gi|291093511|ref|ADBC00000000| Escherichia coli H299 .1, whole genome shotgun sequence. .5248906, GC%: 50.75%, length = 5248906 bps

Total : 14 prophage regions have been identified, of which 7 regions are intact, 3 regions are incomplete, 4 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 15.8Kb incomplete 20 22 87657-103550 Cronobacter phage ENT39118 53.06% Detail
2 34.6Kb intact 120 18 104288-138905 Enterobacteria phage mEp460 53.16% Detail
3 7.3Kb questionable 80 270526-277846 Stx2-converting phage 1717 45.44% Detail
4 13.1Kb incomplete 60 25 780048-793222 Stx2-converting phage 1717 50.21% Detail
5 32.8Kb intact 130 51 1121963-1154824 Enterobacteria phage mEp460 46.62% Detail
6 63.2Kb intact 150 78 1362417-1425713 Enterobacteria phage lambda 49.70% Detail
7 9.4Kb questionable 70 14 2060795-2070209 Enterobacteria phage mEp460 54.43% Detail
8 34.6Kb intact 150 50 2165505-2200119 Enterobacteria phage mEp460 49.60% Detail
9 38.1Kb intact 150 50 2539301-2577439 PHAGE_Yersin_413C 51.51% Detail
10 37.4Kb intact 150 52 2681426-2718903 Salmonella phage ST64B 50.71% Detail
11 6.1Kb incomplete 40 2826534-2832691 Cronobacter phage vB_CskP_GAP227 42.56% Detail
12 19.7Kb questionable 90 42 5027395-5047099 Enterobacteria phage mEp460 48.11% Detail
13 12.6Kb questionable 80 15 5210931-5223588 Stx2-converting phage 1717 53.10% Detail
14 20.4Kb intact 140 36 5228107-5248530 Enterobacteria phage mEp460 54.46% Detail
Legend:
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
#CDS: the number of coding sequnce
REGION_POSITION: the start and end positions of the region on the bacterial chromosome
PHAGE: the phage with the highest number of proteins most similar to those in the region
GC_PERCENTAGE: the percentage of gc nucleotides of the region
DETAIL: detail info of the region


txt file for download


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.