Submission Results

Sequence Name: Not Available

GenBank Accession Number: QVGA00000000.1 open_in_new

GenInfo (GI) Number: 0000000000 open_in_new

Download Results: QVGA00000000.1.PHASTER.zip

gi|00000000|ref|QVGA00000000.1| Klebsiella pneumoniae strain SWKP178, whole genome shotgun 5544954, gc%: 57.34%

Download summary as .txt file: summary.txt file_download

Total: 14 prophage regions have been identified, of which 7 regions are intact, 6 regions are incomplete, and 1 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
138.8Kbintact1203631083-69907 info_outlinePHAGE_Klebsi_phiKO2_NC_005857(23)53.91%Show info_outline
233.3Kbintact15043359702-393027 info_outlinePHAGE_Salmon_Fels_2_NC_010463(35)51.46%Show info_outline
349Kbintact12062845591-894604 info_outlinePHAGE_Escher_phiV10_NC_007804(31)52.74%Show info_outline
441.2Kbintact100272500385-2541642 info_outlinePHAGE_Salmon_ST64B_NC_004313(3)53.94%Show info_outline
531.8Kbincomplete40324199641-4231459 info_outlinePHAGE_Escher_HK639_NC_016158(6)53.35%Show info_outline
642.5Kbintact110454697122-4739710 info_outlinePHAGE_Salmon_SEN34_NC_028699(19)53.70%Show info_outline
742.1Kbintact150514805962-4848103 info_outlinePHAGE_Salmon_118970_sal3_NC_031940(12)51.50%Show info_outline
825Kbintact150334971675-4996731 info_outlinePHAGE_Salmon_RE_2010_NC_019488(25)56.30%Show info_outline
96.3Kbincomplete3095360962-5367318 info_outlinePHAGE_Entero_P4_NC_001609(5)55.25%Show info_outline
1015.2Kbincomplete40225385236-5400438 info_outlinePHAGE_Salmon_SEN34_NC_028699(6)52.90%Show info_outline
1128.7Kbincomplete30215440029-5468802 info_outlinePHAGE_Salmon_Fels_2_NC_010463(10)57.51%Show info_outline
1225Kbincomplete50225482255-5507254 info_outlinePHAGE_Salmon_SJ46_NC_031129(5)54.73%Show info_outline
1312.3Kbincomplete30205504593-5516925 info_outlinePHAGE_Sphing_PAU_NC_019521(4)50.56%Show info_outline
1419.2Kbquestionable70215519857-5539080 info_outlinePHAGE_Entero_P4_NC_001609(2)51.69%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.