gi|320202653|ref|AERU00000000.1| Escherichia coli EC4100B , whole genome shotgun .5111899, GC%: 50.51%, length = 5111899 bps

Total : 14 prophage regions have been identified, of which 8 regions are intact, 5 regions are incomplete, 1 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 5.9Kb incomplete 50 201-6183 PHAGE_Entero_Sf6 49.37% Detail
2 33.4Kb intact 150 38 1101120-1134557 Enterobacteria phage HK629 53.67% Detail
3 20.7Kb questionable 70 28 1213823-1234527 Enterobacteria phage SfV 45.05% Detail
4 38.1Kb incomplete 50 38 1763656-1801759 Enterobacteria phage lambda 48.24% Detail
5 30.1Kb intact 150 37 1821229-1851347 PHAGE_Entero_4795 55.32% Detail
6 24.5Kb incomplete 50 25 2565105-2589687 Enterobacteria phage mEp460 47.75% Detail
7 7.8Kb incomplete 60 3338066-3345955 Enterobacteria phage HK629 48.73% Detail
8 51.4Kb intact 150 47 3672724-3724180 Enterobacteria phage cdtI 48.90% Detail
9 33.5Kb intact 150 44 3797693-3831228 Enterobacteria phage 285P 51.11% Detail
10 22Kb intact 150 32 3809075-3831150 Enterobacteria phage 285P 54.66% Detail
11 26.7Kb incomplete 30 37 3975591-4002341 Enterobacteria phage mEp460 47.80% Detail
12 44Kb intact 140 31 4216258-4260346 PHAGE_Vibrio_kappa 51.64% Detail
13 31.5Kb intact 150 34 4720649-4752183 Enterobacteria phage mEp460 50.96% Detail
14 27Kb intact 150 30 5067991-5095071 Enterobacteria phage HK630 54.91% 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.