gi|345351935|ref|AFDS00000000.1| Escherichia coli 2534-86 .0, whole genome shotgun .5290142, GC%: 50.53%, length = 5290142 bps

Total : 18 prophage regions have been identified, of which 11 regions are intact, 2 regions are incomplete, 5 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 105Kb intact 150 173 5171-110177 PHAGE_Entero_2008 52.50% Detail
2 29.9Kb intact 100 28 619682-649664 PHAGE_Stx2_c_II 50.56% Detail
3 11.1Kb intact 150 16 918781-929915 Enterobacteria phage HK630 54.97% Detail
4 21.2Kb intact 150 30 1160424-1181634 Enterobacteria phage HK630 49.01% Detail
5 28.5Kb questionable 80 32 1405112-1433651 Pectobacterium phage ZF40 47.82% Detail
6 8.3Kb incomplete 50 15 1425047-1433376 PHAGE_Entero_2008 48.28% Detail
7 24.2Kb intact 120 26 1662649-1686872 Stx2-converting phage 1717 52.48% Detail
8 52.1Kb intact 150 79 1804216-1856401 PHAGE_Entero_2008 49.54% Detail
9 31.1Kb questionable 90 43 1952624-1983801 PHAGE_Gifsy_2 46.91% Detail
10 22.7Kb questionable 70 15 2172380-2195130 Stx2-converting phage 1717 47.31% Detail
11 33.6Kb intact 150 47 2383205-2416816 PHAGE_Yersin_413C 52.21% Detail
12 45.2Kb intact 150 50 2681836-2727047 Stx2-converting phage 1717 48.25% Detail
13 52.4Kb intact 120 61 2731648-2784066 PHAGE_Entero_HK620 47.51% Detail
14 40.1Kb questionable 70 21 3014677-3054857 Stx2-converting phage 1717 48.49% Detail
15 40.2Kb incomplete 60 50 3165836-3206035 PHAGE_Stx2_c_II 49.23% Detail
16 22.8Kb questionable 70 19 3470261-3493063 PHAGE_Entero_4795 49.21% Detail
17 30Kb intact 140 42 5062317-5092408 Enterobacteria phage mEp460 49.40% Detail
18 17.6Kb intact 130 25 5261646-5279305 PHAGE_Stx2_c_II 50.50% 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.