Psudo Genome,   chromosome

Definition Streptococcus pyogenes MGAS5005 chromosome, complete genome.
Accession NC_007297
Length 1,838,554
Summary Detailed summary Map Image Text file for download
Total : 3 prophage regions have been identified, of which 2 regions are intact, 0 regions are incomplete, 1 region is questionable.
REGION REGION_LENGTH COMPLETENESS SCORE #CDS REGION_POSITION PHAGE GC_PERCENTAGE DETAIL
1 48.4Kb questionable 87 63 981099-1029543 Streptococcus phage 5093 37.47% Detail
2 35.8Kb intact 106 57 1143271-1179151 Streptococcus pyogenes phage 315.3 37.76% Detail
3 44.2Kb intact 116 57 1385206-1429409 Streptococcus phage P9 39.51% 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.