Submission Results

Sequence Name: Not Available

GenBank Accession Number: NZ_CP061390.1

Download Results: NZ_CP061390.1.PHASTEST.zip

gi|00000000|ref|NC_000000| Klebsiella pneumoniae strain NU-CRE195 plasmid pCRE-195-1, 183887, gc%: 52.87%

Download summary as .txt file:summary.txt file_download

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

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
143.3Kbincomplete5032137057-180415 info_outlinePHAGE_Escher_RCS47_NC_042128(4)54.62%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|NZ_CP061390.1| Klebsiella pneumoniae strain NU-CRE195 plasmid pCRE-195-1, 183887, gc%: 52.87%

Download details as .txt file:detail.txt file_download

Integrase
Transposase
Hypothetical protein
Phage-like protein

incomplete

Region 1, total 14 CDS

#CDS PositionBLAST HitE-ValueSequence
1149901..150938PP_00152;tyrosine-type recombinase/integrase;phage;PHAGE_Bacill_vB_BtS_B83_NC_0487626.85e-11Show info_outline
2153026..153544PP_00156;transposase IS26;phage;PHAGE_Escher_RCS47_NC_0421281.5e-80Show info_outline
3153607..154311PP_00157;transposase IS26;phage;PHAGE_Escher_RCS47_NC_0421281.51e-174Show info_outline
4155267..156088PP_00160;hypothetical protein;phage;PHAGE_Cronob_vB_CsaM_GAP32_NC_0194015.83e-58Show info_outline
5157335..157613PP_00162;gp48;phage;PHAGE_Entero_N15_NC_0019011.14e-13Show info_outline
6157603..157923PP_00163;Gp49;phage;PHAGE_Klebsi_phiKO2_NC_0058571.69e-24Show info_outline
7160819..160941PP_00169;host killer protein;phage;PHAGE_Entero_933W_NC_0009241.0e-05Show info_outline
8161638..161964PP_00172;hypothetical protein;phage;PHAGE_Rhodob_RcapNL_NC_0204897.1e-17Show info_outline
9163162..165219PP_00175;DNA binding protein;phage;PHAGE_Gordon_Hedwig_NC_0310991.95e-06Show info_outline
10165586..166128PP_00177;single stranded DNA-binding protein;phage;PHAGE_Escher_Sortsne_NC_0481782.12e-68Show info_outline
11167276..167530PP_00179;DNA pol III theta;phage;PHAGE_Escher_HK639_NC_0161585.3e-22Show info_outline
12167767..168192PP_00180;hypothetical protein;phage;PHAGE_Pseudo_YuA_NC_0101163.19e-14Show info_outline
13169176..170687PP_00182;reverse transcriptase;phage;PHAGE_Pseudo_phi3_NC_0309401.45e-30Show info_outline
14171089..171514PP_00183;protein umuD;phage;PHAGE_Cronob_ENT39118_NC_0199344.99e-32Show info_outline

gi|00000000|ref|NZ_CP061390.1| Klebsiella pneumoniae strain NU-CRE195 plasmid pCRE-195-1, 183887, gc%: 52.87%

Download details as .txt file:detail.txt file_download

Non phage-like protein
Hypothetical protein
phage system protein ZorA1
phage system protein ZorB1
phage system protein ZorC
phage system protein ZorD

Bacterial, total 137 CDS

#CDS PositionBLAST HitE-ValueSequence
11..1011PP_00001; RepB family plasmid replication initiator protein0.0Showinfo_outline
21729..2469PP_00002; tyrosine-type recombinase/integrase0.0Showinfo_outline
33613..4560PP_00003; sensor domain-containing diguanylate cyclase0.0Showinfo_outline
44587..4898PP_00004; EAL domain-containing protein0.0Showinfo_outline
54918..5886PP_00005; IS5-like element IS903B family transposase0.0Showinfo_outline
66559..6816PP_00006; hypothetical protein0.0Showinfo_outline
77457..7972PP_00007; IS3 family transposase0.0Showinfo_outline
88036..8872PP_00008; EAL domain-containing protein0.0Showinfo_outline
99855..11132PP_00009; DUF2254 domain-containing protein0.0Showinfo_outline
1011195..13192PP_00010; choline BCCT transporter BetT0.0Showinfo_outline
1113344..14041PP_00011; IS1 family transposase0.0Showinfo_outline
1214232..15439PP_00012; IS3 family transposase0.0Showinfo_outline
1315530..16014PP_00013; IS3 family transposase0.0Showinfo_outline
1416030..16572PP_00014; IS3 family transposase0.0Showinfo_outline
1516868..17299PP_00015; silver-binding protein SilE0.0Showinfo_outline
1617550..19025PP_00016; copper/silver sensor histidine kinase SilS0.0Showinfo_outline
1719018..19698PP_00017; copper/silver response regulator transcription factor SilR0.0Showinfo_outline
1819888..21273PP_00018; Cu(+)/Ag(+) efflux RND transporter outer membrane channel SilC0.0Showinfo_outline
1921302..21655PP_00019; cation efflux system protein CusF0.0Showinfo_outline
2021769..23061PP_00020; Cu(+)/Ag(+) efflux RND transporter periplasmic adaptor subunit SilB0.0Showinfo_outline
2123072..26218PP_00021; Cu(+)/Ag(+) efflux RND transporter permease subunit SilA0.0Showinfo_outline
2226305..26745PP_00022; DUF411 domain-containing protein0.0Showinfo_outline
2326872..29319PP_00023; Ag(+)-translocating P-type ATPase SilP0.0Showinfo_outline
2429360..29557PP_00024; DUF2933 domain-containing protein0.0Showinfo_outline
2529591..30328PP_00025; peptidoglycan DD-metalloendopeptidase family protein0.0Showinfo_outline
2630617..31066PP_00026; copper resistance protein0.0Showinfo_outline
2731300..33117PP_00027; multicopper oxidase PcoA0.0Showinfo_outline
2833123..34013PP_00028; copper resistance outer membrane transporter PcoB0.0Showinfo_outline
2934053..34433PP_00029; copper resistance system metallochaperone PcoC0.0Showinfo_outline
3034489..35367PP_00030; copper resistance inner membrane protein PcoD0.0Showinfo_outline
3135422..36102PP_00031; copper response regulator transcription factor PcoR0.0Showinfo_outline
3236099..37499PP_00032; copper resistance membrane spanning protein PcoS0.0Showinfo_outline
3337716..38150PP_00033; copper resistance system metallochaperone PcoE0.0Showinfo_outline
3438382..38561PP_00034; type II toxin-antitoxin system RelE/ParE family toxin0.0Showinfo_outline
3538622..40242PP_00035; IS3 family transposase0.0Showinfo_outline
3640304..40813PP_00036; aquaporin0.0Showinfo_outline
3740863..41360PP_00037; GNAT family N-acetyltransferase0.0Showinfo_outline
3841692..42018PP_00038; helix-turn-helix transcriptional regulator0.0Showinfo_outline
3942015..42728PP_00039; arsenical resistance protein ArsH0.0Showinfo_outline
4042737..43282PP_00040; sigma-70 family RNA polymerase sigma factor0.0Showinfo_outline
4143358..43720PP_00041; arsenic metallochaperone ArsD family protein0.0Showinfo_outline
4243739..45495PP_00042; IS3 family transposase0.0Showinfo_outline
4345617..46153PP_00043; GNAT family N-acetyltransferase0.0Showinfo_outline
4446186..46611PP_00044; glutaredoxin-dependent arsenate reductase0.0Showinfo_outline
4546624..47913PP_00045; arsenite efflux transporter membrane subunit ArsB0.0Showinfo_outline
4647961..49712PP_00046; arsenite efflux transporter ATPase subunit ArsA0.0Showinfo_outline
4749730..50092PP_00047; arsenite efflux transporter metallochaperone ArsD0.0Showinfo_outline
4850142..50492PP_00048; As(III)-sensing metalloregulatory transcriptional repressor ArsR0.0Showinfo_outline
4950850..51119PP_00049; hypothetical protein0.0Showinfo_outline
5051107..51682PP_00050; hypothetical protein0.0Showinfo_outline
5151713..52207PP_00051; DNA-binding protein0.0Showinfo_outline
5252251..52619PP_00052; hypothetical protein0.0Showinfo_outline
5352653..52856PP_00053; HHA domain-containing protein0.0Showinfo_outline
5452905..53162PP_00054; hypothetical protein0.0Showinfo_outline
5553238..53492PP_00055; hypothetical protein0.0Showinfo_outline
5653668..53934PP_00056; DUF1778 domain-containing protein0.0Showinfo_outline
5753922..54404PP_00057; GNAT family N-acetyltransferase0.0Showinfo_outline
5854616..55962PP_00058; ISNCY family transposase0.0Showinfo_outline
5956123..56254PP_00059; hypothetical protein0.0Showinfo_outline
6056463..57628PP_00060; IS3 family transposase0.0Showinfo_outline
6157805..58767PP_00061; zinc metalloprotease HtpX0.0Showinfo_outline
6258754..59242PP_00062; phosphate-starvation-inducible PsiE family protein0.0Showinfo_outline
6359357..59503PP_00063; IS3 family transposase0.0Showinfo_outline
6459741..59938PP_00064; hypothetical protein0.0Showinfo_outline
6559938..62733PP_00065; heat shock survival AAA family ATPase ClpK0.0Showinfo_outline
6662848..63417PP_00066; small heat shock protein sHSP200.0Showinfo_outline
6763452..63733PP_00067; helix-turn-helix domain-containing protein0.0Showinfo_outline
6863977..64240PP_00068; hypothetical protein0.0Showinfo_outline
6964255..64518PP_00069; transposase0.0Showinfo_outline
7064463..64579PP_00070; IS3 family transposase0.0Showinfo_outline
7164764..65461PP_00071; IS1 family transposase0.0Showinfo_outline
7265720..66700PP_00072; IS5-like element ISKpn26 family transposase0.0Showinfo_outline
7367282..67801PP_00073; IS3 family transposase0.0Showinfo_outline
7467909..68778PP_00074; LysR family transcriptional regulator0.0Showinfo_outline
7568772..69782PP_00075; phosphonate dehydrogenase PtxD0.0Showinfo_outline
7669791..70618PP_00076; phosphonate ABC transporter, permease protein PhnE0.0Showinfo_outline
7770627..71490PP_00077; phosphate/phosphite/phosphonate ABC transporter substrate-binding protein0.0Showinfo_outline
7871487..72314PP_00078; phosphonate ABC transporter ATP-binding protein0.0Showinfo_outline
7972656..72964PP_00079; IS3 family transposase0.0Showinfo_outline
8073170..73874PP_00080; IS6-like element IS26 family transposase0.0Showinfo_outline
8174934..76667PP_00081; ABC transporter ATP-binding protein0.0Showinfo_outline
8276675..77622PP_00082; acetamidase/formamidase family protein0.0Showinfo_outline
8377667..79271PP_00083; ABC transporter substrate-binding protein0.0Showinfo_outline
8479284..80204PP_00084; ABC transporter permease0.0Showinfo_outline
8580204..81052PP_00085; ABC transporter permease0.0Showinfo_outline
8681049..81642PP_00086; ANTAR domain-containing response regulator0.0Showinfo_outline
8781639..82766PP_00087; transporter substrate-binding protein0.0Showinfo_outline
8883051..83152PP_00088; IS3 family transposase0.0Showinfo_outline
8983360..83845PP_00089; IS3 family transposase0.0Showinfo_outline
9084115..84184PP_00090; IS3 family transposase0.0Showinfo_outline
9184321..84842PP_00091; RNA polymerase sigma factor FecI0.0Showinfo_outline
9284839..85792PP_00092; ferric citrate uptake sigma factor regulator FecR0.0Showinfo_outline
9385879..88203PP_00093; TonB-dependent Fe(3+) dicitrate receptor FecA0.0Showinfo_outline
9488248..89150PP_00094; Fe(3+) dicitrate ABC transporter substrate-binding protein FecB0.0Showinfo_outline
9589147..90145PP_00095; iron-dicitrate ABC transporter permease FecC0.0Showinfo_outline
9690142..91098PP_00096; Fe(3+) dicitrate ABC transporter permease subunit FecD0.0Showinfo_outline
9791099..91866PP_00097; Fe(3+) dicitrate ABC transporter ATP-binding protein FecE0.0Showinfo_outline
9891965..92258PP_00098; IS66 family insertion sequence element accessory protein TnpB0.0Showinfo_outline
9992333..92560PP_00099; IS3 family transposase0.0Showinfo_outline
10092589..92876PP_00100; EAL domain-containing protein0.0Showinfo_outline
10193210..94220PP_00101; zinc-binding alcohol dehydrogenase family protein0.0Showinfo_outline
10294243..94458PP_00102; hypothetical protein0.0Showinfo_outline
10394681..95763PP_00103; DNA-binding transcriptional repressor LacI0.0Showinfo_outline
10495885..98959PP_00104; beta-galactosidase0.0Showinfo_outline
10599011..100264PP_00105; lactose permease0.0Showinfo_outline
106100330..100470PP_00106; IS3 family transposase0.0Showinfo_outline
107100485..101181PP_00107; IS3 family transposase0.0Showinfo_outline
108101370..101630PP_00108; DUF2534 family protein0.0Showinfo_outline
109101687..103750PP_00109; TonB-dependent copper receptor0.0Showinfo_outline
110103833..104252PP_00110; DUF2946 domain-containing protein0.0Showinfo_outline
111105195..106330PP_00111; IS3-like element ISEc15 family transposase0.0Showinfo_outline
112106716..107036PP_00112; hypothetical protein0.0Showinfo_outline
113107142..108173PP_00113; IS630-like element ISEc33 family transposase0.0Showinfo_outline
114109137..109523PP_00114; IS3 family transposase0.0Showinfo_outline
115109547..110569PP_00115; IS110 family transposase0.0Showinfo_outline
116110990..113566PP_00116; nuclease domain-containing protein0.0Showinfo_outline
117113569..115743PP_00117; AAA family ATPase0.0Showinfo_outline
118116273..117241PP_00118; IS5-like element IS903 family transposase0.0Showinfo_outline
119117579..119768PP_00119; type I Zorya anti-phage system protein ZorA1;phage system protein ZorA10.0Showinfo_outline
120119782..120522PP_00120; type I Zorya anti-phage system protein ZorB1;phage system protein ZorB10.0Showinfo_outline
121120519..122201PP_00121; type I Zorya anti-phage system protein ZorC;phage system protein ZorC0.0Showinfo_outline
122122201..125449PP_00122; type I Zorya anti-phage system protein ZorD;phage system protein ZorD0.0Showinfo_outline
123125557..126630PP_00123; aromatic acid exporter family protein0.0Showinfo_outline
124126896..127393PP_00124; DUF2778 domain-containing protein0.0Showinfo_outline
125127576..128040PP_00125; IS3 family transposase0.0Showinfo_outline
126128095..128487PP_00126; IS3 family transposase0.0Showinfo_outline
127128751..129083PP_00127; helix-turn-helix transcriptional regulator0.0Showinfo_outline
128129089..129802PP_00128; arsenical resistance protein ArsH0.0Showinfo_outline
129129860..130288PP_00129; glutaredoxin-dependent arsenate reductase0.0Showinfo_outline
130130338..131621PP_00130; arsenic transporter0.0Showinfo_outline
131131717..132070PP_00131; metalloregulator ArsR/SmtB family transcription factor0.0Showinfo_outline
132132554..134032PP_00132; SulP family inorganic anion transporter0.0Showinfo_outline
133134051..134878PP_00133; universal stress protein0.0Showinfo_outline
134134950..136146PP_00134; MFS transporter0.0Showinfo_outline
135136675..137049PP_00135; fluoride efflux transporter CrcB0.0Showinfo_outline
136181018..181989PP_00191; ParB/RepB/Spo0J family plasmid partition protein0.0Showinfo_outline
137181989..183155PP_00192; plasmid-partitioning protein SopA0.0Showinfo_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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