gi|295975953|ref|ADUX00000000| Escherichia coli O157:H7 str. EC4192 , whole genome .5349693, GC%: 50.24%, length = 5349693 bps

Total : 28 prophage regions have been identified, of which 7 regions are intact, 17 regions are incomplete, 4 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 18.1Kb incomplete 40 28 108621-126750 Enterobacteria phage HK630 46.17% Detail
2 12.3Kb intact 110 21 410314-422618 Enterobacteria phage HK629 53.48% Detail
3 16.2Kb intact 110 30 1248750-1264965 Enterobacteria phage HK629 51.44% Detail
4 4.1Kb incomplete 20 1374264-1378444 Enterobacteria phage HK022 50.44% Detail
5 28.3Kb questionable 70 22 1625180-1653492 Enterobacteria phage mEp460 55.76% Detail
6 50.5Kb intact 150 66 1657748-1708284 Enterobacteria phage mEp460 49.75% Detail
7 17.6Kb incomplete 40 12 2292788-2310399 Salmonella phage ST64B 41.55% Detail
8 10.4Kb questionable 80 14 2330666-2341109 Stx2-converting phage 1717 49.64% Detail
9 11.7Kb incomplete 50 19 2346244-2358008 PHAGE_Entero_2008 46.72% Detail
10 14.6Kb incomplete 30 19 2505518-2520136 Enterobacteria phage P4 43.06% Detail
11 12.5Kb incomplete 60 16 2553746-2566312 Escherichia phage TL-2011c 49.77% Detail
12 7.8Kb incomplete 50 13 3179505-3187385 PHAGE_Stx2_c_II 50.89% Detail
13 10.1Kb incomplete 50 15 3235728-3245908 Escherichia phage HK639 48.06% Detail
14 39.8Kb questionable 90 23 3327488-3367378 Enterobacteria phage mEp237 50.48% Detail
15 15Kb intact 100 20 3459362-3474372 PHAGE_Entero_4795 49.94% Detail
16 12.9Kb incomplete 20 26 3557024-3570020 Escherichia phage TL-2011c 47.47% Detail
17 16.2Kb incomplete 40 18 3602692-3618923 PHAGE_Entero_2008 53.06% Detail
18 30.4Kb intact 150 43 3637103-3667576 Enterobacteria phage HK630 52.97% Detail
19 10.7Kb incomplete 40 15 3688748-3699503 Stx2-converting phage 1717 48.97% Detail
20 18Kb incomplete 40 14 3755880-3773907 Enterobacteria phage cdtI 48.46% Detail
21 29Kb incomplete 30 29 3797353-3826378 PHAGE_Stx1_converting 51.85% Detail
22 18.4Kb intact 150 25 4235827-4254248 Enterobacteria phage mEp460 52.38% Detail
23 68.9Kb incomplete 60 53 4415942-4484876 PHAGE_Yersin_413C 51.52% Detail
24 22.7Kb incomplete 30 16 4861019-4883788 PHAGE_Entero_2008 50.99% Detail
25 59.6Kb intact 100 50 4883710-4943325 PHAGE_Yersin_413C 50.90% Detail
26 20Kb incomplete 20 15 4996920-5016989 PHAGE_Entero_2008 50.15% Detail
27 28Kb incomplete 60 24 5174138-5202176 Enterobacteria phage mEp460 45.98% Detail
28 17.7Kb questionable 90 17 5317900-5335620 Enterobacteria phage HK630 51.69% 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.