Submission Results

Sequence Name: Bacteriophage GA-1 complete genome sequence.

GenBank Accession Number: X96987.2

GenInfo (GI) Number: 12141271

Download Results: X96987.2.PHASTER.zip

gi|00000000|ref|X96987.2| Bacteriophage GA-1 complete genome sequence. 21129, gc%: 34.65%

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
120.7Kbintact15035193-20943 info_outlinePHAGE_Bacill_GA_1_NC_002649(35)34.63%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|X96987.2| Bacteriophage GA-1 complete genome sequence. 21129, gc%: 34.65%

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 35 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(193..519)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248101)3.63e-77Showinfo_outline
2complement(558..647)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248102)3.37e-13Showinfo_outline
3complement(640..963)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248103)4.12e-76Showinfo_outline
4complement(947..1372)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248104)1.25e-98Showinfo_outline
5complement(1372..1542)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248105)4.43e-33Showinfo_outline
6complement(1896..2180)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248106)2.27e-60Showinfo_outline
7complement(2180..2281)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248107)1.71e-15Showinfo_outline
8complement(2282..2674)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248108)1.02e-91Showinfo_outline
9complement(2765..4501)PHAGE_Bacill_GA_1_NC_002649: DNA polymerase; -; phage(gi12248109)0.0Showinfo_outline
10complement(4529..5326)PHAGE_Bacill_GA_1_NC_002649: terminal protein; -; phage(gi12248110)0.0Showinfo_outline
11complement(5197..5601)PHAGE_Bacill_GA_1_NC_002649: transcriptional regulator; -; phage(gi12248111)6.41e-95Showinfo_outline
12complement(5613..6125)PHAGE_Bacill_GA_1_NC_002649: SSB; -; phage(gi12248112)2.44e-122Showinfo_outline
13complement(6230..6511)PHAGE_Bacill_GA_1_NC_002649: dsDNA binding protein; -; phage(gi12248113)2.87e-60Showinfo_outline
146789..7112PHAGE_Bacill_GA_1_NC_002649: scaffolding protein; -; phage(gi12248114)1.57e-71Showinfo_outline
157137..8555PHAGE_Bacill_GA_1_NC_002649: major head protein; -; phage(gi12248115)0.0Showinfo_outline
168574..10412PHAGE_Bacill_GA_1_NC_002649: tail protein; -; phage(gi12248116)0.0Showinfo_outline
1710414..11334PHAGE_Bacill_GA_1_NC_002649: upper collar protein; -; phage(gi12248117)0.0Showinfo_outline
1811279..12142PHAGE_Bacill_GA_1_NC_002649: lower collar protein; -; phage(gi12248118)0.0Showinfo_outline
1912157..14379PHAGE_Bacill_GA_1_NC_002649: neck appendage protein precursor; -; phage(gi12248119)0.0Showinfo_outline
2014381..15448PHAGE_Bacill_GA_1_NC_002649: morphogenesis protein; -; phage(gi12248120)0.0Showinfo_outline
2115464..15865PHAGE_Bacill_GA_1_NC_002649: holin; -; phage(gi12248121)4.01e-90Showinfo_outline
2215858..16577PHAGE_Bacill_GA_1_NC_002649: peptidoglycan hydrolase; -; phage(gi12248122)3.99e-172Showinfo_outline
2316590..17600PHAGE_Bacill_GA_1_NC_002649: DNA encapsidation protein; -; phage(gi12248123)0.0Showinfo_outline
24complement(17624..17815)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248124)4.88e-40Showinfo_outline
25complement(17802..17948)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248125)5.37e-26Showinfo_outline
26complement(17945..18187)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248126)2.15e-52Showinfo_outline
27complement(18190..18591)PHAGE_Bacill_GA_1_NC_002649: 16.7 protein homologue (phi29); -; phage(gi12248127)1.23e-90Showinfo_outline
28complement(18588..18836)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248128)1.54e-52Showinfo_outline
29complement(18890..19240)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248129)1.82e-79Showinfo_outline
30complement(19318..19395)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248130)3.45e-09Showinfo_outline
31complement(19409..19723)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248131)1.90e-73Showinfo_outline
32complement(19717..20022)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248132)3.55e-69Showinfo_outline
33complement(20028..20312)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248133)5.15e-61Showinfo_outline
34complement(20370..20687)PHAGE_Bacill_GA_1_NC_002649: hypothetical protein; -; phage(gi12248134)1.97e-69Showinfo_outline
35complement(20680..20943)PHAGE_Bacill_GA_1_NC_002649: phi29 gene 17 homologue; -; phage(gi12248135)1.60e-59Showinfo_outline
Bacteriophage GA-1 complete genome sequence
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

Viewer Options
Length: 21129 bps
Phages: 1
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Click on a region in the genome above to show details here.
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Click on a sequence to see details.
Lysis
Terminase
Portal Protein
Protease
Coat Protein
Tail Shaft
Attachment Site
Integrase
Phage-like Protein
Hypotheical Protein
Other
Transposase
Fiber Protein
Plate Protein
tRNA

Download data as .txt file: png_input file_download