gi|323163821|ref|ADUO00000000.1| Escherichia coli E128010 gecE128010.assembly.100, whole genome .5221267, GC%: 50.59%, length = 5221267 bps

Total : 18 prophage regions have been identified, of which 9 regions are intact, 7 regions are incomplete, 2 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 23.2Kb incomplete 30 16 247041-270270 PHAGE_Bacill_36 50.91% Detail
2 21.9Kb incomplete 60 15 1506803-1528750 Stx2-converting phage 1717 49.03% Detail
3 8.2Kb incomplete 50 12 1571207-1579502 Stx2-converting phage 1717 52.48% Detail
4 27.2Kb questionable 70 18 1747969-1775179 PHAGE_Entero_Sf6 49.91% Detail
5 44.9Kb incomplete 40 29 2130178-2175108 PHAGE_Yersin_413C 51.45% Detail
6 52.7Kb intact 150 70 2246495-2299205 Enterobacteria phage mEp460 51.50% Detail
7 46.1Kb intact 150 62 2813130-2859296 Enterobacteria phage mEp460 51.31% Detail
8 32.4Kb intact 150 39 3846149-3878572 Enterobacteria phage HK629 49.59% Detail
9 35Kb intact 150 47 4120771-4155772 Enterobacteria phage mEp460 52.78% Detail
10 47Kb intact 150 64 4366088-4413166 Stx2-converting phage 1717 50.89% Detail
11 6.3Kb questionable 70 10 4538483-4544803 Prophage Escherichia coli CFT073 47.35% Detail
12 15Kb intact 150 27 4561081-4576149 Stx2-converting phage 1717 52.98% Detail
13 19.5Kb incomplete 40 27 4785029-4804603 Enterobacteria phage lambda 46.46% Detail
14 28.2Kb intact 150 36 5040572-5068786 Salmonella phage RE-2010 52.98% Detail
15 11.6Kb intact 120 23 5105246-5116884 Erwinia phage ENT90 50.43% Detail
16 10.6Kb intact 150 19 5129243-5139861 Enterobacteria phage HK630 51.40% Detail
17 8.1Kb incomplete 60 15 5143540-5151639 Enterobacteria phage If1 53.04% Detail
18 6.1Kb incomplete 60 10 5173465-5179650 Stx2-converting phage 1717 50.10% 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.