Submission Results

Sequence Name: Burkholderia mallei JHU, whole genome shotgun sequencing project.

GenBank Accession Number: AAIR00000000.2

GenInfo (GI) Number: 83595722

Download Results: AAIR00000000.2.PHASTER.zip

gi|83595722|ref|AAIR00000000| Burkholderia mallei JHU whole genome shotgun .5713799, gc%: 68.41%

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
14.9Kbincomplete607672770-677689 info_outlinePHAGE_Burkho_263.48%Show info_outline
26.7Kbquestionable80114412330-4419070 info_outlinePROPHAGE_Xantho_3391363.57%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|83595722|ref|AAIR00000000| Burkholderia mallei JHU whole genome shotgun [asmbl_id: NC_000000].5713799, gc%: 68.41%

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
1complement(672770..673600)PROPHAGE_Xantho_33913: IS1477 transposase; PP_00697; phage(gi77747809)4e-88Showinfo_outline
2complement(673627..673890)PROPHAGE_Xantho_33913: IS1477 transposase; PP_00698; phage(gi21230912)6e-28Showinfo_outline
3674698..674994PHAGE_Burkho_2: gp7, putative addiction module killer protein; PP_00699; phage(gi134288691)2e-50Showinfo_outline
4674997..675353PHAGE_Burkho_2: gp6, putative addiction module antidote protein; PP_00700; phage(gi134288715)4e-60Showinfo_outline
5complement(675397..676452)PHAGE_Burkho_2: gp5, phage portal protein, pbsx family; PP_00701; phage(gi134288732)0.0Showinfo_outline
6complement(676449..676763)PHAGE_Burkho_2: gp4, phage terminase, ATPase subunit; PP_00702; phage(gi134288710)1e-55Showinfo_outline
7complement(677072..677147)tRNA0.0Showinfo_outline
8complement(677168..677689)PROPHAGE_Escher_Sakai: ClpXP protease specificity-enhancing factor; PP_00703; phage(gi15833355)3e-24Showinfo_outline

Region 2, total 11 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(4412330..4412524)PHAGE_Ralsto_phiRSA1: transposase IRSO15-like; PP_04560; phage(gi145708108)4e-31Showinfo_outline
2complement(4412631..4413461)PROPHAGE_Xantho_33913: IS1477 transposase; PP_04561; phage(gi77747809)3e-87Showinfo_outline
3complement(4413488..4413751)PROPHAGE_Xantho_33913: IS1477 transposase; PP_04562; phage(gi21230912)6e-28Showinfo_outline
44413847..4414458PHAGE_Staphy_phiPV83: transposase; PP_04563; phage(gi9635722)9e-12Showinfo_outline
5complement(4414571..4415776)lipoprotein [Burkholderia mallei ATCC 23344] gi|53724814|ref|YP_102773.1|; PP_045640.0Showinfo_outline
64415954..4416085hypothetical protein GBP346_A1770 [Burkholderia pseudomallei MSHR346] gi|237812028|ref|YP_002896479.1|; PP_045653e-17Showinfo_outline
74416126..4416326hypothetical protein BPC006_I1797 [Burkholderia pseudomallei BPC006] gi|403518449|ref|YP_006652582.1|; PP_045663e-28Showinfo_outline
84416392..4416655PROPHAGE_Xantho_33913: IS1477 transposase; PP_04567; phage(gi21230912)6e-28Showinfo_outline
94416682..4417512PROPHAGE_Xantho_33913: IS1477 transposase; PP_04568; phage(gi77747809)4e-88Showinfo_outline
104417534..4417857hypothetical protein BMA1084 [Burkholderia mallei ATCC 23344] gi|53724811|ref|YP_102777.1|; PP_045692e-56Showinfo_outline
114417868..4419070PHAGE_Equid__9: envelope glycoprotein J; PP_04570; phage(gi216905924)1e-04Showinfo_outline
Burkholderia mallei JHU 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: 5713799 bps
Phages: 2
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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