gi|217322862|ref|ABKY00000000.2| Escherichia coli O157:H7 str. TW14588 , whole .5670297, GC%: 50.46%, length = 5670297 bps

Total : 19 prophage regions have been identified, of which 13 regions are intact, 3 regions are incomplete, 3 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 34.7Kb intact 150 45 41537-76250 Enterobacteria phage HK630 53.38% Detail
2 19.6Kb incomplete 40 18 194621-214309 Enterobacteria phage P4 48.71% Detail
3 48.1Kb intact 150 42 321339-369531 Enterobacteria phage cdtI 50.11% Detail
4 39.9Kb intact 150 55 822648-862641 Enterobacteria phage Mu 53.69% Detail
5 26.6Kb intact 110 33 973344-999966 Enterobacteria phage P4 44.39% Detail
6 11.7Kb incomplete 20 21 2199200-2210968 PHAGE_Stx2_c_I 49.52% Detail
7 20.8Kb questionable 90 24 3273750-3294566 Stx2-converting phage 1717 41.76% Detail
8 81.9Kb intact 150 91 3559482-3641475 Escherichia phage TL-2011c 49.06% Detail
9 45.3Kb questionable 90 49 3874244-3919549 PHAGE_Stx1_converting 50.47% Detail
10 46.5Kb intact 150 48 4033322-4079878 Enterobacteria phage lambda 51.09% Detail
11 35.9Kb intact 120 32 4067642-4103593 Salmonella phage ST64B 49.67% Detail
12 53.9Kb intact 150 63 4107603-4161543 PHAGE_Entero_2008 51.44% Detail
13 69.6Kb intact 150 86 4378913-4448600 PHAGE_Stx2_c_II 51.43% Detail
14 26Kb questionable 90 31 4499288-4525328 Enterobacteria phage PsP3 49.96% Detail
15 14.6Kb incomplete 50 18 4863282-4877906 PHAGE_Entero_2008 48.09% Detail
16 61Kb intact 150 72 5049409-5110486 PHAGE_Entero_2008 50.25% Detail
17 55.9Kb intact 150 64 5215724-5271706 Enterobacteria phage cdtI 50.84% Detail
18 61.5Kb intact 150 58 5265020-5326563 PHAGE_Entero_2008 50.49% Detail
19 94.7Kb intact 150 123 5488889-5583679 PHAGE_Entero_2008 52.92% 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.