gi|329753721|ref|AEME00000000| Escherichia sp. TW09308 , whole genome shotgun sequence. .4809826, GC%: 50.28%, length = 4809826 bps

Total : 16 prophage regions have been identified, of which 6 regions are intact, 7 regions are incomplete, 3 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 21.4Kb incomplete 40 23 155-21590 PHAGE_Entero_Sf6 47.41% Detail
2 13Kb incomplete 40 19 202878-215959 Salmonella phage ST64B 52.75% Detail
3 35Kb intact 142 49 824826-859849 PHAGE_Yersin_413C 52.38% Detail
4 16.9Kb incomplete 40 10 970866-987852 Planktothrix phage PaV-LD 53.13% Detail
5 13.1Kb questionable 80 17 1831874-1845042 Enterobacteria phage 285P 52.16% Detail
6 29.3Kb incomplete 20 18 2043541-2072920 Salmonella phage SPN3UB 46.16% Detail
7 32.1Kb intact 150 45 3438981-3471099 Enterobacteria phage HK629 50.38% Detail
8 17.2Kb incomplete 20 17 3483177-3500387 Enterobacteria phage P4 55.91% Detail
9 26.2Kb incomplete 30 20 3658290-3684522 PHAGE_Entero_4795 48.76% Detail
10 34.8Kb intact 140 51 3922956-3957803 Escherichia phage D108 54.68% Detail
11 83.6Kb intact 150 121 3922956-4006591 Enterobacteria phage 285P 50.91% Detail
12 56.7Kb intact 130 66 3949870-4006591 Enterobacteria phage 285P 48.33% Detail
13 19Kb questionable 80 22 4444098-4463158 Escherichia phage HK639 46.70% Detail
14 9.2Kb questionable 80 18 4486354-4495569 Enterobacteria phage mEp460 52.34% Detail
15 5.2Kb incomplete 50 11 4508498-4513757 Enterobacteria phage P4 46.79% Detail
16 60.2Kb intact 150 77 4722196-4782452 Enterobacteria phage SfV 49.49% 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.