gi|213928698|ref|ABSM00000000.1| Pseudomonas syringae pv. tomato T1 ptot1_ whole genome .6145942, GC%: 58.63%, length = 6145942 bps

Total : 11 prophage regions have been identified, of which 4 regions are intact, 4 regions are incomplete, 3 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 10Kb incomplete 60 12 791459-801525 Stx2-converting phage 1717 54.54% Detail
2 42.8Kb intact 110 60 906391-949200 Acinetobacter phage Bphi-B1251 58.08% Detail
3 27.4Kb incomplete 40 20 943346-970764 Enterobacteria phage HK225 56.76% Detail
4 17.1Kb intact 110 21 1149473-1166618 Enterobacteria phage SfV 59.83% Detail
5 35.2Kb incomplete 30 24 1611720-1646989 Vibrio phage VvAW1 59.19% Detail
6 27.1Kb questionable 70 34 1809269-1836437 Vibrio phage VHML 57.93% Detail
7 30.3Kb incomplete 40 12 4278332-4308656 Pseudomonas phage F116 58.74% Detail
8 46.6Kb intact 150 43 4340043-4386707 Burkholderia phage KS9 58.39% Detail
9 15.7Kb questionable 90 17 5826498-5842256 Vibrio phage vB_VpaM_MAR 59.52% Detail
10 8.7Kb questionable 80 6063331-6072059 Stx2-converting phage 1717 55.23% Detail
11 31.2Kb intact 110 20 6113159-6144442 Pseudomonas phage phiCTX 55.32% 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.