Submission Results

Sequence Name: Not Available

GenBank Accession Number: 1057340342

GenInfo (GI) Number: 0000000000

Download Results:

gi|00000000|ref|NZ_CP014167.1| Paenibacillus yonginensis strain DCY84 chromosome, complete 4985901, gc%: 51.01%

Download summary as .txt file: summary.txt file_download

Total: 2 prophage regions have been identified, of which 0 regions are intact, 1 regions are incomplete, and 1 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
114.1Kbincomplete3020709943-724109 info_outlinePHAGE_Lister_B054_NC_009813(11)50.35%Show info_outline
210Kbquestionable70131414048-1424050 info_outlinePHAGE_Bacill_G_NC_023719(2)47.98%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|NZ_CP014167.1| Paenibacillus yonginensis strain DCY84 chromosome, complete 4985901, gc%: 51.01%

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 20 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(709943..710428)PHAGE_Thermu_OH2_NC_021784: predicted Zn peptidase; AWM70_RS03205; phage(gi526118363)2.08e-32Showinfo_outline
2complement(710450..710890)PHAGE_Geobac_GBSV1_NC_008376: immunity repressor protein; AWM70_RS03210; phage(gi115334658)5.28e-25Showinfo_outline
3711191..711685PHAGE_Brevib_Jimmer2_NC_041976: hypothetical protein; AWM70_RS03215; phage(gi100100)6.09e-40Showinfo_outline
4711920..712417hypothetical protein; AWM70_RS032200.0Showinfo_outline
5712404..713408PHAGE_Deep_s_D6E_NC_019544: hypothetical protein; AWM70_RS03225; phage(gi423262335)8.30e-43Showinfo_outline
6713436..713837PHAGE_Deep_s_D6E_NC_019544: phage structure protein; AWM70_RS03230; phage(gi423262336)1.58e-09Showinfo_outline
7713929..714231PHAGE_Lister_B054_NC_009813: gp16; AWM70_RS03235; phage(gi157325300)9.10e-10Showinfo_outline
8714197..714379hypothetical protein; AWM70_RS032400.0Showinfo_outline
9714394..716517PHAGE_Clostr_phiCD111_NC_028905: Tail tape measure; AWM70_RS03245; phage(gi971820061)4.65e-46Showinfo_outline
10716517..717065PHAGE_Deep_s_D6E_NC_019544: hypothetical protein; AWM70_RS03250; phage(gi423262338)1.75e-05Showinfo_outline
11717068..717403PHAGE_Deep_s_D6E_NC_019544: hypothetical protein; AWM70_RS03255; phage(gi423262339)5.44e-25Showinfo_outline
12717396..718196PHAGE_Deep_s_D6E_NC_019544: hypothetical protein; AWM70_RS03260; phage(gi423262340)3.48e-53Showinfo_outline
13718178..718585PHAGE_Lister_B054_NC_009813: gp22; AWM70_RS03265; phage(gi157325306)6.31e-11Showinfo_outline
14718573..718923PHAGE_Deep_s_D6E_NC_019544: hypothetical protein; AWM70_RS03270; phage(gi423262341)1.63e-12Showinfo_outline
15718913..720088PHAGE_Deep_s_D6E_NC_019544: baseplate protein; AWM70_RS03275; phage(gi423262343)7.18e-126Showinfo_outline
16720081..720722PHAGE_Deep_s_D6E_NC_019544: hypothetical protein; AWM70_RS03280; phage(gi423262344)4.08e-72Showinfo_outline
17720744..722300PHAGE_Deep_s_D6E_NC_019544: tail fiber protein; AWM70_RS03285; phage(gi423262345)5.50e-11Showinfo_outline
18722315..722629hypothetical protein; AWM70_RS032900.0Showinfo_outline
19723254..723481PHAGE_Brevib_Abouo_NC_029029: hypothetical protein; AWM70_RS03295; phage(gi971767202)1.16e-12Showinfo_outline
20723489..724109PHAGE_Bacill_phi29_NC_011048: peptidoglycan hydrolase; AWM70_RS03300; phage(gi194186889)1.10e-38Showinfo_outline

Region 2, total 13 CDS

#CDS PositionBLAST HitE-ValueSequence
1complement(1414048..1414299)PHAGE_Hypert_2_NC_014321: IS element Dka2 orfA; AWM70_RS06505; phage(gi300116744)1.64e-06Showinfo_outline
21414381..1414671PROPHAGE_Shewan_MR-1: ISSod1, transposase OrfA; AWM70_RS06510; phage(gi24373865)2.29e-06Showinfo_outline
31414695..1415555PROPHAGE_Escher_CFT073: transposase insF; AWM70_RS06515; phage(gi26249410)1.62e-48Showinfo_outline
4complement(1415607..1415750)PROPHAGE_Salmon_Ty2: transposase; AWM70_RS22610; phage(gi29143766)7.60e-10Showinfo_outline
51415820..1416971PROPHAGE_Escher_MG1655: IS3 transposase B; AWM70_RS06520; phage(gi16128284)4.66e-77Showinfo_outline
6complement(1417001..1417087)PROPHAGE_Salmon_Ty2: transposase; AWM70_RS22615; phage(gi29143766)2.17e-07Showinfo_outline
71417258..1418384PHAGE_Bacter_Diva_NC_028788: transposase-like protein; AWM70_RS06530; phage(gi971743572)6.70e-126Showinfo_outline
81418785..1419738PHAGE_Bacill_G_NC_023719: gp344; AWM70_RS06535; phage(gi593777800)4.55e-70Showinfo_outline
91419810..1420328thiol peroxidase; AWM70_RS065400.0Showinfo_outline
101420538..1421392PHAGE_Plankt_PaV_LD_NC_016564: ABC transporter; AWM70_RS06545; phage(gi371496158)8.95e-09Showinfo_outline
111421385..1422041ABC-2 transporter permease; AWM70_RS065500.0Showinfo_outline
121422038..1422403GntR family transcriptional regulator; AWM70_RS065550.0Showinfo_outline
13complement(1422578..1424050)PHAGE_Mycoba_Enkosi_NC_028936: transporter-like protein; AWM70_RS06560; phage(gi971757643)2.03e-25Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 4985901 bps
Phages: 2
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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