Submission Results

Sequence Name: Not Available

GenBank Accession Number: PSYC01000020.1

GenInfo (GI) Number: 0000000000

Download Results:

gi|00000000|ref|PSYC01000020.1| Pseudoclavibacter sp. RFBG4 RFBG4_5, whole genome shotgun 255643, gc%: 67.45%

Download summary as .txt file: summary.txt file_download

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

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
120.5Kbincomplete501848313-68904 info_outlinePHAGE_Strept_Amela_NC_028904(3)64.81%Show info_outline
211.2Kbincomplete3019242471-253670 info_outlinePHAGE_Microb_Min1_NC_009603(5)67.54%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|PSYC01000020.1| Pseudoclavibacter sp. RFBG4 RFBG4_5, whole genome shotgun 255643, gc%: 67.45%

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 23 CDS

#CDS PositionBLAST HitE-ValueSequence
2complement(52561..53742)PHAGE_Brocho_BL3_NC_015254: gp26; C5E10_05300; phage(gi327409418)7.29e-30Showinfo_outline
3complement(54363..54674)PHAGE_Gordon_Bantam_NC_031074: hypothetical protein; C5E10_05305; phage(gi100132)1.07e-13Showinfo_outline
4complement(54737..55288)PHAGE_Lactoc_bIL311_NC_002670: Orf21; C5E10_05310; phage(gi13095679)5.25e-12Showinfo_outline
5complement(55522..55788)PHAGE_Arthro_Molivia_NC_042001: rnaseH; C5E10_05315; phage(gi100048)3.29e-10Showinfo_outline
6complement(55785..56480)PHAGE_Strept_phiHau3_NC_018836: putative portal; C5E10_05320; phage(gi410490964)1.37e-30Showinfo_outline
7complement(56499..58187)PHAGE_Gordon_GMA4_NC_030939: hypothetical protein; C5E10_05325; phage(gi100002)9.84e-149Showinfo_outline
8complement(58213..58620)PHAGE_Mycoba_Brujita_NC_011291: gp1; C5E10_05330; phage(gi206599545)2.72e-12Showinfo_outline
9complement(58824..59540)hypothetical protein; C5E10_053350.0Showinfo_outline
10complement(59720..60037)PHAGE_Strept_SF3_NC_028952: hypothetical protein; C5E10_05340; phage(gi971759878)5.85e-26Showinfo_outline
1160065..60553hypothetical protein; C5E10_053450.0Showinfo_outline
1360966..62480hypothetical protein; C5E10_053550.0Showinfo_outline
1462660..62959hypothetical protein; C5E10_053600.0Showinfo_outline
15complement(62981..63178)hypothetical protein; C5E10_053650.0Showinfo_outline
16complement(63175..63402)hypothetical protein; C5E10_053700.0Showinfo_outline
1763742..64197hypothetical protein; C5E10_053750.0Showinfo_outline
18complement(64247..65851)PHAGE_Mycoba_Severus_NC_021307: integrase, s-int; C5E10_05380; phage(gi508179854)3.56e-28Showinfo_outline
20complement(66040..66675)PHAGE_Mycoba_PegLeg_NC_021299: integrase; C5E10_05385; phage(gi508177970)7.02e-20Showinfo_outline
22complement(66715..67377)PHAGE_Strept_Caliburn_NC_028892: serine integrase; C5E10_05390; phage(gi971753190)6.42e-27Showinfo_outline

Region 2, total 20 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(242471..242803)PHAGE_Mycoba_SkinnyPete_NC_041882: membrane-associated initiation of head vertex; C5E10_06195; phage(gi100034)4.38e-05Showinfo_outline
2242892..243107PHAGE_Acidia_virus_NC_029316: transposase; C5E10_06200; phage(gi1002166849)3.97e-05Showinfo_outline
3complement(243293..243517)hypothetical protein; C5E10_062050.0Showinfo_outline
4243742..244533PHAGE_Gordon_Attis_NC_041883: RNA polymerase binding protein; C5E10_06210; phage(gi100043)8.13e-49Showinfo_outline
5244728..245111hypothetical protein; C5E10_062150.0Showinfo_outline
6245108..245494hypothetical protein; C5E10_062200.0Showinfo_outline
7245491..246495PHAGE_Microb_Min1_NC_009603: hypothetical protein; C5E10_06225; phage(gi149882795)5.03e-21Showinfo_outline
8246498..247178PHAGE_Microb_Min1_NC_009603: hypothetical protein; C5E10_06230; phage(gi149882796)1.32e-15Showinfo_outline
9247175..247519PHAGE_Microb_Min1_NC_009603: hypothetical protein; C5E10_06235; phage(gi149882797)1.60e-20Showinfo_outline
10247516..248325PHAGE_Rhizob_vB_RleM_PPF1_NC_025427: putative adenine-specific methyltransferase; C5E10_06240; phage(gi712912781)3.03e-43Showinfo_outline
11248322..248732hypothetical protein; C5E10_062450.0Showinfo_outline
12249087..249764PHAGE_Microb_Min1_NC_009603: hypothetical protein; C5E10_06250; phage(gi149882802)1.06e-46Showinfo_outline
13249739..250068hypothetical protein; C5E10_062550.0Showinfo_outline
14250068..250355hypothetical protein; C5E10_062600.0Showinfo_outline
15250355..250885PHAGE_Microb_Min1_NC_009603: single-stranded DNA-binding protein; C5E10_06265; phage(gi149882804)5.63e-69Showinfo_outline
16251118..251486PHAGE_Mycoba_Theia_NC_028960: hypothetical protein; C5E10_06270; phage(gi971760938)1.88e-15Showinfo_outline
17251479..252081hypothetical protein; C5E10_062750.0Showinfo_outline
18252349..253215hypothetical protein; C5E10_062800.0Showinfo_outline
20253359..253670PHAGE_Gordon_Gustav_NC_042088: hypothetical protein; C5E10_06285; phage(gi100068)9.27e-18Showinfo_outline
Pseudoclavibacter sp
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 255643 bps
Phages: 2
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Click on a sequence to see details.
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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