||Aggregatibacter phage S1249
||Clostridium phage phiMMP04
||Prophage Escherichia coli str. K-12 substr. MG1655
|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):
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.
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).
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.