Submission Results

Sequence Name: Not Available

GenBank Accession Number: WUUI01000014.1

GenInfo (GI) Number: 0000000000

Download Results: WUUI01000014.1.PHASTER.zip

gi|00000000|ref|WUUI01000014.1| Clostridioides difficile strain TMD0138 135990, gc%: 27.55%

Download summary as .txt file: summary.txt file_download

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

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
142.6Kbintact140474745-47397 info_outlinePHAGE_Clostr_phiMMP01_NC_028883(11)28.66%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|WUUI01000014.1| Clostridioides difficile strain TMD0138 135990, gc%: 27.55%

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 49 CDS

#CDS PositionBLAST HitE-ValueSequence
14745..4764attL0.0Showinfo_outline
25435..5620PHAGE_Clostr_phiCD111_NC_028905: hypothetical protein; GSM30_13825; phage(gi971820076)7.94e-14Showinfo_outline
3complement(5665..6471)PHAGE_Clostr_phiCD111_NC_028905: Endolysine; GSM30_13830; phage(gi971820068)3.00e-175Showinfo_outline
4complement(6471..6737)PHAGE_Clostr_phiCD111_NC_028905: putative holin; GSM30_13835; phage(gi971820067)3.71e-53Showinfo_outline
5complement(6979..7314)PHAGE_Clostr_phiCD211_NC_029048: hypothetical protein; GSM30_13840; phage(gi981220885)5.44e-46Showinfo_outline
6complement(7320..9659)PHAGE_Clostr_phiCD211_NC_029048: Putative tail fiber protein (fragment); GSM30_13845; phage(gi981220880)7.95e-29Showinfo_outline
7complement(9684..11666)PHAGE_Clostr_phiCD111_NC_028905: Tail fiber protein; GSM30_13850; phage(gi971820066)0.0Showinfo_outline
8complement(11666..13885)PHAGE_Clostr_phiCD111_NC_028905: Tail fiber protein; GSM30_13855; phage(gi971820065)2.06e-33Showinfo_outline
9complement(13892..16660)PHAGE_Clostr_phiCD111_NC_028905: Tail protein/endopeptidase; GSM30_13860; phage(gi971820063)6.74e-164Showinfo_outline
10complement(16662..17417)PHAGE_Clostr_phiCD111_NC_028905: Tail component protein; GSM30_13865; phage(gi971820062)3.42e-52Showinfo_outline
11complement(17578..17727)PHAGE_Clostr_phiCD111_NC_028905: hypothetical protein; GSM30_13870; phage(gi971820079)1.81e-19Showinfo_outline
12complement(17855..23608)PHAGE_Clostr_phiCD6356_NC_015262: putative phage tail tape measure protein; GSM30_13875; phage(gi326536862)0.0Showinfo_outline
13complement(23688..24059)hypothetical protein; GSM30_138800.0Showinfo_outline
14complement(24740..24949)PHAGE_Clostr_phiCTP1_NC_014457: hypothetical protein; GSM30_13885; phage(gi304360683)2.90e-05Showinfo_outline
15complement(24930..25406)PHAGE_Clostr_phiCT19406A_NC_030950: late promoter transcription; GSM30_13890; phage(gi100046)3.49e-15Showinfo_outline
16complement(25462..26268)PHAGE_Clostr_phiCTP1_NC_014457: hypothetical protein; GSM30_13895; phage(gi304360680)4.93e-34Showinfo_outline
17complement(26274..26618)PHAGE_Clostr_phiCT19406A_NC_030950: ssDNA binding protein; GSM30_13900; phage(gi100044)3.71e-18Showinfo_outline
18complement(26626..27060)PHAGE_Clostr_phiMMP02_NC_019421: putative tail component; GSM30_13905; phage(gi414090375)1.74e-24Showinfo_outline
19complement(27062..27424)PHAGE_Clostr_phiCT19406A_NC_030950: sliding clamp DNA polymerase; GSM30_13910; phage(gi100042)5.24e-07Showinfo_outline
20complement(27421..27675)PHAGE_Clostr_phiCT19406A_NC_030950: clamp-loader subunit; GSM30_13915; phage(gi100041)1.28e-08Showinfo_outline
21complement(27700..28668)PHAGE_Clostr_phiCT9441A_NC_029022: coat protein; GSM30_13920; phage(gi971821685)3.89e-170Showinfo_outline
22complement(28686..29321)PHAGE_Clostr_phiCT9441A_NC_029022: minor structural protein; GSM30_13925; phage(gi971821684)5.01e-22Showinfo_outline
23complement(29458..29697)hypothetical protein; GSM30_139300.0Showinfo_outline
24complement(29691..31094)PHAGE_Clostr_phiCT19406A_NC_030950: membrane-associated initiation of head vertex; GSM30_13935; phage(gi100034)8.31e-83Showinfo_outline
25complement(31094..32578)PHAGE_Strept_Dp_1_NC_015274: portal protein; GSM30_13940; phage(gi327198352)1.81e-38Showinfo_outline
26complement(32589..33851)PHAGE_Brevib_Jimmer2_NC_041976: hypothetical protein; GSM30_13945; phage(gi100002)0.0Showinfo_outline
27complement(33844..34284)PHAGE_Thermu_OH2_NC_021784: terminase small subunit; GSM30_13950; phage(gi526118336)1.99e-40Showinfo_outline
28complement(34710..34916)PHAGE_Clostr_phiMMP01_NC_028883: hypothetical protein; GSM30_13955; phage(gi971820038)7.64e-44Showinfo_outline
29complement(35337..35837)PHAGE_Clostr_phiMMP01_NC_028883: hypothetical protein; GSM30_13960; phage(gi971820036)3.53e-115Showinfo_outline
30complement(35856..36272)PHAGE_Clostr_phiMMP01_NC_028883: hypothetical protein; GSM30_13965; phage(gi971820035)3.97e-91Showinfo_outline
31complement(36299..36496)PHAGE_Clostr_phiMMP01_NC_028883: hypothetical protein; GSM30_13970; phage(gi971820034)1.73e-40Showinfo_outline
32complement(36672..36791)PHAGE_Clostr_phiMMP01_NC_028883: hypothetical protein; GSM30_13975; phage(gi971820032)1.36e-20Showinfo_outline
33complement(36909..37271)PHAGE_Clostr_phiCD27_NC_011398: hypothetical protein; GSM30_13980; phage(gi209901296)6.53e-47Showinfo_outline
34complement(37301..37720)PHAGE_Clostr_phiCD111_NC_028905: Single-stranded DNA-binding protein 2; GSM30_13985; phage(gi971820092)7.79e-50Showinfo_outline
35complement(37740..38636)PHAGE_Clostr_phiMMP01_NC_028883: putative DnaD; GSM30_13990; phage(gi971820025)1.22e-19Showinfo_outline
36complement(38646..39284)PHAGE_Clostr_phiCD505_NC_028764: putative phage essential recombination function protein; GSM30_13995; phage(gi971819888)9.21e-99Showinfo_outline
37complement(39271..39552)hypothetical protein; GSM30_140000.0Showinfo_outline
38complement(39631..39873)PHAGE_Clostr_phiCD505_NC_028764: hypothetical protein; GSM30_14005; phage(gi971819886)1.53e-45Showinfo_outline
39complement(40163..40555)PHAGE_Clostr_phiC2_NC_009231: hypothetical protein; GSM30_14010; phage(gi134287391)2.01e-25Showinfo_outline
4040725..40961hypothetical protein; GSM30_140150.0Showinfo_outline
41complement(40919..41101)hypothetical protein; GSM30_140200.0Showinfo_outline
42complement(41149..41964)PHAGE_Lister_B054_NC_009813: gp72; GSM30_14025; phage(gi157325355)5.39e-71Showinfo_outline
43complement(41967..42188)PHAGE_Clostr_CDMH1_NC_024144: putative transcriptional regulator protein; GSM30_14030; phage(gi640884901)1.09e-14Showinfo_outline
4442341..42904PHAGE_Brevib_Abouo_NC_029029: transcriptional regulator; GSM30_14035; phage(gi971767217)9.92e-24Showinfo_outline
4542916..43461PHAGE_Clostr_phiMMP01_NC_028883: putative repressor; GSM30_14040; phage(gi971820010)1.42e-27Showinfo_outline
4643485..45074PHAGE_Bacill_phBC6A51_NC_004820: hypothetical protein; GSM30_14045; phage(gi31415804)2.89e-80Showinfo_outline
4745336..45842PHAGE_Lister_LP_030_2_NC_021539: DUF955 domain containing protein; GSM30_14050; phage(gi514051963)4.35e-09Showinfo_outline
4846082..47212PHAGE_Clostr_phiMMP01_NC_028883: putative integrase; GSM30_14055; phage(gi971820006)3.68e-164Showinfo_outline
4947397..47416attR0.0Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 135990 bps
Phages: 1
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Click on a region in the genome above to show details here.
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Click on a sequence to see details.
Lysis
Terminase
Portal Protein
Protease
Coat Protein
Tail Shaft
Attachment Site
Integrase
Phage-like Protein
Hypotheical Protein
Other
Transposase
Fiber Protein
Plate Protein
tRNA

Download data as .txt file: png_input file_download