gi|159531150|ref|ABHR00000000.1| Escherichia coli O157:H7 str. EC4401 , whole .5733133, GC%: 50.46%, length = 5733133 bps

Total : 18 prophage regions have been identified, of which 9 regions are intact, 4 regions are incomplete, 5 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 34Kb intact 150 39 1094901-1128971 Enterobacteria phage HK630 53.47% Detail
2 28.8Kb questionable 80 39 1958790-1987680 PHAGE_Stx2_c_II 51.00% Detail
3 29Kb incomplete 50 20 2032049-2061140 Enterobacteria phage mEp460 47.56% Detail
4 42.6Kb questionable 80 22 2185180-2227836 Stx2-converting phage 1717 43.71% Detail
5 24.1Kb questionable 80 12 2605838-2630013 Enterobacteria phage HK97 49.11% Detail
6 38.1Kb intact 97 38 3129241-3167416 PHAGE_Yersin_413C 50.15% Detail
7 28.1Kb intact 150 31 3210308-3238481 Enterobacteria phage cdtI 54.03% Detail
8 26Kb questionable 90 20 3228803-3254870 PHAGE_Entero_4795 48.77% Detail
9 50.9Kb intact 150 49 3273448-3324415 Enterobacteria phage lambda 50.34% Detail
10 38.5Kb intact 150 40 3831573-3870163 Enterobacteria phage cdtI 49.39% Detail
11 31.3Kb incomplete 50 14 4016414-4047735 Enterobacteria phage lambda 50.09% Detail
12 41.7Kb incomplete 60 30 4080297-4121999 Stx2-converting phage 86 46.17% Detail
13 27.9Kb incomplete 50 35 4218631-4246626 Stx2-converting phage 1717 47.85% Detail
14 89.4Kb intact 150 69 4285427-4374881 PHAGE_Entero_2008 50.10% Detail
15 51.7Kb intact 110 46 4474088-4525819 PHAGE_Entero_2008 52.28% Detail
16 65.3Kb intact 150 77 4618188-4683569 PHAGE_Entero_2008 52.94% Detail
17 21.3Kb questionable 90 20 5220205-5241522 PHAGE_Entero_2008 53.32% Detail
18 22.1Kb intact 150 25 5258019-5280187 Enterobacteria phage HK630 53.96% 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.