Submission Results

Sequence Name: Not Available

GenBank Accession Number: AM406671 open_in_new

GenInfo (GI) Number: 0000000000 open_in_new

Download Results: AM406671.PHASTER.zip

gi|00000000|ref|AM406671.1| Lactococcus lactis subsp. cremoris MG1363, complete genome. 2529478, gc%: 35.75%

Download summary as .txt file: summary.txt file_download

Total: 16 prophage regions have been identified, of which 2 regions are intact, 13 regions are incomplete, and 1 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
134.7Kbintact983025908-60657 info_outlinePHAGE_Lactoc_bIL310_NC_002669(19)35.18%Show info_outline
29.5Kbincomplete2013545001-554598 info_outlinePHAGE_Shigel_SfIV_NC_022749(2)33.93%Show info_outline
327.4Kbincomplete5016593485-620935 info_outlinePHAGE_Lactob_phiAT3_NC_005893(2)35.40%Show info_outline
413.6Kbincomplete6013667479-681171 info_outlinePHAGE_Staphy_SPbeta_like_NC_029119(2)34.08%Show info_outline
514.7Kbincomplete4011693054-707763 info_outlinePHAGE_Shigel_SfIV_NC_022749(2)32.94%Show info_outline
643Kbincomplete5060778852-821910 info_outlinePHAGE_Lactoc_PLgT_1_NC_031016(22)35.05%Show info_outline
710.5Kbincomplete2013861704-872284 info_outlinePHAGE_Lactob_phiAT3_NC_005893(2)35.08%Show info_outline
837.4Kbincomplete4029932389-969852 info_outlinePHAGE_Prochl_P_SSM2_NC_006883(3)36.81%Show info_outline
97.6Kbincomplete2081107609-1115264 info_outlinePHAGE_Shigel_SfIV_NC_022749(2)32.88%Show info_outline
106Kbincomplete3091198699-1204779 info_outlinePHAGE_Paenib_Leyra_NC_048692(2)33.05%Show info_outline
1116.4Kbquestionable90181226569-1243023 info_outlinePHAGE_Entero_fiAA91_ss_NC_022750(2)34.94%Show info_outline
1225.7Kbincomplete60211310020-1335809 info_outlinePHAGE_Acinet_vB_AbaM_ME3_NC_041884(4)34.09%Show info_outline
1310.3Kbincomplete10101685283-1695666 info_outlinePHAGE_Lactob_phiAT3_NC_005893(2)33.98%Show info_outline
1415.2Kbincomplete4091822453-1837732 info_outlinePHAGE_Lactob_phiAT3_NC_005893(2)36.26%Show info_outline
1514.9Kbincomplete50101867286-1882273 info_outlinePHAGE_Lactoc_bIL312_NC_002671(2)35.58%Show info_outline
1649.4Kbintact150682061037-2110526 info_outlinePHAGE_Lactoc_lato_NC_004746(21)35.83%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.