Submission Results

Sequence Name: Not Available

GenBank Accession Number: 1027763306

GenInfo (GI) Number: 0000000000

Download Results:

gi|00000000|ref|NZ_LXOM01000222.1| Salmonella enterica strain CU013109 PROKKA_contig000224, whole 382780, gc%: 52.20%

Download summary as .txt file: summary.txt file_download

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

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
139.9Kbquestionable8031208726-248655 info_outlinePHAGE_Phage_Gifsy_2_NC_010393(18)51.12%Show info_outline
28.3Kbincomplete6012257793-266144 info_outlinePHAGE_Phage_Gifsy_2_NC_010393(3)46.05%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_LXOM01000222.1| Salmonella enterica strain CU013109 PROKKA_contig000224, whole 382780, gc%: 52.20%

Download details as .txt file: detail.txt file_download

Hits against Virus and Prophage Database
Hits against Bacterial Database or GenBank File

Region 1, total 33 CDS

#CDS PositionBLAST HitE-ValueSequence
2complement(220741..221943)PHAGE_Agroba_Atu_ph07_NC_042013: hypothetical protein; A7K97_RS20510; phage(gi100242)1.94e-49Showinfo_outline
3complement(222138..223430)PHAGE_Phage_Gifsy_2_NC_010393: bacteriophage integrase; A7K97_RS20515; phage(gi169257268)0.0Showinfo_outline
4complement(223475..223723)PHAGE_Phage_Gifsy_2_NC_010393: bacteriophage excisionase; A7K97_RS20520; phage(gi169257269)2.25e-55Showinfo_outline
5complement(223764..224003)PHAGE_Phage_Gifsy_2_NC_010393: hypothetical protein; A7K97_RS20525; phage(gi169257270)1.91e-52Showinfo_outline
6complement(224046..225205)PHAGE_Phage_Gifsy_2_NC_010393: conserved hypothetical bacteriophage protein; A7K97_RS20530; phage(gi169257271)1.25e-72Showinfo_outline
7complement(225168..228356)PHAGE_Phage_Gifsy_2_NC_010393: putatitive bacteriophage exodeoxyribonuclease VIII; A7K97_RS20535; phage(gi169257272)0.0Showinfo_outline
8complement(228497..228667)PHAGE_Phage_Gifsy_2_NC_010393: hypothetical protein; A7K97_RS28415; phage(gi169257274)1.00e-13Showinfo_outline
9complement(229066..229470)PHAGE_Phage_Gifsy_2_NC_010393: putative bacteriophage regulatory protein; repressor; Lambda gpCI analog; A7K97_RS20545; phage(gi169257276)2.39e-18Showinfo_outline
10229600..229836PHAGE_Phage_Gifsy_2_NC_010393: putative bacteriophage regulatory protein; Lambda gpCro analog; A7K97_RS26990; phage(gi169257277)9.25e-17Showinfo_outline
11229802..230176PHAGE_Phage_Gifsy_2_NC_010393: bacteriophage transcriptional activator; Lambda gpCII analog; A7K97_RS20550; phage(gi169257278)6.23e-72Showinfo_outline
12230261..231244PHAGE_Phage_Gifsy_2_NC_010393: bacteriophage DNA replication protein; Lambda gpo homolog; A7K97_RS20555; phage(gi169257279)0.0Showinfo_outline
13231247..231996PHAGE_Phage_Gifsy_2_NC_010393: bacteriophage DNA replication protein; A7K97_RS20560; phage(gi169257280)0.0Showinfo_outline
14232007..232354PHAGE_Phage_Gifsy_2_NC_010393: hypothetical protein; A7K97_RS20565; phage(gi169257281)5.91e-79Showinfo_outline
15232351..232875PHAGE_Phage_Gifsy_2_NC_010393: conserved hypothetical bacteriophage protein; A7K97_RS20570; phage(gi169257282)7.32e-44Showinfo_outline
16232875..233348PHAGE_Gordon_Nymphadora_NC_031061: capsid maturation protease; A7K97_RS20575; phage(gi100067)5.88e-68Showinfo_outline
17233352..233924PHAGE_Salmon_ST64T_NC_004348: hypothetical protein; A7K97_RS20580; phage(gi24371543)7.39e-66Showinfo_outline
18234440..234679PHAGE_Phage_Gifsy_2_NC_010393: bacteriophage damage-inducible protein DinI; A7K97_RS20590; phage(gi169257284)3.26e-50Showinfo_outline
19234735..234974PHAGE_Salmon_SPN3UB_NC_019545: hypothetical protein; A7K97_RS20595; phage(gi423262436)3.00e-53Showinfo_outline
20235014..235616PHAGE_Phage_Gifsy_2_NC_010393: hypothetical protein; A7K97_RS20600; phage(gi169257286)9.08e-145Showinfo_outline
21235825..236436PHAGE_Phage_Gifsy_2_NC_010393: NinG; A7K97_RS20610; phage(gi169257288)7.98e-144Showinfo_outline
22236433..236579PHAGE_Phage_Gifsy_2_NC_010393: hypothetical protein; A7K97_RS27695; phage(gi169257289)1.76e-26Showinfo_outline
23236569..237366PHAGE_Phage_Gifsy_2_NC_010393: prophage antitermination protein; late gene regulator; Lamba gpQ homolog; A7K97_RS20620; phage(gi169257290)0.0Showinfo_outline
24237771..238112PHAGE_Entero_SfV_NC_003444: holin; A7K97_RS20625; phage(gi19549036)1.83e-48Showinfo_outline
25238115..238729PHAGE_Salmon_118970_sal3_NC_031940: portal protein; A7K97_RS20630; phage(gi100069)1.35e-88Showinfo_outline
26238726..239277PROPHAGE_Salmon_LT2: phage-tail assembly-like protein; A7K97_RS20635; phage(gi16765210)1.97e-17Showinfo_outline
27239267..239680hypothetical protein; A7K97_RS206400.0Showinfo_outline
28239742..240716PHAGE_Burkho_BcepMigl_NC_019917: terminase small subunit; A7K97_RS20645; phage(gi431809885)3.39e-46Showinfo_outline
29240706..241977PHAGE_Salmon_SSU5_NC_018843: putative terminase large subunit; A7K97_RS20650; phage(gi410491412)5.86e-16Showinfo_outline
30241977..243407DUF1073 domain-containing protein; A7K97_RS206550.0Showinfo_outline
31243379..244254hypothetical protein; A7K97_RS206600.0Showinfo_outline
32244255..245829PHAGE_Burkho_Bcep1_NC_005263: gp18; A7K97_RS20665; phage(gi38638625)2.48e-22Showinfo_outline

Region 2, total 12 CDS

#CDS PositionBLAST HitE-ValueSequence
1257793..259019PHAGE_Vibrio_CP_T1_NC_019457: putative baseplate protein; A7K97_RS20745; phage(gi418489249)1.11e-06Showinfo_outline
2259003..259629hypothetical protein; A7K97_RS207500.0Showinfo_outline
3259626..261335PHAGE_Phage_Gifsy_2_NC_010393: bacteriophage side tail fiber protein; Lambda gpStf (gpN) homolog; A7K97_RS20755; phage(gi169257320)0.0Showinfo_outline
4261335..261916PHAGE_Phage_Gifsy_2_NC_010393: bacteriophage side tail fiber assembly protein; Lambda gpTfa analog; A7K97_RS20760; phage(gi169257321)1.16e-142Showinfo_outline
5complement(261920..262135)PHAGE_Salmon_SJ46_NC_031129: holin; A7K97_RS26995; phage(gi100034)8.16e-25Showinfo_outline
6262139..262225phage tail protein; A7K97_RS270000.0Showinfo_outline
7262394..263362PHAGE_Phage_Gifsy_2_NC_010393: prophage virulence determinant; secreted effector protein; A7K97_RS20765; phage(gi169257322)0.0Showinfo_outline
8263460..263878PHAGE_Stx2_c_Stx2a_F451_NC_049924: tail assembly protein; A7K97_RS27700; phage(gi100053)1.18e-05Showinfo_outline
9complement(264010..264636)PHAGE_Erwini_vB_EhrS_59_NC_048198: holin; A7K97_RS20775; phage(gi100034)1.82e-90Showinfo_outline
10complement(264705..265011)hypothetical protein; A7K97_RS270050.0Showinfo_outline
11complement(264996..265682)hypothetical protein; A7K97_RS207850.0Showinfo_outline
12complement(265953..266144)PHAGE_Entero_mEp390_NC_019721: DinI-like family protein; A7K97_RS20790; phage(gi428782688)3.35e-33Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 382780 bps
Phages: 2
Click on a region in the genome above to show details here.
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Click on a sequence to see details.
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Click on a sequence to see details.
Portal Protein
Coat Protein
Tail Shaft
Attachment Site
Phage-like Protein
Hypotheical Protein
Fiber Protein
Plate Protein

Download data as .txt file: png_input file_download