gi|192940712|ref|AAJV00000000.2| Escherichia coli E22 , whole genome shotgun .5528238, GC%: 50.62%, length = 5528238 bps

Total : 15 prophage regions have been identified, of which 11 regions are intact, 4 regions are incomplete, 0 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 27.6Kb incomplete 30 16 584311-612005 Enterobacteria phage mEp460 50.50% Detail
2 32.2Kb intact 150 41 883743-915998 PHAGE_Gifsy_1 52.18% Detail
3 22.2Kb incomplete 20 17 1010645-1032920 PHAGE_Gifsy_2 45.65% Detail
4 32.7Kb intact 150 36 1029320-1062117 Enterobacteria phage cdtI 48.05% Detail
5 33.1Kb intact 100 33 1280616-1313767 Haemophilus phage HP2 50.49% Detail
6 47.1Kb intact 150 33 1887336-1934447 Enterobacteria phage HK629 51.60% Detail
7 22.7Kb intact 150 33 2952851-2975581 Salmonella phage ST64B 53.79% Detail
8 49.2Kb intact 150 64 3435998-3485248 Enterobacteria phage mEp237 50.57% Detail
9 24.2Kb intact 140 33 3905102-3929314 PHAGE_Yersin_413C 52.99% Detail
10 30.9Kb incomplete 50 34 4052113-4083013 Salmonella phage 19 47.20% Detail
11 43Kb intact 100 39 4207631-4250684 Enterobacteria phage lambda 49.72% Detail
12 35.6Kb intact 96 53 4817793-4853408 Burkholderia phage BcepMu 54.94% Detail
13 29.5Kb incomplete 40 20 4947494-4977071 Enterobacteria phage HK106 48.45% Detail
14 27.3Kb intact 130 27 5075587-5102954 Enterobacteria phage mEp460 55.07% Detail
15 18.4Kb intact 140 23 5247878-5266375 Enterobacteria phage HK630 52.17% 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.