gi|259042952|ref|ACZD00000000.1| Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884 .5280675, GC%: 57.23%, length = 5280675 bps

Total : 11 prophage regions have been identified, of which 5 regions are intact, 5 regions are incomplete, 1 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 38.8Kb intact 150 52 9118-47992 Cronobacter phage ENT47670 52.52% Detail
2 21.5Kb incomplete 30 31 432570-454126 PHAGE_Entero_epsilon15 53.18% Detail
3 36.3Kb questionable 90 38 965345-1001742 Escherichia phage HK639 52.72% Detail
4 37.8Kb incomplete 40 33 1068250-1106112 Cronobacter phage phiES15 55.27% Detail
5 24.3Kb intact 150 34 2531845-2556186 Salmonella phage RE-2010 55.25% Detail
6 36.5Kb intact 130 43 3336811-3373386 PHAGE_Acyrth_1 54.42% Detail
7 26Kb incomplete 60 33 3481043-3507069 PHAGE_Entero_phiV10 53.94% Detail
8 46Kb intact 120 62 3555790-3601872 Pectobacterium phage ZF40 50.88% Detail
9 19.8Kb incomplete 10 32 3625123-3645002 Enterobacteria phage mEp237 53.71% Detail
10 23.6Kb incomplete 30 30 3674717-3698326 Salmonella phage 19 55.24% Detail
11 39.4Kb intact 120 34 4407172-4446580 Enterobacteria phage mEpX2 53.02% 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.