gi|159530691|ref|ABHP00000000.1| Escherichia coli O157:H7 str. EC4113 , whole .5655847, GC%: 50.60%, length = 5655847 bps

Total : 20 prophage regions have been identified, of which 12 regions are intact, 8 regions are incomplete, 0 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 36.9Kb intact 140 35 1074559-1111519 Salmonella phage RE-2010 51.15% Detail
2 23.7Kb incomplete 30 1212292-1236059 PHAGE_Entero_2008 49.61% Detail
3 65.3Kb intact 140 89 1327251-1392602 PHAGE_Stx2_c_II 47.83% Detail
4 19.4Kb incomplete 50 2151342-2170769 PHAGE_Stx2_c_II 46.18% Detail
5 18.8Kb intact 110 18 2740531-2759370 PHAGE_Entero_2008 53.24% Detail
6 10.9Kb incomplete 20 16 2772563-2783541 Enterobacteria phage N15 49.21% Detail
7 46.5Kb intact 150 42 2783359-2829911 Enterobacteria phage lambda 51.07% Detail
8 18.6Kb intact 140 19 3098361-3116982 Enterobacteria phage cdtI 56.14% Detail
9 32.4Kb incomplete 60 10 3232673-3265133 Enterobacteria phage lambda 50.43% Detail
10 38.5Kb intact 150 40 3280084-3318674 Enterobacteria phage cdtI 49.40% Detail
11 35.7Kb incomplete 60 28 3459290-3495018 PHAGE_Entero_4795 48.44% Detail
12 35.3Kb incomplete 60 18 3828546-3863930 Stx2-converting phage 1717 44.59% Detail
13 29.4Kb intact 150 34 4073383-4102863 Enterobacteria phage cdtI 54.56% Detail
14 76.4Kb intact 140 86 4188811-4265302 PHAGE_Entero_2008 49.99% Detail
15 46Kb intact 150 48 4407783-4453857 PHAGE_Entero_2008 53.35% Detail
16 18.4Kb incomplete 40 15 4549738-4568154 Stx2-converting phage 1717 49.36% Detail
17 31.6Kb intact 130 37 4641218-4672868 PHAGE_Entero_2008 53.22% Detail
18 29.4Kb intact 150 29 4787472-4816881 Enterobacteria phage HK630 55.08% Detail
19 15.2Kb incomplete 30 21 5160408-5175632 PHAGE_Yersin_413C 53.27% Detail
20 53Kb intact 150 51 5214430-5267516 Stx2-converting phage 1717 51.46% 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.