gi|332099014|ref|AFFZ00000000.1| Shigella dysenteriae 155-74 .0, whole genome shotgun .5162596, GC%: 50.77%, length = 5162596 bps

Total : 26 prophage regions have been identified, of which 14 regions are intact, 8 regions are incomplete, 4 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 71.8Kb intact 150 92 3490-75304 Enterobacteria phage mEp460 52.06% Detail
2 27.5Kb questionable 70 24 349259-376776 Salmonella phage ST64B 50.99% Detail
3 25.5Kb questionable 90 18 428218-453719 Burkholderia phage Bcep43 49.85% Detail
4 26.5Kb intact 110 37 872119-898637 Enterobacteria phage phiP27 48.61% Detail
5 20.1Kb questionable 90 26 1065644-1085798 PHAGE_Gifsy_2 48.49% Detail
6 10.5Kb incomplete 30 1096726-1107284 Salmonella phage SSU5 50.59% Detail
7 17.3Kb incomplete 50 19 1155976-1173314 PHAGE_Gifsy_1 49.88% Detail
8 16.5Kb intact 110 17 1229974-1246491 Enterobacteria phage phiP27 49.92% Detail
9 24.3Kb intact 100 15 1332715-1357021 Enterobacteria phage phiP27 50.08% Detail
10 70.7Kb intact 150 75 1499485-1570193 Enterobacteria phage mEp460 51.19% Detail
11 20.5Kb intact 150 18 1667725-1688254 Prophage Escherichia coli CFT073 47.91% Detail
12 35.6Kb intact 150 33 1802054-1837732 Escherichia phage P13374 49.20% Detail
13 48.7Kb intact 150 50 1868148-1916945 Prophage Escherichia coli CFT073 48.22% Detail
14 7.7Kb incomplete 20 2066545-2074275 PHAGE_Yersin_413C 55.03% Detail
15 43.2Kb intact 130 25 2186372-2229586 Prophage Escherichia coli CFT073 48.54% Detail
16 15.7Kb incomplete 60 17 2438223-2453980 Psychrobacter phage pOW20-A 49.17% Detail
17 60.8Kb intact 150 59 2527974-2588786 PHAGE_Yersin_413C 52.50% Detail
18 6.1Kb incomplete 30 2811221-2817391 Planktothrix phage PaV-LD 54.29% Detail
19 28.5Kb intact 140 18 2838775-2867277 Enterobacteria phage phiP27 50.90% Detail
20 7.6Kb incomplete 30 3008812-3016502 Lactobacillus prophage Lj771 50.88% Detail
21 30.9Kb intact 150 28 3701793-3732766 Prophage Escherichia coli CFT073 47.82% Detail
22 19.9Kb incomplete 40 16 4103832-4123757 Enterobacteria phage phiP27 49.04% Detail
23 8.6Kb incomplete 30 4319641-4328242 Enterobacteria phage phiP27 51.92% Detail
24 23.3Kb intact 140 24 4851599-4874906 Stx2-converting phage 1717 49.68% Detail
25 28.5Kb questionable 70 28 5078313-5106835 Enterobacteria phage SfV 48.64% Detail
26 29.9Kb intact 150 27 5123105-5153014 Prophage Escherichia coli CFT073 47.33% 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.