gi|188491671|ref|AAKB00000000.2| Escherichia coli 53638 , whole genome shotgun .5071018, GC%: 51.10%, length = 5071018 bps

Total : 16 prophage regions have been identified, of which 10 regions are intact, 5 regions are incomplete, 1 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 7.6Kb incomplete 60 12 34-7698 Stx2-converting phage 1717 50.23% Detail
2 20.7Kb incomplete 30 11 8573-29316 PHAGE_Gifsy_2 48.13% Detail
3 68.5Kb intact 150 55 44403-112951 Enterobacteria phage mEp460 51.16% Detail
4 35.8Kb questionable 70 27 362913-398750 PHAGE_Gifsy_1 51.20% Detail
5 9.8Kb intact 107 14 949585-959433 Enterobacteria phage P4 55.17% Detail
6 37.7Kb intact 96 53 1121698-1159430 Burkholderia phage BcepMu 54.38% Detail
7 36.5Kb intact 123 46 1832647-1869235 PHAGE_Yersin_413C 51.98% Detail
8 12Kb incomplete 60 11 2038959-2050998 Prophage Escherichia coli str. K-12 substr. MG1655 51.58% Detail
9 9.1Kb incomplete 30 10 3212914-3222068 Enterococcus phage phiEF24C 50.09% Detail
10 29.2Kb intact 110 36 3328202-3357442 Burkholderia phage Bcep43 51.59% Detail
11 62.6Kb intact 150 73 3700803-3763449 Aggregatibacter phage S1249 50.09% Detail
12 34.2Kb intact 100 49 3905690-3939953 Enterobacteria phage phiP27 48.95% Detail
13 10.1Kb incomplete 60 14 3950721-3960897 PHAGE_Gifsy_1 50.41% Detail
14 72.9Kb intact 150 99 4192498-4265416 Enterobacteria phage Mu 51.89% Detail
15 48.9Kb intact 150 65 4303022-4351984 Enterobacteria phage mEp460 51.26% Detail
16 14.2Kb intact 110 19 5056750-5071018 PHAGE_Entero_4795 50.42% 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.