gi|296493501|ref|ADTK00000000.1| Escherichia coli MS 84-1 .1, whole genome .5287926, GC%: 50.55%, length = 5287926 bps

Total : 13 prophage regions have been identified, of which 5 regions are intact, 6 regions are incomplete, 2 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 30.7Kb questionable 70 27 84537-115314 Escherichia phage phAPEC8 48.15% Detail
2 19.2Kb incomplete 60 25 280647-299877 PHAGE_Gifsy_1 48.69% Detail
3 22.7Kb intact 140 17 498218-520923 Salmonella phage RE-2010 51.80% Detail
4 26.3Kb incomplete 40 33 661561-687890 Enterobacteria phage mEp460 49.78% Detail
5 30.2Kb incomplete 40 29 1202083-1232344 PHAGE_Entero_4795 48.76% Detail
6 17Kb questionable 70 33 1887592-1904632 Enterobacteria phage mEp460 46.95% Detail
7 11.1Kb incomplete 40 16 2036671-2047841 Enterobacteria phage mEp460 48.38% Detail
8 35.4Kb intact 150 54 2803196-2838662 Enterobacteria phage P4 47.96% Detail
9 71Kb intact 150 117 2877947-2949039 Enterobacteria phage HK629 49.52% Detail
10 16.7Kb incomplete 50 20 3314448-3331174 Enterobacteria phage HK630 51.89% Detail
11 46.8Kb intact 150 73 4513227-4560035 Enterobacteria phage HK544 50.27% Detail
12 34.8Kb intact 150 39 4638636-4673516 Salmonella phage RE-2010 50.72% Detail
13 11.6Kb incomplete 50 19 5275189-5286845 Cronobacter phage vB_CsaM_GAP32 48.81% 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.