gi|308171891|ref|NC_014551.1| Bacillus amyloliquefaciens DSM 7, complete genome. .3980199, gc%: 46.08%,   chromosome

Definition Bacillus amyloliquefaciens DSM 7, complete genome.
Accession NC_014551
Length 3,980,199
Summary Detailed summary Map Image Text file for download
Total : 8 prophage regions have been identified, of which 4 regions are intact, 3 regions are incomplete, 1 region is questionable.
REGION REGION_LENGTH COMPLETENESS SCORE #CDS REGION_POSITION PHAGE GC_PERCENTAGE DETAIL
1 45.8Kb questionable 70 63 572646-618509 43.67% Detail
2 43.7Kb intact 150 46 869860-913622 40.95% Detail
3 28.5Kb incomplete 50 24 949583-978087 48.62% Detail
4 12.7Kb incomplete 60 18 1267193-1279966 46.68% Detail
5 38.3Kb intact 130 49 1332960-1371295 45.72% Detail
6 37.7Kb intact 100 27 2937280-2975047 37.06% Detail
7 26.7Kb intact 110 29 3127689-3154425 44.31% Detail
8 14.7Kb incomplete 50 17 3670019-3684807 49.96% 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

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.