gi|343142175|ref|AFWP00000000| Escherichia coli O104:H4 str. GOS2, whole genome shotgun sequence. .5308815, GC%: 50.59%, length = 5308815 bps

Total : 15 prophage regions have been identified, of which 6 regions are intact, 8 regions are incomplete, 1 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 36.6Kb incomplete 40 20 339377-376028 PHAGE_Entero_Sf6 47.09% Detail
2 13Kb intact 100 16 887696-900756 Enterobacteria phage HK630 49.78% Detail
3 50.2Kb intact 140 68 1606179-1656415 Escherichia phage P13374 49.44% Detail
4 18.5Kb incomplete 50 17 1694209-1712781 Escherichia phage P13374 51.95% Detail
5 46.5Kb intact 150 50 2187181-2233688 Enterobacteria phage lambda 49.29% Detail
6 25.9Kb incomplete 40 34 2785050-2810997 Enterobacteria phage mEp460 48.94% Detail
7 23.6Kb incomplete 20 35 2885518-2909147 Enterobacteria phage mEp460 48.48% Detail
8 9.1Kb questionable 80 3011763-3020954 PHAGE_Gifsy_1 52.68% Detail
9 7.7Kb intact 100 12 4015189-4022924 Enterobacteria phage HK630 46.37% Detail
10 23.1Kb intact 150 26 4074186-4097335 PHAGE_Yersin_413C 51.33% Detail
11 35.6Kb incomplete 30 25 4471189-4506795 Enterobacteria phage phiP27 49.18% Detail
12 29.8Kb incomplete 60 30 4628036-4657909 PHAGE_Yersin_413C 50.99% Detail
13 18.1Kb incomplete 60 20 4734080-4752250 PHAGE_Gifsy_1 44.84% Detail
14 53.2Kb intact 150 46 4783660-4836887 Escherichia phage TL-2011c 50.39% Detail
15 24.1Kb incomplete 10 24 4926378-4950562 Escherichia phage TL-2011c 51.20% 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.