Submission Results

Sequence Name: Not Available

GenBank Accession Number: 1532593903 open_in_new

GenInfo (GI) Number: 0000000000 open_in_new

Download Results: 1532593903.PHASTER.zip

gi|00000000|ref|NZ_CP032146.1| Bacillus amyloliquefaciens strain YP6 chromosome, complete genome. 4009619, gc%: 45.92%

Download summary as .txt file: summary.txt file_download

Total: 6 prophage regions have been identified, of which 1 regions are intact, 3 regions are incomplete, and 2 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
134.6Kbquestionable90241124506-1159201 info_outlinePHAGE_Bacill_G_NC_023719(2)45.37%Show info_outline
212Kbincomplete2091153986-1166040 info_outlinePHAGE_Bacill_SPbeta_NC_001884(3)43.12%Show info_outline
332.7Kbincomplete60431207447-1240167 info_outlinePHAGE_Brevib_Jimmer2_NC_041976(9)46.55%Show info_outline
411.4Kbincomplete20121828652-1840133 info_outlinePHAGE_Bacill_PBS1_NC_043027(4)41.91%Show info_outline
5151.9Kbquestionable701882121021-2272972 info_outlinePHAGE_Bacill_SPbeta_NC_001884(77)36.38%Show info_outline
648.9Kbintact100622628798-2677758 info_outlinePHAGE_Bacill_phi105_NC_004167(17)42.98%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.