Submission Results

Sequence Name: Not Available

GenBank Accession Number: UGHB01000001.1

GenInfo (GI) Number: 0000000000

Download Results: UGHB01000001.1.PHASTER.zip

gi|00000000|ref|UGHB01000001.1| Gordonia bronchialis strain NCTC10667 genome assembly, contig: 5217573, gc%: 67.07%

Download summary as .txt file: summary.txt file_download

Total: 3 prophage regions have been identified, of which 0 regions are intact, 2 regions are incomplete, and 1 regions are questionable.

RegionRegion LengthCompletenessScore# Total ProteinsRegion PositionMost Common PhageGC %Details
125.9Kbquestionable7023402331-428317 info_outlinePHAGE_Gordon_Blueberry_NC_030943(2)63.97%Show info_outline
223.1Kbincomplete409747553-770694 info_outlinePHAGE_Gordon_Blueberry_NC_030943(2)66.16%Show info_outline
321.7Kbincomplete10101227245-1249022 info_outlinePHAGE_Gordon_Blueberry_NC_030943(2)62.32%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|UGHB01000001.1| Gordonia bronchialis strain NCTC10667 genome assembly, contig: 5217573, gc%: 67.07%

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 25 CDS

#CDS PositionBLAST HitE-ValueSequence
1402331..404862PHAGE_Mycoba_Bernardo_NC_022983: type III restriction helicase; NCTC10667_00365; phage(gi563399135)1.09e-11Showinfo_outline
2404865..406421PHAGE_Entero_fiAA91_ss_NC_022750: IS21 transposase; NCTC10667_00366; phage(gi557307612)1.25e-19Showinfo_outline
3406474..407235PHAGE_Entero_fiAA91_ss_NC_022750: IS21 transposition protein; NCTC10667_00367; phage(gi557307613)2.97e-33Showinfo_outline
4complement(407828..408946)PHAGE_Strept_TP1604_NC_028818: DNA methylase; NCTC10667_00368; phage(gi971746061)1.12e-90Showinfo_outline
5complement(408946..409266)Uncharacterised protein; NCTC10667_003690.0Showinfo_outline
6complement(409478..410272)PHAGE_Burkho_Bcep22_NC_005262: ISL3 family transposase; NCTC10667_00370; phage(gi38640338)5.08e-07Showinfo_outline
7complement(410235..411197)PROPHAGE_Xantho_306: transposase; NCTC10667_00371; phage(gi21243165)2.53e-87Showinfo_outline
8complement(411200..411466)PHAGE_Gordon_Cucurbita_NC_031029: hypothetical protein; NCTC10667_00372; phage(gi100019)1.10e-46Showinfo_outline
9411983..412249PHAGE_Gordon_Cucurbita_NC_031029: hypothetical protein; NCTC10667_00373; phage(gi100019)1.10e-46Showinfo_outline
10412252..413214PROPHAGE_Xantho_306: transposase; NCTC10667_00374; phage(gi21243165)2.53e-87Showinfo_outline
11complement(413165..413527)Transposase and inactivated derivatives; NCTC10667_003750.0Showinfo_outline
12413754..414395PHAGE_Mycoba_Mufasa_NC_028759: hypothetical protein; NCTC10667_00376; phage(gi971740757)7.90e-11Showinfo_outline
13414507..414995Uncharacterised protein; NCTC10667_003770.0Showinfo_outline
14complement(415152..416372)PHAGE_Ralsto_RSA1_NC_009382: transposase IRSO15-like; NCTC10667_00378; phage(gi145708108)3.31e-26Showinfo_outline
15416837..417130Uncharacterised protein; NCTC10667_003790.0Showinfo_outline
16417282..420761PHAGE_Gordon_Katyusha_NC_041950: hypothetical protein; NCTC10667_00380; phage(gi100058)3.38e-47Showinfo_outline
17complement(420846..421631)PAP2 superfamily; NCTC10667_003810.0Showinfo_outline
18421719..422234Uncharacterised protein; NCTC10667_003820.0Showinfo_outline
19422252..423766Predicted integral membrane protein; NCTC10667_003830.0Showinfo_outline
20complement(423813..424331)N-acyltransferase YncA; NCTC10667_003840.0Showinfo_outline
21424414..425202arylformamidase; NCTC10667_003850.0Showinfo_outline
22425199..426863Sulfoacetaldehyde acetyltransferase; NCTC10667_003860.0Showinfo_outline
23426931..426944attL0.0Showinfo_outline
24complement(426972..427856)PHAGE_Burkho_phiE125_NC_003309: putative transposase OrfB; NCTC10667_00387; phage(gi17975200)1.40e-73Showinfo_outline
25428317..428330attR0.0Showinfo_outline

Region 2, total 11 CDS

#CDS PositionBLAST HitE-ValueSequence
1747553..747570attL0.0Showinfo_outline
2762153..763778PHAGE_Cellul_phi14:2_NC_021806: chaperonin GroEL; NCTC10667_00722; phage(gi526178751)5.08e-103Showinfo_outline
3764044..764508PHAGE_Brevib_Jenst_NC_028805: putative major virion structural protein; NCTC10667_00723; phage(gi971744883)1.22e-05Showinfo_outline
4complement(764623..765579)Uncharacterized ABC transporter solute-binding protein yclQ precursor; NCTC10667_007240.0Showinfo_outline
5complement(765662..766408)transcriptional regulator BetI; NCTC10667_007250.0Showinfo_outline
6766517..767725PHAGE_Mycoba_Enkosi_NC_028936: transporter-like protein; NCTC10667_00726; phage(gi971757643)2.27e-46Showinfo_outline
7complement(767754..768080)PROPHAGE_Xantho_306: transposase; NCTC10667_00727; phage(gi21243165)2.31e-20Showinfo_outline
8768100..769362PROPHAGE_Escher_MG1655: IS30 transposase; NCTC10667_00728; phage(gi16132105)1.33e-65Showinfo_outline
9769463..769729PHAGE_Gordon_Cucurbita_NC_031029: hypothetical protein; NCTC10667_00729; phage(gi100019)1.10e-46Showinfo_outline
10769518..769535attR0.0Showinfo_outline
11769732..770694PHAGE_Gordon_Cucurbita_NC_031029: hypothetical protein; NCTC10667_00730; phage(gi100020)0.0Showinfo_outline

Region 3, total 12 CDS

#CDS PositionBLAST HitE-ValueSequence
11227245..1227289attL0.0Showinfo_outline
2complement(1229927..1231375)PHAGE_Gordon_Eyre_NC_031122: hypothetical protein; NCTC10667_01200; phage(gi100015)9.35e-112Showinfo_outline
3complement(1231415..1232377)PHAGE_Gordon_Cucurbita_NC_031029: hypothetical protein; NCTC10667_01201; phage(gi100020)0.0Showinfo_outline
4complement(1232380..1232646)PHAGE_Gordon_Cucurbita_NC_031029: hypothetical protein; NCTC10667_01202; phage(gi100019)1.10e-46Showinfo_outline
5complement(1232664..1236695)PHAGE_Gordon_BritBrat_NC_030942: exonuclease A; NCTC10667_01203; phage(gi100018)0.0Showinfo_outline
6complement(1236774..1237268)PHAGE_Rhodoc_REQ3_NC_016654: hypothetical protein; NCTC10667_01204; phage(gi372450005)9.52e-20Showinfo_outline
7complement(1237340..1237756)PHAGE_Gordon_Cucurbita_NC_031029: hypothetical protein; NCTC10667_01205; phage(gi100020)7.49e-91Showinfo_outline
8complement(1238182..1239144)PHAGE_Gordon_Cucurbita_NC_031029: hypothetical protein; NCTC10667_01206; phage(gi100020)0.0Showinfo_outline
9complement(1239147..1239413)PHAGE_Gordon_Cucurbita_NC_031029: hypothetical protein; NCTC10667_01207; phage(gi100019)1.10e-46Showinfo_outline
10complement(1239431..1240657)Uncharacterised protein; NCTC10667_012080.0Showinfo_outline
11complement(1240712..1241320)PHAGE_Gordon_Blueberry_NC_030943: hypothetical protein; NCTC10667_01209; phage(gi100084)5.49e-110Showinfo_outline
121249022..1249066attR0.0Showinfo_outline
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 5217573 bps
Phages: 3
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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