Submission Results

Sequence Name: Not Available

GenBank Accession Number: NZ_WMCJ01000032.1

Download Results: NZ_WMCJ01000032.1.PHASTEST.zip

gi|00000000|ref|NC_000000| Xanthomonas perforans strain BAV6163 32, whole genome shotgun 13537, gc%: 63.06%

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
113.5Kbintact140181-13537 info_outlinePHAGE_Stenot_Smp131_NC_023588(14)63.06%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_WMCJ01000032.1| Xanthomonas perforans strain BAV6163 32, whole genome shotgun 13537, gc%: 63.06%

Download details as .txt file:detail.txt file_download

Phage-like protein
Tail protein
Plate protein
Hypothetical protein
Fiber protein

intact

Region 1, total 16 CDS

#CDS PositionBLAST HitE-ValueSequence
11..115PP_00001;phage late gene control protein;phage;PHAGE_Stenot_Smp131_NC_0235883.01e-10Show info_outline
2112..513PP_00002;phage tail protein;phage;PHAGE_Stenot_Smp131_NC_0235881.11e-52Show info_outline
3526..3396PP_00003;phage tail tape measure protein;phage;PHAGE_Stenot_Smp131_NC_0235880.0Show info_outline
43426..3539PP_00004;tail protein;phage;PHAGE_Klebsi_ST147_VIM1phi7.1_NC_0494511.04e-10Show info_outline
53548..3850PP_00005;tail protein;phage;PHAGE_Stenot_Smp131_NC_0235881.14e-35Show info_outline
63896..4405PP_00006;tail core protein;phage;PHAGE_Stenot_Smp131_NC_0235882.99e-97Show info_outline
74435..5601PP_00007;tail sheath protein;phage;PHAGE_Erwini_ENT90_NC_0199323.84e-164Show info_outline
85613..5972PP_00008;baseplate assembly protein;phage;PHAGE_Stenot_Smp131_NC_0235884.23e-47Show info_outline
95969..6532PP_00009;baseplate assembly protein;phage;PHAGE_Stenot_Smp131_NC_0235885.98e-46Show info_outline
106676..7350PP_00010;hypothetical protein;phage;PHAGE_Stenot_Smp131_NC_0235884.09e-13Show info_outline
117725..9524PP_00012;putative phage tail fiber protein;phage;PHAGE_Stenot_Smp131_NC_0235881.17e-97Show info_outline
129537..10082PP_00013;baseplate assembly protein;phage;PHAGE_Stenot_Smp131_NC_0235882.54e-64Show info_outline
1310075..10965PP_00014;baseplate assembly protein;phage;PHAGE_Stenot_Smp131_NC_0235881.84e-106Show info_outline
1412470..12919PP_00016;tail completion protein;phage;PHAGE_Stenot_Smp131_NC_0235882.3e-46Show info_outline
1512907..13326PP_00017;predicted tail completion;phage;PHAGE_Pseudo_phiCTX_NC_0032783.62e-43Show info_outline
1613323..13537PP_00018;gp31;phage;PHAGE_Burkho_KS5_NC_0152652.87e-05Show info_outline

gi|00000000|ref|NZ_WMCJ01000032.1| Xanthomonas perforans strain BAV6163 32, whole genome shotgun 13537, gc%: 63.06%

Download details as .txt file:detail.txt file_download

Bacterial, total 0 CDS

#CDS PositionBLAST HitE-ValueSequence

Phage Genes

Bacterial Genes

Phage Regions

GC Skew

GC Content

lock_open

Phage Genes

Bacterial Genes

Phage Regions

GC Skew

GC Content

lock_open
Click on a region or gene to view details

We require the use of cookies for essential features like storing your previously submitted PHASTEST queries. Rejecting the usage of cookies will result in certain features being disabled. By clicking ACCEPT or continuing to use the website you are agreeing to our use of cookies.

ACCEPT