Submission Results

Sequence Name: Not Available

GenBank Accession Number: CP056025.1

Download Results: CP056025.1.PHASTEST.zip

gi|00000000|ref|NC_000000| Klebsiella pneumoniae strain 39428 plasmid pKPN39428.1, complete 211775, gc%: 52.90%

Download summary as .txt file:summary.txt file_download

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

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
139.9Kbintact1303580378-120328 info_outlinePHAGE_Stx2_c_1717_NC_011357(3)55.53%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|CP056025.1| Klebsiella pneumoniae strain 39428 plasmid pKPN39428.1, complete 211775, gc%: 52.90%

Download details as .txt file:detail.txt file_download

Transposase
Phage-like protein
Integrase

intact

Region 1, total 17 CDS

#CDS PositionBLAST HitE-ValueSequence
180378..81142PP_00085;transposase IS26;phage;PHAGE_Escher_RCS47_NC_0421282.6e-104Show info_outline
284210..84557PP_00091;putative quaternary ammonium compound-resistance protein qacE;phage;PHAGE_Acinet_Acj61_NC_0146611.46e-08Show info_outline
385920..86417PP_00094;putative dihydrofolate reductase;phage;PHAGE_Bacill_Bp8p_T_NC_0477441.86e-33Show info_outline
486562..87575PP_00095;integrase;phage;PHAGE_Mycoba_Butters_NC_0210613.63e-12Show info_outline
588254..88475PP_00097;site-specific recombinase;phage;PHAGE_Salmon_SJ46_NC_0311294.86e-16Show info_outline
688534..89238PP_00098;transposase IS26;phage;PHAGE_Escher_RCS47_NC_0421283.1e-175Show info_outline
789292..89642PP_00099;resolvase;phage;PHAGE_Salmon_SJ46_NC_0311291.17e-63Show info_outline
889645..92611PP_00100;transposase;phage;PHAGE_Salmon_SJ46_NC_0311290.0Show info_outline
993256..93915PP_00102;Cat;phage;PHAGE_Stx2_vB_EcoP_24B_NC_0279845.0e-167Show info_outline
1094194..94891PP_00103;transposase IS1;phage;PHAGE_Escher_RCS47_NC_0421281.1e-54Show info_outline
1195123..96511PP_00105;radical SAM domain-containing protein;phage;PHAGE_Campyl_CP21_NC_0195078.33e-06Show info_outline
1296504..97616PP_00106;radical SAM domain-containing protein;phage;PHAGE_Campyl_CP21_NC_0195075.09e-07Show info_outline
1398796..99182PP_00108;truncated transposase;phage;PHAGE_Stx2_c_1717_NC_0113574.25e-78Show info_outline
1499179..99526PP_00109;transposase;phage;PHAGE_Escher_SH2026Stx1_NC_0499191.42e-75Show info_outline
1599576..101113PP_00110;transposase;phage;PHAGE_Escher_SH2026Stx1_NC_0499190.0Show info_outline
16101151..101528PP_00111;transposase;phage;PHAGE_Escher_SH2026Stx1_NC_0499191.62e-74Show info_outline
17103349..105082PP_00112;ABC transporter;phage;PHAGE_Plankt_PaV_LD_NC_0165642.46e-19Show info_outline

gi|00000000|ref|CP056025.1| Klebsiella pneumoniae strain 39428 plasmid pKPN39428.1, complete 211775, gc%: 52.90%

Download details as .txt file:detail.txt file_download

Non phage-like protein
Hypothetical protein

Bacterial, total 181 CDS

#CDS PositionBLAST HitE-ValueSequence
11..1011PP_00001; replication initiation protein0.0Showinfo_outline
21728..2468PP_00002; site-specific integrase0.0Showinfo_outline
33612..4559PP_00003; sensor domain-containing diguanylate cyclase0.0Showinfo_outline
44586..4897PP_00004; EAL domain-containing protein0.0Showinfo_outline
54917..5885PP_00005; IS5 family transposase0.0Showinfo_outline
66558..6815PP_00006; hypothetical protein0.0Showinfo_outline
77417..7944PP_00007; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
88091..9071PP_00008; IS5-like element ISKpn26 family transposase0.0Showinfo_outline
99235..10071PP_00009; EAL domain-containing protein0.0Showinfo_outline
1011054..12331PP_00010; DUF2254 domain-containing protein0.0Showinfo_outline
1112394..14391PP_00011; choline BCCT transporter BetT0.0Showinfo_outline
1214543..15240PP_00012; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
1315431..16638PP_00013; IS3 family transposase0.0Showinfo_outline
1416729..17213PP_00014; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
1517229..17771PP_00015; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
1618067..18498PP_00016; silver-binding protein SilE0.0Showinfo_outline
1718749..20224PP_00017; copper/silver sensor histidine kinase SilS0.0Showinfo_outline
1820217..20897PP_00018; copper/silver response regulator transcription factor SilR0.0Showinfo_outline
1921087..22472PP_00019; Cu(+)/Ag(+) efflux RND transporter outer membrane channel SilC0.0Showinfo_outline
2022501..22854PP_00020; cation efflux system protein CusF0.0Showinfo_outline
2122968..24260PP_00021; Cu(+)/Ag(+) efflux RND transporter periplasmic adaptor subunit SilB0.0Showinfo_outline
2224271..27417PP_00022; Cu(+)/Ag(+) efflux RND transporter permease subunit SilA0.0Showinfo_outline
2327504..27944PP_00023; hypothetical protein0.0Showinfo_outline
2428071..30518PP_00024; Ag(+)-translocating P-type ATPase SilP0.0Showinfo_outline
2530559..30756PP_00025; DUF2933 domain-containing protein0.0Showinfo_outline
2630790..31527PP_00026; peptidoglycan DD-metalloendopeptidase family protein0.0Showinfo_outline
2731816..32265PP_00027; copper resistance protein0.0Showinfo_outline
2832499..34310PP_00028; multicopper oxidase PcoA0.0Showinfo_outline
2934316..35206PP_00029; copper resistance outer membrane transporter PcoB0.0Showinfo_outline
3035246..35626PP_00030; copper resistance system metallochaperone PcoC0.0Showinfo_outline
3135631..36560PP_00031; copper resistance inner membrane protein PcoD0.0Showinfo_outline
3236615..37295PP_00032; copper response regulator transcription factor PcoR0.0Showinfo_outline
3337292..38692PP_00033; copper resistance membrane spanning protein PcoS0.0Showinfo_outline
3438909..39343PP_00034; copper resistance system metallochaperone PcoE0.0Showinfo_outline
3539575..39754PP_00035; type II toxin-antitoxin system RelE/ParE family toxin0.0Showinfo_outline
3639815..41435PP_00036; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
3741497..42006PP_00037; aquaporin0.0Showinfo_outline
3842056..42553PP_00038; N-acetyltransferase family protein0.0Showinfo_outline
3942885..43211PP_00039; helix-turn-helix transcriptional regulator0.0Showinfo_outline
4043208..43921PP_00040; arsenical resistance protein ArsH0.0Showinfo_outline
4143930..44475PP_00041; sigma-70 family RNA polymerase sigma factor0.0Showinfo_outline
4244551..44913PP_00042; arsenic metallochaperone ArsD family protein0.0Showinfo_outline
4344938..46688PP_00043; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
4446810..47346PP_00044; N-acetyltransferase family protein0.0Showinfo_outline
4547379..47804PP_00045; glutaredoxin-dependent arsenate reductase0.0Showinfo_outline
4647817..49106PP_00046; arsenite efflux transporter membrane subunit ArsB0.0Showinfo_outline
4749154..50905PP_00047; arsenite efflux transporter ATPase subunit ArsA0.0Showinfo_outline
4850923..51285PP_00048; arsenite efflux transporter metallochaperone ArsD0.0Showinfo_outline
4951335..51685PP_00049; As(III)-sensing metalloregulatory transcriptional repressor ArsR0.0Showinfo_outline
5052043..52312PP_00050; hypothetical protein0.0Showinfo_outline
5152300..52875PP_00051; hypothetical protein0.0Showinfo_outline
5252906..53400PP_00052; DNA-binding protein0.0Showinfo_outline
5353444..53812PP_00053; hypothetical protein0.0Showinfo_outline
5453846..54049PP_00054; hemolysin expression modulator Hha0.0Showinfo_outline
5554098..54355PP_00055; hypothetical protein0.0Showinfo_outline
5654431..54685PP_00056; hypothetical protein0.0Showinfo_outline
5754861..55127PP_00057; DUF1778 domain-containing protein0.0Showinfo_outline
5855115..55597PP_00058; GNAT family N-acetyltransferase0.0Showinfo_outline
5955809..57155PP_00059; ISNCY family transposase0.0Showinfo_outline
6057656..58910PP_00060; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
6158998..59960PP_00061; M48 family metalloprotease0.0Showinfo_outline
6259947..60696PP_00062; phosphate-starvation-inducible PsiE family protein0.0Showinfo_outline
6360934..61131PP_00063; hypothetical protein0.0Showinfo_outline
6461131..63926PP_00064; heat shock survival AAA family ATPase ClpK0.0Showinfo_outline
6564041..64610PP_00065; small heat shock protein sHSP200.0Showinfo_outline
6664645..64926PP_00066; helix-turn-helix domain-containing protein0.0Showinfo_outline
6765170..65433PP_00067; hypothetical protein0.0Showinfo_outline
6865448..65711PP_00068; transposase0.0Showinfo_outline
6965656..65772PP_00069; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
7065957..66654PP_00070; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
7166913..67893PP_00071; IS5-like element ISKpn26 family transposase0.0Showinfo_outline
7268475..68994PP_00072; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
7369102..69971PP_00073; LysR family transcriptional regulator0.0Showinfo_outline
7469965..70975PP_00074; phosphonate dehydrogenase PtxD0.0Showinfo_outline
7570984..71811PP_00075; phosphonate ABC transporter, permease protein PhnE0.0Showinfo_outline
7671820..72683PP_00076; phosphate/phosphite/phosphonate ABC transporter substrate-binding protein0.0Showinfo_outline
7772680..73507PP_00077; phosphonate ABC transporter ATP-binding protein0.0Showinfo_outline
7873849..74157PP_00078; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
7974363..75067PP_00079; IS6-like element IS26 family transposase0.0Showinfo_outline
8075130..76323PP_00080; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
8176371..77039PP_00081; IS6 family transposase0.0Showinfo_outline
8277161..78066PP_00082; Mph(A) family macrolide 2'-phosphotransferase0.0Showinfo_outline
8378063..79301PP_00083; MFS transporter0.0Showinfo_outline
8479301..79885PP_00084; TetR/AcrR family transcriptional regulator0.0Showinfo_outline
85120379..120672PP_00129; IS66 family insertion sequence element accessory protein TnpB0.0Showinfo_outline
86120747..120974PP_00130; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
87121003..121290PP_00131; EAL domain-containing protein0.0Showinfo_outline
88121624..122634PP_00132; zinc-binding alcohol dehydrogenase family protein0.0Showinfo_outline
89123095..124177PP_00133; DNA-binding transcriptional repressor LacI0.0Showinfo_outline
90124299..127373PP_00134; beta-galactosidase0.0Showinfo_outline
91127425..128678PP_00135; lactose permease0.0Showinfo_outline
92128770..129738PP_00136; IS5 family transposase0.0Showinfo_outline
93130383..132692PP_00137; TerB N-terminal domain-containing protein0.0Showinfo_outline
94132696..134012PP_00138; ATP-binding protein0.0Showinfo_outline
95134009..136204PP_00139; DEAD/DEAH box helicase0.0Showinfo_outline
96137652..138509PP_00140; incFII family plasmid replication initiator RepA0.0Showinfo_outline
97138502..138579PP_00141; RepA leader peptide Tap0.0Showinfo_outline
98138811..139080PP_00142; replication regulatory protein RepA0.0Showinfo_outline
99139198..139677PP_00143; phospholipase D family protein0.0Showinfo_outline
100139853..140161PP_00144; hypothetical protein0.0Showinfo_outline
101140158..140808PP_00145; DUF2726 domain-containing protein0.0Showinfo_outline
102140864..141508PP_00146; hypothetical protein0.0Showinfo_outline
103141558..142160PP_00147; hypothetical protein0.0Showinfo_outline
104142321..142914PP_00148; fertility inhibition protein FinO0.0Showinfo_outline
105142986..143711PP_00149; type-F conjugative transfer system pilin acetylase TraX0.0Showinfo_outline
106143792..149053PP_00150; conjugative transfer relaxase/helicase TraI0.0Showinfo_outline
107149053..150282PP_00151; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
108150310..153315PP_00152; Tn3-like element Tn3 family transposase0.0Showinfo_outline
109153477..154034PP_00153; recombinase family protein0.0Showinfo_outline
110154217..155077PP_00154; class A broad-spectrum beta-lactamase TEM-10.0Showinfo_outline
111155224..156318PP_00155; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
112156447..157136PP_00156; hypothetical protein0.0Showinfo_outline
113157328..158059PP_00157; complement resistance protein TraT0.0Showinfo_outline
114158243..158791PP_00158; conjugal transfer entry exclusion protein TraS0.0Showinfo_outline
115158804..161653PP_00159; conjugal transfer mating pair stabilization protein TraG0.0Showinfo_outline
116161653..163032PP_00160; conjugal transfer protein TraH0.0Showinfo_outline
117163010..163453PP_00161; F-type conjugal transfer protein TrbF0.0Showinfo_outline
118163499..164056PP_00162; type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB0.0Showinfo_outline
119164028..164267PP_00163; type-F conjugative transfer system pilin chaperone TraQ0.0Showinfo_outline
120164278..165030PP_00164; type-F conjugative transfer system pilin assembly protein TraF0.0Showinfo_outline
121165051..165377PP_00165; hypothetical protein0.0Showinfo_outline
122165390..165638PP_00166; hypothetical protein0.0Showinfo_outline
123165616..165870PP_00167; conjugal transfer protein TrbE0.0Showinfo_outline
124165902..167857PP_00168; type-F conjugative transfer system mating-pair stabilization protein TraN0.0Showinfo_outline
125167916..168554PP_00169; type-F conjugative transfer system pilin assembly protein TrbC0.0Showinfo_outline
126168567..169556PP_00170; conjugal transfer pilus assembly protein TraU0.0Showinfo_outline
127169553..169942PP_00171; hypothetical protein0.0Showinfo_outline
128169984..170610PP_00172; type-F conjugative transfer system protein TraW0.0Showinfo_outline
129170610..170999PP_00173; type-F conjugative transfer system protein TrbI0.0Showinfo_outline
130170999..173638PP_00174; type IV secretion system protein TraC0.0Showinfo_outline
131173710..174108PP_00175; hypothetical protein0.0Showinfo_outline
132174404..174808PP_00176; hypothetical protein0.0Showinfo_outline
133174875..175192PP_00177; hypothetical protein0.0Showinfo_outline
134175193..175411PP_00178; hypothetical protein0.0Showinfo_outline
135175435..175725PP_00179; hypothetical protein0.0Showinfo_outline
136175730..176140PP_00180; lipase chaperone0.0Showinfo_outline
137176272..176841PP_00181; type IV conjugative transfer system lipoprotein TraV0.0Showinfo_outline
138176864..177460PP_00182; conjugal transfer protein TraP0.0Showinfo_outline
139177453..178877PP_00183; conjugal transfer protein TraB0.0Showinfo_outline
140178877..179617PP_00184; type-F conjugative transfer system secretin TraK0.0Showinfo_outline
141179604..180170PP_00185; type IV conjugative transfer system protein TraE0.0Showinfo_outline
142180190..180495PP_00186; type IV conjugative transfer system protein TraL0.0Showinfo_outline
143180509..180877PP_00187; type IV conjugative transfer system pilin TraA0.0Showinfo_outline
144180931..181302PP_00188; TraY domain-containing protein0.0Showinfo_outline
145181386..182072PP_00189; conjugal transfer protein TraJ0.0Showinfo_outline
146182295..182687PP_00190; relaxosome protein TraM0.0Showinfo_outline
147183121..183606PP_00191; transglycosylase SLT domain-containing protein0.0Showinfo_outline
148183639..183968PP_00192; hypothetical protein0.0Showinfo_outline
149184001..184822PP_00193; DUF945 domain-containing protein0.0Showinfo_outline
150185656..186069PP_00194; helix-turn-helix domain-containing protein0.0Showinfo_outline
151186070..186348PP_00195; helix-turn-helix transcriptional regulator0.0Showinfo_outline
152186338..186658PP_00196; type II toxin-antitoxin system RelE/ParE family toxin0.0Showinfo_outline
153186739..186963PP_00197; hypothetical protein0.0Showinfo_outline
154186974..187186PP_00198; hypothetical protein0.0Showinfo_outline
155187247..187603PP_00199; hypothetical protein0.0Showinfo_outline
156188239..188589PP_00200; hypothetical protein0.0Showinfo_outline
157188586..188858PP_00201; hypothetical protein0.0Showinfo_outline
158189558..189719PP_00202; type I toxin-antitoxin system Hok family toxin0.0Showinfo_outline
159189791..190870PP_00203; IS481-like element ISKpn28 family transposase0.0Showinfo_outline
160191048..191422PP_00204; hypothetical protein0.0Showinfo_outline
161191478..191804PP_00205; theronine dehydrogenase0.0Showinfo_outline
162191801..192529PP_00206; plasmid SOS inhibition protein A0.0Showinfo_outline
163192526..192957PP_00207; conjugation system SOS inhibitor PsiB0.0Showinfo_outline
164193024..195060PP_00208; ParB/RepB/Spo0J family partition protein0.0Showinfo_outline
165195130..195378PP_00209; DUF905 domain-containing protein0.0Showinfo_outline
166195427..195969PP_00210; single-stranded DNA-binding protein0.0Showinfo_outline
167196745..197308PP_00211; methyltransferase0.0Showinfo_outline
168197356..198711PP_00212; DUF3560 domain-containing protein0.0Showinfo_outline
169198763..198993PP_00213; hypothetical protein0.0Showinfo_outline
170199085..199312PP_00214; hypothetical protein0.0Showinfo_outline
171200096..200413PP_00215; hypothetical protein0.0Showinfo_outline
172200448..200702PP_00216; DNA polymerase III subunit theta0.0Showinfo_outline
173200939..201364PP_00217; antirestriction protein0.0Showinfo_outline
174201885..202115PP_00218; hypothetical protein0.0Showinfo_outline
175202349..203836PP_00219; group II intron reverse transcriptase/maturase0.0Showinfo_outline
176204239..204664PP_00220; translesion error-prone DNA polymerase V autoproteolytic subunit0.0Showinfo_outline
177204664..205935PP_00221; Y-family DNA polymerase0.0Showinfo_outline
178206014..206229PP_00222; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
179206252..207450PP_00223; IS200/IS605 family element transposase accessory protein TnpB0.0Showinfo_outline
180208887..209858PP_00224; ParB/RepB/Spo0J family plasmid partition protein0.0Showinfo_outline
181209858..211024PP_00225; plasmid-partitioning protein SopA0.0Showinfo_outline

Phage Genes

Bacterial Genes

Phage Regions

GC Skew

GC Content

lock_open

Phage Genes

Bacterial Genes

Phage Regions

GC Skew

GC Content

lock_open
Click on a region or gene to view details

We require the use of cookies for essential features like storing your previously submitted PHASTEST queries. Rejecting the usage of cookies will result in certain features being disabled. By clicking ACCEPT or continuing to use the website you are agreeing to our use of cookies.

ACCEPT