Submission Results

Sequence Name: Brevibacterium linens BL2, whole genome shotgun sequencing project.

GenBank Accession Number: AAGP00000000.1

GenInfo (GI) Number: 62362144

Download Results: AAGP00000000.1.PHASTER.zip

gi|62362144|ref|AAGP00000000| Brevibacterium linens BL2 , whole genome shotgun .4366969, gc%: 62.77%

Download summary as .txt file: summary.txt file_download

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

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
116.4Kbincomplete206739244-755656 info_outlinePHAGE_Entero_phiEF24C62.21%Show info_outline
27.9Kbincomplete4082834336-2842263 info_outlinePROPHAGE_Escher_CFT07360.89%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|62362144|ref|AAGP00000000| Brevibacterium linens BL2 , whole genome shotgun [asmbl_id: NC_000000].4366969, gc%: 62.77%

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 8 CDS

#CDS PositionBLAST HitE-ValueSequence
1739244..739258attL0.0Showinfo_outline
2complement(745605..746600)PHAGE_Acidia_virus: hypothetical protein ATV_gp66; PP_00673; phage(gi75750456)4e-08Showinfo_outline
3747189..747437PHAGE_Rhodoc_REQ2: hypothetical protein; PP_00674; phage(gi372449877)2e-11Showinfo_outline
4747439..747852PHAGE_Staphy_JD007: ribonucleotide reductase stimulatory protein; PP_00675; phage(gi428783205)4e-13Showinfo_outline
5747822..749984PHAGE_Entero_phiEF24C: putative ribonucleotide reductase; PP_00676; phage(gi158079505)0.0Showinfo_outline
6750130..751110PHAGE_Mycoba_Myrna: gp256; PP_00677; phage(gi203454817)3e-142Showinfo_outline
7751476..752792PHAGE_Mycoba_SWU1: integrase; PP_00678; phage(gi388570553)1e-21Showinfo_outline
8755656..755670attR0.0Showinfo_outline

Region 2, total 8 CDS

#CDS PositionBLAST HitE-ValueSequence
12834336..2835706PHAGE_Singap_iridovirus: hypothetical protein ORF141R; PP_02607; phage(gi56692778)1e-05Showinfo_outline
22835962..2836573PHAGE_Staphy_phi5967PVL: S14 family endopeptidase ClpP; PP_02608; phage(gi431810271)5e-15Showinfo_outline
32836609..2837241PHAGE_Staphy_phi5967PVL: S14 family endopeptidase ClpP; PP_02609; phage(gi431810271)2e-10Showinfo_outline
42837489..2838808PROPHAGE_Escher_Sakai: ATP-dependent protease ATP-binding subunit HslU; PP_02610; phage(gi15834112)1e-16Showinfo_outline
52838973..2839203PROPHAGE_Escher_CFT073: transposase insF; PP_02611; phage(gi26249410)2e-07Showinfo_outline
6complement(2839187..2839771)Conserved protein of unknown function [Mycobacterium canettii CIPT 140070017] gi|433636653|ref|YP_007270280.1|; PP_026128e-59Showinfo_outline
72839970..2841520ABC-type phosphate transport system, ATPase component [Corynebacterium callunae DSM 20147] gi|470159966|ref|YP_007531895.1|; PP_026130.0Showinfo_outline
82841517..2842263PROPHAGE_Escher_CFT073: transposase/IS protein; PP_02614; phage(gi26248359)2e-07Showinfo_outline
Brevibacterium linens BL2 , whole genome shotgun
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 4366969 bps
Phages: 2
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Click on a region in the genome above to show details here.
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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