gi|159530375|ref|ABHO00000000.1| Escherichia coli O157:H7 str. EC4196 , whole .5620606, GC%: 50.55%, length = 5620606 bps

Total : 19 prophage regions have been identified, of which 11 regions are intact, 5 regions are incomplete, 3 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 81.1Kb intact 140 86 557067-638261 PHAGE_Stx2_c_II 47.62% Detail
2 50.7Kb intact 150 67 1807567-1858298 PHAGE_Entero_2008 51.80% Detail
3 29Kb incomplete 50 20 2039220-2068311 Enterobacteria phage mEp460 47.56% Detail
4 20.5Kb questionable 70 23 2493693-2514195 Stx2-converting phage 1717 42.35% Detail
5 27.4Kb intact 150 31 2674356-2701837 Enterobacteria phage cdtI 54.74% Detail
6 17.2Kb questionable 70 16 3059225-3076521 PHAGE_Yersin_413C 47.76% Detail
7 36.2Kb incomplete 50 28 3161178-3197443 Stx2-converting phage 1717 48.27% Detail
8 44.4Kb intact 97 39 3531875-3576342 PHAGE_Yersin_413C 48.99% Detail
9 46.5Kb intact 150 48 3579135-3625664 Enterobacteria phage lambda 51.04% Detail
10 22Kb questionable 70 13 3649640-3671738 Enterobacteria phage lambda 48.01% Detail
11 39.8Kb intact 150 38 3977847-4017693 Enterobacteria phage mEp460 49.56% Detail
12 24.7Kb intact 130 34 4041140-4065931 Salmonella phage RE-2010 50.13% Detail
13 20.9Kb incomplete 50 36 4244513-4265467 PHAGE_Entero_2008 51.81% Detail
14 17.1Kb intact 150 18 4550496-4567657 Enterobacteria phage HK630 57.18% Detail
15 24.4Kb incomplete 50 24 4783528-4807928 PHAGE_Entero_4795 45.87% Detail
16 29.2Kb intact 150 38 4899487-4928712 Enterobacteria phage HK630 52.54% Detail
17 6.2Kb incomplete 40 11 5224984-5231238 PHAGE_Entero_4795 48.19% Detail
18 61Kb intact 150 44 5303127-5364214 Enterobacteria phage HK630 51.05% Detail
19 39.6Kb intact 150 38 5373465-5413090 Enterobacteria phage HK629 51.84% 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.