Submission Results

Sequence Name: Not Available

GenBank Accession Number: PSUA01000012.1

GenInfo (GI) Number: 0000000000

Download Results:

gi|00000000|ref|PSUA01000012.1| Pseudoclavibacter sp. RFBA6 RFBA6_1, whole genome shotgun 735225, gc%: 68.04%

Download summary as .txt file: summary.txt file_download

Total: 1 prophage regions have been identified, of which 0 regions are intact, 1 regions are incomplete, and 0 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
147.4Kbincomplete3038359818-407253 info_outlinePHAGE_Arthro_Joann_NC_041942(4)66.59%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.

gi|00000000|ref|PSUA01000012.1| Pseudoclavibacter sp. RFBA6 RFBA6_1, whole genome shotgun 735225, gc%: 68.04%

Download details as .txt file: detail.txt file_download

Hits against Virus and Prophage Database
Hits against Bacterial Database or GenBank File

Region 1, total 42 CDS

#CDS PositionBLAST HitE-ValueSequence
2373188..374570PHAGE_Strept_phiCAM_NC_041856: RNA polymerase sigma factor; C5C17_11690; phage(gi100049)3.22e-72Showinfo_outline
3374742..376289PHAGE_Mycoba_Benedict_NC_042331: hypothetical protein; C5C17_11695; phage(gi100032)2.29e-28Showinfo_outline
4complement(376341..377483)hypothetical protein; C5C17_117000.0Showinfo_outline
5377720..378292hypothetical protein; C5C17_117050.0Showinfo_outline
6378289..379767hypothetical protein; C5C17_117100.0Showinfo_outline
9380258..380503hypothetical protein; C5C17_117250.0Showinfo_outline
10complement(380549..381037)hypothetical protein; C5C17_117300.0Showinfo_outline
11381065..381382PHAGE_Strept_SF3_NC_028952: hypothetical protein; C5C17_11735; phage(gi971759878)6.79e-26Showinfo_outline
12complement(381420..381665)hypothetical protein; C5C17_117400.0Showinfo_outline
13381961..382278hypothetical protein; C5C17_117450.0Showinfo_outline
14382482..382889PHAGE_Mycoba_Brujita_NC_011291: gp1; C5C17_11750; phage(gi206599545)3.05e-12Showinfo_outline
15382915..384603PHAGE_Gordon_GMA4_NC_030939: hypothetical protein; C5C17_11755; phage(gi100002)6.20e-150Showinfo_outline
16384622..385977PHAGE_Strept_phiELB20_NC_041849: hypothetical protein; C5C17_11760; phage(gi100007)8.19e-88Showinfo_outline
17385977..386723PHAGE_Gordon_Lucky10_NC_031267: DNA topoisomerase medium subunit; C5C17_11765; phage(gi100004)7.33e-10Showinfo_outline
18386787..387293hypothetical protein; C5C17_117700.0Showinfo_outline
19387323..388282PHAGE_Mycoba_Gardann_NC_031124: hypothetical protein; C5C17_11775; phage(gi100008)1.44e-45Showinfo_outline
20388343..388738PHAGE_Strept_phiELB20_NC_041849: hypothetical protein; C5C17_11780; phage(gi100011)5.55e-07Showinfo_outline
21388838..389197hypothetical protein; C5C17_117850.0Showinfo_outline
22389205..389486hypothetical protein; C5C17_117900.0Showinfo_outline
23389483..389881hypothetical protein; C5C17_117950.0Showinfo_outline
24389892..390449PHAGE_Gordon_Mahdia_NC_042089: hypothetical protein; C5C17_11800; phage(gi100011)6.15e-23Showinfo_outline
25390843..391172PHAGE_Gordon_Bowser_NC_030930: hypothetical protein; C5C17_11805; phage(gi100015)9.11e-10Showinfo_outline
26391184..393814PHAGE_Arthro_Joann_NC_041942: hypothetical protein; C5C17_11810; phage(gi100019)4.95e-69Showinfo_outline
27393825..394640PHAGE_Arthro_Abidatro_NC_042002: exonuclease A; C5C17_11815; phage(gi100018)1.14e-14Showinfo_outline
28394701..395849PHAGE_Arthro_Abidatro_NC_042002: hypothetical protein; C5C17_11820; phage(gi100019)5.96e-28Showinfo_outline
29395846..397141PHAGE_Lactob_phig1e_NC_004305: minor capsid protein; C5C17_11825; phage(gi23455811)1.61e-14Showinfo_outline
30397141..397572PHAGE_Bacill_G_NC_023719: gp183; C5C17_11830; phage(gi593777640)4.42e-15Showinfo_outline
31397565..397768hypothetical protein; C5C17_118350.0Showinfo_outline
32397768..398217hypothetical protein; C5C17_118400.0Showinfo_outline
33398227..399501PHAGE_Gordon_CarolAnn_NC_031118: hypothetical protein; C5C17_11845; phage(gi100031)5.06e-60Showinfo_outline
34399503..400183PHAGE_Gordon_CarolAnn_NC_031118: hypothetical protein; C5C17_11850; phage(gi100032)5.09e-17Showinfo_outline
35400196..400564hypothetical protein; C5C17_118550.0Showinfo_outline
36400561..401484PHAGE_Arthro_Joann_NC_041942: hypothetical protein; C5C17_11860; phage(gi100002)1.58e-09Showinfo_outline
37401499..401720PHAGE_Arthro_Glenn_NC_041940: hypothetical protein; C5C17_11865; phage(gi100003)2.52e-07Showinfo_outline
38401785..402471PHAGE_Leucon_1_A4_NC_027987: phage-related amidase; C5C17_11870; phage(gi937533154)1.23e-26Showinfo_outline
39402474..402965PHAGE_Microb_Dismas_NC_042099: hypothetical protein; C5C17_11875; phage(gi100022)2.48e-10Showinfo_outline
40402958..403380hypothetical protein; C5C17_118800.0Showinfo_outline
41403389..403658PHAGE_Arthro_Molivia_NC_042001: rnaseH; C5C17_11885; phage(gi100048)3.20e-10Showinfo_outline
Pseudoclavibacter sp
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

Viewer Options
Length: 735225 bps
Phages: 1
Click on a region in the genome above to show details here.
Viewer Options
Click on a sequence to see details.
Portal Protein
Coat Protein
Tail Shaft
Attachment Site
Phage-like Protein
Hypotheical Protein
Fiber Protein
Plate Protein

Download data as .txt file: png_input file_download