Submission Results

Sequence Name: Not Available

GenBank Accession Number: NZ_RBRE01000044.1

Download Results: NZ_RBRE01000044.1.PHASTEST.zip

gi|00000000|ref|NC_000000| Pseudomonas cichorii strain ICMP 3353 PchICMP3353_Contig_24, whole 88249, gc%: 57.91%

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
146.8Kbintact1505540979-87825 info_outlinePHAGE_Vibrio_VP58.5_NC_027981(7)57.53%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|NZ_RBRE01000044.1| Pseudomonas cichorii strain ICMP 3353 PchICMP3353_Contig_24, whole 88249, gc%: 57.91%

Download details as .txt file:detail.txt file_download

Phage-like protein
Integrase
Hypothetical protein
Head protein
Regulatory protein
Lysis protein
Terminase
Portal protein
Tail protein
Plate protein
Fiber protein

intact

Region 1, total 34 CDS

#CDS PositionBLAST HitE-ValueSequence
148092..48427PP_00044;sulfur transfer protein, DsrC;phage;PHAGE_Podovi_Lau218_NC_0243297.32e-07Show info_outline
250605..51672PP_00049;Integrase;phage;PHAGE_Pseudo_F10_NC_0078058.02e-123Show info_outline
351676..51924PP_00050;hypothetical protein;phage;PHAGE_Pseudo_F10_NC_0078057.26e-25Show info_outline
451921..53009PP_00051;DNA methyltransferase;phage;PHAGE_Pseudo_phiPSA1_NC_0243653.07e-161Show info_outline
553173..53850PP_00052;capsid scaffolding protein;phage;PHAGE_Pectob_DU_PP_V_NC_0478871.37e-07Show info_outline
653847..55469PP_00053;hypothetical protein;phage;PHAGE_Pseudo_phiCTX_NC_0032780.0Show info_outline
757093..57410PP_00058;excisionase;phage;PHAGE_Burkho_AH2_NC_0182838.75e-07Show info_outline
859066..59848PP_00062;HTH-type transcriptional regulator PrtR;phage;PHAGE_Pseudo_phi2_NC_0309319.63e-58Show info_outline
960524..61042PP_00064;gp14;phage;PHAGE_Burkho_Bcep176_NC_0074973.75e-10Show info_outline
1061035..61259PP_00065;hypothetical protein;phage;PHAGE_Erwini_ENT90_NC_0199329.44e-14Show info_outline
1161249..63465PP_00066;primase;phage;PHAGE_Escher_vB_EcoM_ep3_NC_0254305.35e-76Show info_outline
1264389..64706PP_00069;bacteriophage lysis protein;holin;phage;PHAGE_Salmon_Fels_1_NC_0103916.33e-15Show info_outline
1366022..68049PP_00073;large terminase subunit;phage;PHAGE_Synech_S_CBS3_NC_0154655.83e-139Show info_outline
1468254..69735PP_00075;portal protein;phage;PHAGE_Vibrio_vB_VpaM_MAR_NC_0197228.43e-103Show info_outline
1569732..70877PP_00076;head maturation protease;phage;PHAGE_Entero_c_1_NC_0197067.92e-44Show info_outline
1670880..71227PP_00077;head decoration protein D;phage;PHAGE_Aurant_AmM_1_NC_0273343.95e-15Show info_outline
1771291..72292PP_00078;major capsid protein;phage;PHAGE_Rheinh_vB_RspM_Barba19A_NC_0481903.19e-28Show info_outline
1872606..73256PP_00080;gp09 protein;phage;PHAGE_Vibrio_VP58.5_NC_0279811.29e-13Show info_outline
1973249..73761PP_00081;putative minor tail protein;phage;PHAGE_Entero_Arya_NC_0310487.64e-11Show info_outline
2073758..74324PP_00082;phage baseplate assembly protein V;phage;PHAGE_Burkho_ST79_NC_0213438.0e-20Show info_outline
2174621..74947PP_00084;baseplate assembly protein;phage;PHAGE_Vibrio_vB_VpaM_MAR_NC_0197222.28e-28Show info_outline
2274944..75825PP_00085;baseplate assembly protein;phage;PHAGE_Pseudo_Dobby_NC_0481095.5e-89Show info_outline
2375827..76432PP_00086;tail protein I;phage;PHAGE_Pseudo_Dobby_NC_0481099.97e-88Show info_outline
2476429..77778PP_00087;tail fiber protein;phage;PHAGE_Pseudo_Dobby_NC_0481095.46e-71Show info_outline
2577793..78227PP_00088;tail protein;phage;PHAGE_Pseudo_Dobby_NC_0481093.06e-26Show info_outline
2678322..79482PP_00089;tail sheath protein;phage;PHAGE_Vibrio_vB_VpaM_MAR_NC_0197225.69e-104Show info_outline
2779495..80004PP_00090;tail protein;phage;PHAGE_Escher_vB_EcoM_ep3_NC_0254301.23e-44Show info_outline
2880040..80312PP_00091;hypothetical protein;phage;PHAGE_Pseudo_PPpW_3_NC_0230067.46e-13Show info_outline
2980454..83165PP_00092;bacteriophage tail length determination protein;phage;PHAGE_Haemop_SuMu_NC_0194555.72e-16Show info_outline
3083175..84020PP_00093;putative tail protein;phage;PHAGE_Vibrio_vB_VpaM_MAR_NC_0197227.75e-28Show info_outline
3183995..84201PP_00094;putative tail protein X;phage;PHAGE_Entero_Arya_NC_0310481.38e-12Show info_outline
3285237..86280PP_00096;gene D protein;phage;PHAGE_Salmon_RE_2010_NC_0194883.37e-60Show info_outline
3386307..86852PP_00097;glycoside hydrolase family 19 protein;phage;PHAGE_Pseudo_phiPSA1_NC_0243652.09e-80Show info_outline
3487031..87825PP_00098;DNA adenine methylase gp25;phage;PHAGE_Burkho_KS9_NC_0130551.45e-124Show info_outline

gi|00000000|ref|NZ_RBRE01000044.1| Pseudomonas cichorii strain ICMP 3353 PchICMP3353_Contig_24, whole 88249, gc%: 57.91%

Download details as .txt file:detail.txt file_download

Non phage-like protein

Bacterial, total 37 CDS

#CDS PositionBLAST HitE-ValueSequence
1110..466PP_00001; 6-carboxytetrahydropterin synthase QueD0.0Showinfo_outline
2653..961PP_00002; PepSY domain-containing protein0.0Showinfo_outline
3961..1269PP_00003; PepSY domain-containing protein0.0Showinfo_outline
41269..1937PP_00004; response regulator transcription factor0.0Showinfo_outline
51934..3256PP_00005; sensor histidine kinase0.0Showinfo_outline
63374..5053PP_00006; methyl-accepting chemotaxis protein0.0Showinfo_outline
75151..6608PP_00007; NADH-quinone oxidoreductase subunit NuoN0.0Showinfo_outline
86616..8148PP_00008; NADH-quinone oxidoreductase subunit M0.0Showinfo_outline
98188..10041PP_00009; NADH-quinone oxidoreductase subunit L0.0Showinfo_outline
1010038..10346PP_00010; NADH-quinone oxidoreductase subunit NuoK0.0Showinfo_outline
1110343..10852PP_00011; NADH-quinone oxidoreductase subunit J0.0Showinfo_outline
1210863..11411PP_00012; NADH-quinone oxidoreductase subunit NuoI0.0Showinfo_outline
1311423..12430PP_00013; NADH-quinone oxidoreductase subunit NuoH0.0Showinfo_outline
1412427..15141PP_00014; NADH-quinone oxidoreductase subunit NuoG0.0Showinfo_outline
1515276..16631PP_00015; NADH-quinone oxidoreductase subunit NuoF0.0Showinfo_outline
1616628..17125PP_00016; NADH-quinone oxidoreductase subunit NuoE0.0Showinfo_outline
1717128..18909PP_00017; NADH-quinone oxidoreductase subunit C/D0.0Showinfo_outline
1818983..19657PP_00018; NADH-quinone oxidoreductase subunit B family protein0.0Showinfo_outline
1919668..20081PP_00019; NADH-quinone oxidoreductase subunit A0.0Showinfo_outline
2020535..21860PP_00020; isocitrate lyase0.0Showinfo_outline
2122364..23104PP_00021; secretin N-terminal domain-containing protein0.0Showinfo_outline
2223290..23712PP_00022; GNAT family N-acetyltransferase0.0Showinfo_outline
2323705..24871PP_00023; cupin domain-containing protein0.0Showinfo_outline
2424932..26302PP_00024; adenylosuccinate lyase0.0Showinfo_outline
2526433..27053PP_00025; high frequency lysogenization protein HflD0.0Showinfo_outline
2627053..28183PP_00026; tRNA 2-thiouridine(34) synthase MnmA0.0Showinfo_outline
2728244..28690PP_00027; NUDIX hydrolase0.0Showinfo_outline
2828830..31055PP_00028; NADP-dependent isocitrate dehydrogenase0.0Showinfo_outline
2931573..32829PP_00029; NADP-dependent isocitrate dehydrogenase0.0Showinfo_outline
3032909..33181PP_00030; cold shock domain-containing protein CspD0.0Showinfo_outline
3133406..33768PP_00031; ATP-dependent Clp protease adapter ClpS0.0Showinfo_outline
3233799..36072PP_00032; ATP-dependent Clp protease ATP-binding subunit ClpA0.0Showinfo_outline
3336165..36383PP_00033; translation initiation factor IF-10.0Showinfo_outline
3436485..37192PP_00034; arginyltransferase0.0Showinfo_outline
3537241..37930PP_00035; leucyl/phenylalanyl-tRNA--protein transferase0.0Showinfo_outline
3638425..40833PP_00036; DNA translocase FtsK0.0Showinfo_outline
3740903..41526PP_00037; outer membrane lipoprotein chaperone LolA0.0Showinfo_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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