hypothetical protein;phage;PHAGE_Rhizob_RHEph10_NC_0342489.35e-10Show info_outline
1718582..19682PP_00018;bacteriophage integrase protein;phage;PHAGE_Phage_Gifsy_1_NC_0103924.01e-23Show info_outline
1820457..20867PP_00020;hypothetical protein;phage;PHAGE_Escher_HK639_NC_0161581.22e-17Show info_outline
1921589..21834PP_00022;putative glutaredoxin;phage;PHAGE_Pseudo_OBP_NC_0165712.21e-14Show info_outline
2021831..22217PP_00023;hypothetical protein;phage;PHAGE_Shigel_Sf6_NC_0053442.58e-62Show info_outline
2122227..23003PP_00024;PhoH;phage;PHAGE_Erwini_PhiEaH1_NC_0236102.05e-121Show info_outline
2224313..24612PP_00025;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.3e-39Show info_outline
2324609..24761PP_00026;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188433.61e-24Show info_outline
2424785..25006PP_00027;putative DNA ligase;phage;PHAGE_Salmon_SSU5_NC_0188432.62e-35Show info_outline
2525006..25473PP_00028;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188432.98e-66Show info_outline
2625553..26341PP_00029;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188438.56e-92Show info_outline
2726462..27583PP_00030;putative DNA primase;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
2827730..28332PP_00031;putative DNA helicase;phage;PHAGE_Salmon_SSU5_NC_0188432.7e-137Show info_outline
2928542..29987PP_00032;aerotaxis sensor receptor protein;phage;PHAGE_Salmon_SJ46_NC_0311291.86e-71Show info_outline
3030070..30774PP_00033;transposase IS26;phage;PHAGE_Escher_RCS47_NC_0421283.1e-175Show info_outline
3132749..34272PP_00036;transposase;phage;PHAGE_Salmon_SJ46_NC_0311294.45e-145Show info_outline
3234334..35086PP_00037;transposase, putative;phage;PROPHAGE_Brucel_13302.19e-50Show info_outline
3335194..35433PP_00038;hypothetical protein;phage;PHAGE_Bacill_SPbeta_NC_0018841.03e-28Show info_outline
3436762..37538PP_00040;hypothetical protein;phage;PHAGE_Bacill_SPbeta_NC_0018842.31e-19Show info_outline
3537652..38356PP_00041;transposase IS26;phage;PHAGE_Escher_RCS47_NC_0421283.1e-175Show info_outline
3638814..39677PP_00043;hypothetical protein;phage;PHAGE_Prochl_P_TIM68_NC_0289556.59e-10Show info_outline
3746860..47702PP_00053;gp58;phage;PHAGE_Mycoba_Wile_NC_0237092.89e-11Show info_outline
3847869..48882PP_00054;integrase;phage;PHAGE_Mycoba_Butters_NC_0210613.3e-12Show info_outline
3949611..50171PP_00056;resolvase;phage;PHAGE_Salmon_SJ46_NC_0311295.65e-83Show info_outline
4050175..53141PP_00057;transposase;phage;PHAGE_Salmon_SJ46_NC_0311290.0Show info_outline
4153118..53897PP_00058;putative DNA helicase;phage;PHAGE_Salmon_SSU5_NC_0188432.59e-170Show info_outline

intact

Region 2, total 48 CDS

#CDS PositionBLAST HitE-ValueSequence
153962..54687PP_00059;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188432.02e-163Show info_outline
254981..56039PP_00060;hypothetical protein;phage;PHAGE_Vibrio_1.202.O._10N.222.45.E8_NC_0480661.33e-74Show info_outline
356099..56455PP_00061;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188436.66e-63Show info_outline
456461..57126PP_00062;putative ParA family protein;phage;PHAGE_Salmon_SSU5_NC_0188436.31e-132Show info_outline
557299..58048PP_00063;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188438.52e-19Show info_outline
658033..58425PP_00064;hypothetical protein;phage;PHAGE_Escher_RCS47_NC_0421282.72e-20Show info_outline
758842..59093PP_00065;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188432.51e-36Show info_outline
859096..59788PP_00066;putative endolysin;phage;PHAGE_Salmon_SSU5_NC_0188434.13e-155Show info_outline
959802..60125PP_00067;putative holin;phage;PHAGE_Salmon_SSU5_NC_0188435.91e-70Show info_outline
1060221..61666PP_00068;tail fiber;phage;PHAGE_Klebsi_Sushi_NC_0287747.92e-49Show info_outline
1161789..73923PP_00069;putative phage tail protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
1273940..74551PP_00070;putative phage tail protein;phage;PHAGE_Salmon_SSU5_NC_0188431.73e-112Show info_outline
1374539..75336PP_00071;putative phage tail protein;phage;PHAGE_Salmon_SSU5_NC_0188434.69e-175Show info_outline
1475329..76027PP_00072;putative minor tail protein L;phage;PHAGE_Salmon_SSU5_NC_0188434.02e-158Show info_outline
1576114..76449PP_00073;putative minor tail protein M;phage;PHAGE_Salmon_SSU5_NC_0188433.76e-67Show info_outline
1676493..81031PP_00074;putative tail tape measure protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
1781039..81263PP_00075;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.2e-42Show info_outline
1881389..81706PP_00076;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188432.75e-64Show info_outline
1981768..82514PP_00077;putative tail protein;phage;PHAGE_Rhizob_RHEph10_NC_0342482.06e-24Show info_outline
2082582..82974PP_00078;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188433.26e-63Show info_outline
2182976..83449PP_00079;putative head-to-tail joining protein;phage;PHAGE_Rhizob_RHEph10_NC_0342481.73e-08Show info_outline
2283440..83784PP_00080;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188435.99e-73Show info_outline
2383882..84715PP_00081;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.41e-176Show info_outline
2484715..85149PP_00082;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188432.83e-84Show info_outline
2585197..85625PP_00083;tail assembly protein;phage;PHAGE_Salmon_SE4_NC_0487643.42e-22Show info_outline
2685704..86582PP_00084;putative major capsid protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
2786609..87508PP_00085;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
2887531..89105PP_00086;putative phage portal protein;phage;PHAGE_Rhizob_RHEph10_NC_0342481.26e-166Show info_outline
2989138..90394PP_00087;putative terminase large subunit;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
3090397..91038PP_00088;putative DNA-binding protein;phage;PHAGE_Salmon_SSU5_NC_0188432.24e-109Show info_outline
3191214..91480PP_00089;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.29e-41Show info_outline
3291490..92380PP_00090;putative ABC transporter ATP-binding protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
3392386..92640PP_00091;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.68e-53Show info_outline
3492633..93271PP_00092;putative ABC transporter ATP-binding protein;phage;PHAGE_Salmon_SSU5_NC_0188435.69e-151Show info_outline
3593268..93936PP_00093;putative ParB-like nuclease domain-containing protein;phage;PHAGE_Salmon_SSU5_NC_0188431.18e-144Show info_outline
3693936..94640PP_00094;putative ParB-like nuclease domain-containing protein;phage;PHAGE_Salmon_SSU5_NC_0188431.31e-145Show info_outline
3794700..96259PP_00095;putative helicase;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
3896262..96540PP_00096;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188437.64e-41Show info_outline
3997912..98268PP_00099;hypothetical protein;phage;PHAGE_Pseudo_PAJU2_NC_0113738.22e-05Show info_outline
4098318..98848PP_00100;putative repressor of phase 1 flagellin;phage;PHAGE_Salmon_SSU5_NC_0188436.62e-74Show info_outline
4199165..99815PP_00101;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188433.01e-144Show info_outline
4299863..100093PP_00102;hypothetical protein;phage;PHAGE_Pseudo_Zigelbrucke_NC_0419041.05e-05Show info_outline
43100731..101213PP_00103;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188433.92e-85Show info_outline
44101419..101700PP_00104;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188435.71e-54Show info_outline
45101827..102234PP_00105;Gp62;phage;PHAGE_Klebsi_phiKO2_NC_0058571.25e-31Show info_outline
46102354..102653PP_00106;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188436.66e-44Show info_outline
47102802..103014PP_00107;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188439.01e-33Show info_outline
48103027..103245PP_00108;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188435.03e-37Show info_outline

gi|00000000|ref|CP129187.1| Klebsiella pneumoniae strain YZE1-3D plasmid pYZE1-3D-2, complete 135702, gc%: 50.41%

Download details as .txt file:detail.txt file_download

Non phage-like protein
Hypothetical protein
phage N-6-adenine-methyltransferase

Bacterial, total 29 CDS

#CDS PositionBLAST HitE-ValueSequence
1105122..106987PP_00109; DUF262 domain-containing protein0.0Showinfo_outline
2107191..108747PP_00110; type I restriction-modification system subunit M0.0Showinfo_outline
3108744..109940PP_00111; restriction endonuclease subunit S0.0Showinfo_outline
4110016..113132PP_00112; HsdR family type I site-specific deoxyribonuclease0.0Showinfo_outline
5113194..113409PP_00113; hypothetical protein0.0Showinfo_outline
6113538..114116PP_00114; hypothetical protein0.0Showinfo_outline
7114244..114399PP_00115; DUF3927 family protein0.0Showinfo_outline
8114399..114824PP_00116; tellurite/colicin resistance protein0.0Showinfo_outline
9115125..115757PP_00117; hypothetical protein0.0Showinfo_outline
10115811..116479PP_00118; ribonuclease HI0.0Showinfo_outline
11117009..117242PP_00119; hypothetical protein0.0Showinfo_outline
12117445..118038PP_00120; phage N-6-adenine-methyltransferase;phage N-6-adenine-methyltransferase0.0Showinfo_outline
13118223..119056PP_00121; hypothetical protein0.0Showinfo_outline
14119182..119739PP_00122; 3'-5' exonuclease0.0Showinfo_outline
15119749..120168PP_00123; hypothetical protein0.0Showinfo_outline
16120232..120876PP_00124; AAA family ATPase0.0Showinfo_outline
17120876..121346PP_00125; dihydrofolate reductase0.0Showinfo_outline
18121349..121744PP_00126; hypothetical protein0.0Showinfo_outline
19121764..122867PP_00127; thymidylate synthase0.0Showinfo_outline
20123061..123936PP_00128; nucleoside triphosphate pyrophosphohydrolase family protein0.0Showinfo_outline
21124014..125156PP_00129; class Ia ribonucleoside-diphosphate reductase subunit beta0.0Showinfo_outline
22125287..127590PP_00130; class 1a ribonucleoside-diphosphate reductase subunit alpha0.0Showinfo_outline
23127666..128235PP_00131; hypothetical protein0.0Showinfo_outline
24128245..128955PP_00132; hypothetical protein0.0Showinfo_outline
25128981..130897PP_00133; AAA family ATPase0.0Showinfo_outline
26130894..131127PP_00134; hypothetical protein0.0Showinfo_outline
27131127..132212PP_00135; metallophosphoesterase0.0Showinfo_outline
28132865..134424PP_00136; DUF4041 domain-containing protein0.0Showinfo_outline
29134738..135382PP_00137; hypothetical protein0.0Showinfo_outline

Phage Genes

Bacterial Genes

Phage Regions

GC Skew

GC Content

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Phage Genes

Bacterial Genes

Phage Regions

GC Skew

GC Content

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Click on a region or gene to view details

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