gi|315619884|ref|ADUM00000000.1| Escherichia coli 3431 gec3431.assembly.100, whole genome shotgun .5223419, GC%: 50.92%, length = 5223419 bps

Total : 19 prophage regions have been identified, of which 12 regions are intact, 0 regions are incomplete, 7 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 90.9Kb intact 150 109 117204-208126 Enterobacteria phage Mu 50.29% Detail
2 22.8Kb intact 140 32 345588-368441 Stx2-converting phage 1717 51.54% Detail
3 8.3Kb questionable 90 15 490503-498825 Enterobacteria phage HK630 49.09% Detail
4 19.4Kb questionable 70 28 683397-702824 PHAGE_Entero_4795 48.35% Detail
5 35.3Kb questionable 80 25 706793-742158 Salmonella phage ST64B 50.84% Detail
6 24Kb questionable 70 17 1558071-1582169 Enterobacteria phage cdtI 49.72% Detail
7 28.8Kb questionable 70 41 1778495-1807387 Salmonella phage ST64B 50.94% Detail
8 3.7Kb questionable 70 1827219-1830993 PHAGE_Entero_2008 55.18% Detail
9 11.5Kb intact 100 17 2106181-2117720 Stx2-converting phage 1717 50.30% Detail
10 30.6Kb intact 140 18 2553805-2584463 Stx2-converting phage 1717 50.81% Detail
11 9Kb questionable 70 10 2894089-2903132 PHAGE_Entero_4795 48.57% Detail
12 37.3Kb intact 150 58 3778582-3815929 PHAGE_Entero_4795 52.01% Detail
13 62.1Kb intact 150 84 3927610-3989769 Enterobacteria phage phiP27 51.77% Detail
14 21Kb intact 140 28 4532290-4553364 Enterobacteria phage 285P 55.01% Detail
15 51.7Kb intact 150 63 4529754-4581467 Enterobacteria phage 285P 51.09% Detail
16 25Kb intact 100 32 4556035-4581057 Salmonella phage RE-2010 49.45% Detail
17 34.1Kb intact 100 27 4813284-4847385 Prophage Escherichia coli CFT073 51.86% Detail
18 33.6Kb intact 150 59 4986700-5020330 Stx2-converting phage 1717 51.21% Detail
19 45.9Kb intact 150 39 5176047-5222042 Enterobacteria phage mEp460 50.63% 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.