gi|323191713|ref|ADUS00000000.1| Escherichia coli RN587/1 RN587.assembly.10, whole genome shotgun .5061577, GC%: 50.61%, length = 5061577 bps

Total : 14 prophage regions have been identified, of which 11 regions are intact, 2 regions are incomplete, 1 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 49.3Kb intact 150 60 675367-724738 Enterobacteria phage HK629 50.36% Detail
2 52.9Kb intact 110 42 757569-810565 Haemophilus phage HP2 50.15% Detail
3 31.9Kb intact 150 43 834209-866186 Enterobacteria phage 285P 51.53% Detail
4 20.8Kb intact 140 28 845312-866120 Enterobacteria phage 285P 55.09% Detail
5 41.2Kb intact 150 49 998229-1039499 Salmonella phage ST64B 50.11% Detail
6 23.6Kb incomplete 20 34 1181276-1204875 PHAGE_Gifsy_2 49.08% Detail
7 60.2Kb intact 150 62 1446038-1506317 Enterobacteria phage cdtI 50.66% Detail
8 9.3Kb questionable 90 13 3352199-3361581 Enterobacteria phage mEp460 46.08% Detail
9 47.1Kb intact 150 50 3475884-3523069 Burkholderia phage KS5 52.63% Detail
10 11.7Kb incomplete 60 12 3975548-3987284 PHAGE_Entero_Sf6 45.33% Detail
11 44.4Kb intact 150 65 4098736-4143145 Enterobacteria phage HK630 49.95% Detail
12 43.1Kb intact 150 58 4154410-4197554 Salmonella phage ST64B 49.16% Detail
13 23.7Kb intact 150 33 4745774-4769567 Salmonella phage RE-2010 53.73% Detail
14 60.9Kb intact 150 70 4995960-5056877 Enterobacteria phage HK630 50.43% 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.