gi|291084348|ref|ADAV00000000| Escherichia coli M605 .1, whole genome shotgun sequence. .5446689, GC%: 50.43%, length = 5446689 bps

Total : 19 prophage regions have been identified, of which 12 regions are intact, 4 regions are incomplete, 3 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 10.8Kb questionable 80 12 306922-317765 Stx2-converting phage 1717 51.00% Detail
2 43.4Kb questionable 90 58 868570-912054 Burkholderia phage Bcep1 46.06% Detail
3 34.7Kb intact 150 48 990543-1025319 Enterobacteria phage 285P 51.16% Detail
4 52.2Kb intact 150 69 1304574-1356778 Enterobacteria phage HK630 50.50% Detail
5 42Kb intact 100 47 1668430-1710444 Enterobacteria phage P1 46.49% Detail
6 19.1Kb intact 150 36 1716071-1735189 Stx2-converting phage 1717 48.55% Detail
7 37.4Kb intact 150 37 1751442-1788939 Prophage Ralstonia solanacearum GMI1000 43.42% Detail
8 12.4Kb intact 100 21 1803719-1816179 Prophage Escherichia coli str. K-12 substr. MG1655 46.22% Detail
9 19.6Kb questionable 90 42 1840148-1859809 Enterobacteria phage SfV 47.24% Detail
10 6.8Kb incomplete 40 2142734-2149630 PHAGE_Entero_4795 41.95% Detail
11 24.3Kb incomplete 20 26 2183351-2207692 PHAGE_Gifsy_2 48.24% Detail
12 31.5Kb intact 120 22 2790400-2821926 Enterobacteria phage HK022 42.59% Detail
13 53.9Kb intact 130 55 2929289-2983190 PHAGE_Entero_phiV10 49.74% Detail
14 37.5Kb intact 140 49 3056223-3093775 PHAGE_Bacter_2 49.96% Detail
15 10.5Kb intact 96 12 3147200-3157767 Enterobacteria phage P4 51.22% Detail
16 11.7Kb incomplete 50 16 3165661-3177376 Enterobacteria phage HK022 49.50% Detail
17 121.4Kb intact 150 139 4688033-4809467 Enterobacteria phage P1 50.21% Detail
18 38.6Kb intact 150 55 5283756-5322365 Enterobacteria phage Mu 52.90% Detail
19 8.3Kb incomplete 60 11 5414148-5422546 Prophage Escherichia coli CFT073 48.03% 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.