gi|208730286|ref|ABHK00000000.2| Escherichia coli O157:H7 str. EC4206 , whole .5629932, GC%: 50.47%, length = 5629932 bps

Total : 19 prophage regions have been identified, of which 14 regions are intact, 2 regions are incomplete, 3 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 41.1Kb intact 110 49 179-41302 Stx2-converting phage 1717 49.90% Detail
2 24Kb questionable 86 31 125886-149964 PHAGE_Yersin_413C 53.41% Detail
3 35.7Kb intact 120 46 125757-161525 PHAGE_Yersin_413C 50.66% Detail
4 73.5Kb intact 150 62 200291-273867 PHAGE_Entero_4795 51.51% Detail
5 66.2Kb intact 140 89 515195-581465 PHAGE_Stx2_c_II 48.04% Detail
6 20.5Kb questionable 70 23 858008-878516 Stx2-converting phage 1717 42.37% Detail
7 29Kb incomplete 50 21 2443619-2472710 Enterobacteria phage mEp460 47.56% Detail
8 26.1Kb intact 120 18 3150226-3176329 Enterobacteria phage HK106 44.56% Detail
9 38.5Kb intact 150 31 3743590-3782181 Enterobacteria phage mEp460 49.39% Detail
10 34Kb intact 150 39 4027820-4061892 Enterobacteria phage HK630 53.47% Detail
11 50.5Kb intact 150 55 4330136-4380658 PHAGE_Entero_2008 49.26% Detail
12 10.9Kb incomplete 20 16 4383532-4394509 Enterobacteria phage N15 49.22% Detail
13 49.6Kb intact 150 48 4400127-4449781 Enterobacteria phage lambda 50.25% Detail
14 36.5Kb questionable 80 23 4511586-4548120 PHAGE_Entero_2008 49.50% Detail
15 44Kb intact 150 46 4589955-4633998 Enterobacteria phage HK630 51.98% Detail
16 27.3Kb intact 130 31 4682871-4710229 Salmonella phage RE-2010 50.11% Detail
17 113.3Kb intact 150 117 5033984-5147328 PHAGE_Entero_2008 51.75% Detail
18 42.9Kb intact 150 58 5158820-5201799 Enterobacteria phage cdtI 52.84% Detail
19 38.4Kb intact 150 41 5489802-5528209 PHAGE_Entero_2008 54.19% 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.