gi|208736083|ref|ABHL00000000.2| Escherichia coli O157:H7 str. EC4045 , whole .5634850, GC%: 50.47%, length = 5634850 bps

Total : 18 prophage regions have been identified, of which 15 regions are intact, 2 regions are incomplete, 1 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 29.3Kb intact 97 40 571-29969 PHAGE_Yersin_413C 49.70% Detail
2 73.5Kb intact 150 62 68735-142311 PHAGE_Entero_4795 51.50% Detail
3 81.1Kb intact 140 90 381894-463089 PHAGE_Stx2_c_II 47.63% Detail
4 20.5Kb questionable 70 23 726421-746929 Stx2-converting phage 1717 42.37% Detail
5 29Kb incomplete 50 21 2311950-2341041 Enterobacteria phage mEp460 47.56% Detail
6 28.5Kb intact 150 23 3018527-3047122 Enterobacteria phage HK106 44.85% Detail
7 38.5Kb intact 150 39 3614470-3653060 Enterobacteria phage cdtI 49.40% Detail
8 34Kb intact 150 38 3898640-3932712 Enterobacteria phage HK630 53.47% Detail
9 50.5Kb intact 150 57 4200931-4251454 PHAGE_Entero_2008 49.26% Detail
10 10.9Kb incomplete 20 16 4254328-4265305 Enterobacteria phage N15 49.22% Detail
11 49.6Kb intact 150 47 4270923-4320577 Enterobacteria phage lambda 50.25% Detail
12 30.2Kb intact 150 36 4409259-4439488 Enterobacteria phage HK630 54.18% Detail
13 45.4Kb intact 150 58 4454531-4499954 Enterobacteria phage cdtI 52.48% Detail
14 60Kb intact 150 63 4787095-4847151 PHAGE_Entero_2008 52.08% Detail
15 22.4Kb intact 130 33 5178275-5200711 Salmonella phage RE-2010 50.28% Detail
16 53.4Kb intact 150 47 5254640-5308135 Enterobacteria phage HK630 51.51% Detail
17 50.8Kb intact 140 60 5336415-5387236 Stx2-converting phage 1717 49.72% Detail
18 77.7Kb intact 150 86 5472673-5550391 PHAGE_Entero_2008 53.25% 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.