Submission Results

Sequence Name: Clostridium difficile 630 complete genome.

GenBank Accession Number: AM180355.1 open_in_new

GenInfo (GI) Number: 115249003 open_in_new

Download Results: AM180355.1.PHASTER.zip

gi|115249003|ref|AM180355.1| Clostridium difficile 630 complete genome. .4290252, gc%: 29.06%

Download summary as .txt file: summary.txt file_download

Total: 5 prophage regions have been identified, of which 2 regions are intact, 3 regions are incomplete, and 0 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
129Kbincomplete2018428477-457542 info_outlinePHAGE_Ectoca_siliculosus_virus_1(3)38.49%Show info_outline
228.4Kbincomplete3011507851-536329 info_outlinePHAGE_Plankt_PaV_LD(1)30.76%Show info_outline
355.8Kbintact140881088001-1143874 info_outlinePHAGE_Clostr_phiC2(46)28.45%Show info_outline
427.3Kbincomplete60301571945-1599297 info_outlinePHAGE_Clostr_phi_CD119(14)28.01%Show info_outline
557.3Kbintact140683377033-3434358 info_outlinePHAGE_Clostr_phiC2(41)29.45%Show info_outline
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)
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.
# Total Proteins: The number of ORFs present in the region.
Region Position: The start and end positions of the region on the bacterial chromosome.
Most Common Phage: The phage(s) with the highest number of proteins most similar to those in the region.
GC %: The percentage of GC nucleotides 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.