Submission Results

Sequence Name: Not Available

GenBank Accession Number: CP029898.1

Download Results: CP029898.1.PHASTEST.zip

gi|00000000|ref|NC_000000| Salmonella enterica subsp. enterica serovar Typhi strain 106705, gc%: 50.63%

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
174.8Kbintact110973412-78245 info_outlinePHAGE_Salmon_SSU5_NC_018843(84)50.95%Show info_outline
224.6Kbquestionable902582064-106695 info_outlinePHAGE_Salmon_SSU5_NC_018843(23)49.79%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|CP029898.1| Salmonella enterica subsp. enterica serovar Typhi strain 106705, gc%: 50.63%

Download details as .txt file:detail.txt file_download

Hypothetical protein
Tail protein
Head protein
Portal protein
Terminase
Phage-like protein
DNA Helicase
Repressor
Antirepressor
Exonuclease
Replication protein
Integrase
Holin
Fiber protein

intact

Region 1, total 90 CDS

#CDS PositionBLAST HitE-ValueSequence
13412..3681PP_00001;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188438.48e-50Show info_outline
23762..4079PP_00002;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.98e-68Show info_outline
34139..4885PP_00003;putative tail protein;phage;PHAGE_Rhizob_RHEph10_NC_0342481.58e-22Show info_outline
44960..5343PP_00004;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.09e-89Show info_outline
55345..5818PP_00005;putative head-to-tail joining protein;phage;PHAGE_Rhizob_RHEph10_NC_0342482.61e-07Show info_outline
65809..6153PP_00006;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188432.15e-77Show info_outline
76251..7084PP_00007;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
87084..7518PP_00008;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.55e-100Show info_outline
97562..8485PP_00009;tail assembly protein;phage;PHAGE_Salmon_SE4_NC_0487642.26e-33Show info_outline
108560..9435PP_00010;putative major capsid protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
119462..10358PP_00011;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
1210381..11955PP_00012;putative phage portal protein;phage;PHAGE_Rhizob_RHEph10_NC_0342484.64e-170Show info_outline
1311989..13245PP_00013;putative terminase large subunit;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
1413248..13889PP_00014;putative DNA-binding protein;phage;PHAGE_Salmon_SSU5_NC_0188432.61e-149Show info_outline
1514085..14351PP_00015;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.49e-57Show info_outline
1614361..15260PP_00016;putative ABC transporter ATP-binding protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
1715257..15511PP_00017;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.6e-55Show info_outline
1815504..16142PP_00018;putative ABC transporter ATP-binding protein;phage;PHAGE_Salmon_SSU5_NC_0188437.99e-153Show info_outline
1916139..16807PP_00019;putative ParB-like nuclease domain-containing protein;phage;PHAGE_Salmon_SSU5_NC_0188431.19e-156Show info_outline
2016807..17487PP_00020;putative ParB-like nuclease domain-containing protein;phage;PHAGE_Salmon_SSU5_NC_0188432.19e-163Show info_outline
2117570..19129PP_00021;putative helicase;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
2219132..19410PP_00022;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188439.43e-60Show info_outline
2319470..19892PP_00023;putative lipoprotein;phage;PHAGE_Salmon_SSU5_NC_0188431.49e-86Show info_outline
2419897..20424PP_00024;putative repressor of phase 1 flagellin;phage;PHAGE_Salmon_SSU5_NC_0188435.79e-104Show info_outline
2521059..21709PP_00025;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.23e-155Show info_outline
2621794..22021PP_00026;hypothetical protein;phage;PHAGE_Pseudo_Zigelbrucke_NC_0419042.69e-09Show info_outline
2722653..23135PP_00027;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188432.29e-113Show info_outline
2823341..23628PP_00028;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188435.91e-61Show info_outline
2923749..24141PP_00029;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188432.54e-57Show info_outline
3024270..24581PP_00030;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188434.87e-65Show info_outline
3125067..25285PP_00032;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188434.16e-45Show info_outline
3225296..25511PP_00033;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.19e-44Show info_outline
3325654..25899PP_00034;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188436.02e-49Show info_outline
3427336..28526PP_00035;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188436.29e-155Show info_outline
3528536..28853PP_00036;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188434.39e-59Show info_outline
3628938..29219PP_00037;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.03e-40Show info_outline
3729393..29596PP_00038;putative selenium-binding protein YdfZ;phage;PHAGE_Salmon_SSU5_NC_0188431.77e-41Show info_outline
3829657..29944PP_00039;hypothetical protein;phage;PHAGE_Escher_HK75_NC_0161601.83e-34Show info_outline
3930261..30803PP_00041;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188435.88e-118Show info_outline
4030800..31441PP_00042;putative guanosine polyphosphate pyrophospho hydrolase/synthetase;phage;PHAGE_Salmon_SSU5_NC_0188431.2e-155Show info_outline
4131533..31904PP_00043;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188435.4e-86Show info_outline
4232015..32188PP_00044;putative Eaa protein;phage;PHAGE_Salmon_SSU5_NC_0188435.52e-35Show info_outline
4332185..32874PP_00045;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188439.47e-166Show info_outline
4432933..34636PP_00046;putative DNA modification methylase;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
4534760..35332PP_00047;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188433.62e-136Show info_outline
4635441..36283PP_00048;putative phage antirepressor family protein;phage;PHAGE_Salmon_SSU5_NC_0188432.7e-92Show info_outline
4736392..36580PP_00049;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.1e-35Show info_outline
4836590..37084PP_00050;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188432.33e-103Show info_outline
4937227..37835PP_00051;putative ribonuclease H;phage;PHAGE_Salmon_SSU5_NC_0188433.38e-151Show info_outline
5038421..38651PP_00052;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188432.41e-50Show info_outline
5138854..39447PP_00053;putative N-6-adenine-methyltransferase;phage;PHAGE_Salmon_SSU5_NC_0188436.73e-144Show info_outline
5239632..40558PP_00054;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
5340603..41160PP_00055;putative exonuclease;phage;PHAGE_Salmon_SSU5_NC_0188431.66e-133Show info_outline
5441170..41589PP_00056;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188434.78e-95Show info_outline
5541653..42297PP_00057;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188438.02e-156Show info_outline
5642297..42773PP_00058;putative dihydrofolate reductase;phage;PHAGE_Salmon_SSU5_NC_0188431.22e-114Show info_outline
5742770..43183PP_00059;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.41e-92Show info_outline
5843185..44300PP_00060;putative thymidylate synthase;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
5944416..45345PP_00061;putative phosphoribosyl-ATP pyrophosphohydrolase-like domain-containing protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
6045428..46570PP_00062;putative ribonucleotide-diphosphate reductase, beta subunit;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
6146678..48993PP_00063;putative ribonucleotide-diphosphate reductase, alpha subunit;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
6249071..49640PP_00064;putative ribonuclease H-like domain-containing protein;phage;PHAGE_Salmon_SSU5_NC_0188438.21e-139Show info_outline
6349653..50399PP_00065;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
6450389..52305PP_00066;putative exonuclease subunit 2;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
6552302..52538PP_00067;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188435.69e-39Show info_outline
6652535..53620PP_00068;putative exonuclease subunit 1;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
6754047..54352PP_00069;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188434.75e-67Show info_outline
6854384..54878PP_00070;putative GNAT family acetyltransferase;phage;PHAGE_Salmon_SSU5_NC_0188435.71e-118Show info_outline
6954954..55598PP_00071;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.33e-155Show info_outline
7056343..57398PP_00072;putative replication protein RepA;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
7157927..58130PP_00073;putative Cre-associated protein;phage;PHAGE_Salmon_SSU5_NC_0188432.57e-39Show info_outline
7258130..58435PP_00074;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188434.18e-43Show info_outline
7358476..58751PP_00075;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.86e-59Show info_outline
7458820..59230PP_00076;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188437.63e-95Show info_outline
7559214..59585PP_00077;putative NinX-like protein;phage;PHAGE_Salmon_SSU5_NC_0188431.17e-88Show info_outline
7659748..60590PP_00078;putative SPFH domain / band 7 protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
7760886..61962PP_00079;putative RecA-like recombinase;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
7861965..62231PP_00080;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188432.77e-57Show info_outline
7962231..63175PP_00081;DNA polymerase I;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
8063236..64264PP_00082;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
8164384..64815PP_00083;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188434.76e-101Show info_outline
8265745..66188PP_00085;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188435.27e-98Show info_outline
8366185..69703PP_00086;DNA polymerase III alpha subunit;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
8469884..71119PP_00087;putative porphyrin biosynthetic protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
8571216..73573PP_00088;putative porphyrin biosynthetic protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
8674157..74543PP_00090;hypothetical protein;phage;PHAGE_Rhizob_RHEph10_NC_0342484.72e-10Show info_outline
8774535..75425PP_00091;bacteriophage integrase protein;phage;PHAGE_Phage_Gifsy_1_NC_0103921.78e-21Show info_outline
8876558..76803PP_00095;putative glutaredoxin;phage;PHAGE_Pseudo_OBP_NC_0165711.83e-14Show info_outline
8976803..77183PP_00096;hypothetical protein;phage;PHAGE_Shigel_Sf6_NC_0053448.75e-53Show info_outline
9077412..78245PP_00097;PhoH;phage;PHAGE_Erwini_PhiEaH1_NC_0236103.75e-119Show info_outline

questionable

Region 2, total 24 CDS

#CDS PositionBLAST HitE-ValueSequence
182064..82369PP_00101;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.26e-66Show info_outline
282366..82518PP_00102;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188433.29e-27Show info_outline
382518..82724PP_00103;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188435.99e-44Show info_outline
482890..84212PP_00104;putative DNA ligase;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
584247..84504PP_00105;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.32e-50Show info_outline
684805..85599PP_00106;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
785783..86835PP_00107;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.44e-120Show info_outline
886837..88048PP_00108;putative DNA primase;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
988111..89451PP_00109;putative DNA helicase;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
1089512..90237PP_00110;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188431.76e-178Show info_outline
1190515..91570PP_00111;hypothetical protein;phage;PHAGE_Vibrio_1.202.O._10N.222.45.E8_NC_0480669.15e-76Show info_outline
1291640..92395PP_00112;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188433.14e-69Show info_outline
1392444..92803PP_00113;hypothetical protein;phage;PHAGE_Salmon_SSU5_NC_0188438.83e-64Show info_outline
1492803..93468PP_00114;putative ParA family protein;phage;PHAGE_Salmon_SSU5_NC_0188438.67e-148Show info_outline
1594401..94745PP_00116;putative Rz1 protein;phage;PHAGE_Salmon_SSU5_NC_0188433.64e-37Show info_outline
1694814..95533PP_00117;putative endolysin;phage;PHAGE_Salmon_SSU5_NC_0188431.61e-162Show info_outline
1795520..95843PP_00118;putative holin;phage;PHAGE_Salmon_SSU5_NC_0188433.08e-71Show info_outline
1895958..98510PP_00119;tail fiber protein;phage;PHAGE_Citrob_Stevie_NC_0273509.07e-180Show info_outline
1998593..102981PP_00120;putative phage tail protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
20102996..103583PP_00121;putative phage tail protein;phage;PHAGE_Salmon_SSU5_NC_0188431.48e-135Show info_outline
21103571..104368PP_00122;putative phage tail protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline
22104361..105092PP_00123;putative minor tail protein L;phage;PHAGE_Salmon_SSU5_NC_0188431.73e-175Show info_outline
23105149..105484PP_00124;putative minor tail protein M;phage;PHAGE_Salmon_SSU5_NC_0188438.54e-77Show info_outline
24105526..106695PP_00125;putative tail tape measure protein;phage;PHAGE_Salmon_SSU5_NC_0188430.0Show info_outline

gi|00000000|ref|CP029898.1| Salmonella enterica subsp. enterica serovar Typhi strain 106705, gc%: 50.63%

Download details as .txt file:detail.txt file_download

Hypothetical protein

Bacterial, total 3 CDS

#CDS PositionBLAST HitE-ValueSequence
178299..78853PP_00098; hypothetical protein0.0Showinfo_outline
279131..79685PP_00099; hypothetical protein0.0Showinfo_outline
379764..80492PP_00100; 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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