Submission Results

Sequence Name: Not Available

GenBank Accession Number: PRDN01000001.1

GenInfo (GI) Number: 0000000000

Download Results:

gi|00000000|ref|PRDN01000001.1| Xanthomonas sp. CFBP 7698 X-CFBP7698-G101, whole genome shotgun 1853199, gc%: 65.60%

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
134.9Kbincomplete5035215979-250889 info_outlinePHAGE_Pseudo_F116_NC_006552(2)62.87%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|PRDN01000001.1| Xanthomonas sp. CFBP 7698 X-CFBP7698-G101, whole genome shotgun 1853199, gc%: 65.60%

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 39 CDS

#CDS PositionBLAST HitE-ValueSequence
3220533..221495PHAGE_Rhodoc_ReqiDocB7_NC_023706: tyrosine recombinase/integrase; XnspCFBP7698_00795; phage(gi593775993)4.87e-10Showinfo_outline
4complement(221497..221928)PHAGE_Salmon_II_E1_NC_010495: bacterial type single-stranded DNA-binding protein; XnspCFBP7698_00800; phage(gi170676317)4.06e-16Showinfo_outline
5complement(221925..223973)PHAGE_Pseudo_F116_NC_006552: DNA cytosine methyltransferase; XnspCFBP7698_00805; phage(gi56692910)9.90e-106Showinfo_outline
6complement(223966..224238)hypothetical protein; XnspCFBP7698_008100.0Showinfo_outline
7complement(224235..224456)hypothetical protein; XnspCFBP7698_008150.0Showinfo_outline
8complement(224449..224997)PHAGE_Escher_TL_2011b_NC_019445: hypothetical protein; XnspCFBP7698_00820; phage(gi418487651)2.53e-33Showinfo_outline
9complement(224997..225722)hypothetical protein; XnspCFBP7698_008250.0Showinfo_outline
10complement(225715..226104)hypothetical protein; XnspCFBP7698_008300.0Showinfo_outline
11complement(226101..226364)PHAGE_Burkho_BcepMigl_NC_019917: hypothetical protein; XnspCFBP7698_00835; phage(gi431809877)1.46e-07Showinfo_outline
12complement(226375..227475)hypothetical protein; XnspCFBP7698_008400.0Showinfo_outline
13complement(227475..227867)hypothetical protein; XnspCFBP7698_008450.0Showinfo_outline
14complement(227867..228130)hypothetical protein; XnspCFBP7698_008500.0Showinfo_outline
15complement(228118..229086)PHAGE_Mycoba_Goku_NC_022085: integrase; XnspCFBP7698_00855; phage(gi530786876)8.53e-12Showinfo_outline
16complement(229277..230251)PHAGE_Pseudo_F116_NC_006552: RdgC exonuclease; XnspCFBP7698_00860; phage(gi56692914)2.82e-42Showinfo_outline
17complement(230255..230482)hypothetical protein; XnspCFBP7698_008650.0Showinfo_outline
18complement(230486..230716)hypothetical protein; XnspCFBP7698_008700.0Showinfo_outline
20complement(230881..231099)hypothetical protein; XnspCFBP7698_008750.0Showinfo_outline
21complement(231096..231701)hypothetical protein; XnspCFBP7698_008800.0Showinfo_outline
22complement(231698..231934)hypothetical protein; XnspCFBP7698_008850.0Showinfo_outline
23complement(231931..232863)PHAGE_Staphy_StB20_NC_019915: integrase; XnspCFBP7698_00890; phage(gi431809731)9.31e-28Showinfo_outline
24complement(232749..232985)hypothetical protein; XnspCFBP7698_008950.0Showinfo_outline
25233017..233385PHAGE_Bacill_vB_BhaS_171_NC_030904: hypothetical protein; XnspCFBP7698_00900; phage(gi100037)1.29e-09Showinfo_outline
26233413..233601hypothetical protein; XnspCFBP7698_009050.0Showinfo_outline
27233598..234329PHAGE_Strept_PH15_NC_010945: hypothetical protein; XnspCFBP7698_00910; phage(gi190151422)4.83e-54Showinfo_outline
28complement(234398..234796)hypothetical protein; XnspCFBP7698_009150.0Showinfo_outline
29complement(234793..235284)PHAGE_Xantho_OP2_NC_007710: hypothetical protein; XnspCFBP7698_00920; phage(gi84662680)1.43e-27Showinfo_outline
30complement(235281..235469)hypothetical protein; XnspCFBP7698_009250.0Showinfo_outline
31complement(235502..235858)hypothetical protein; XnspCFBP7698_009300.0Showinfo_outline
32complement(235918..236454)PHAGE_Pseudo_PEV2_NC_031063: hypothetical protein; XnspCFBP7698_00935; phage(gi100051)1.72e-41Showinfo_outline
33236598..237044PHAGE_Xantho_phiL7_NC_012742: P24; XnspCFBP7698_00940; phage(gi238695611)2.15e-11Showinfo_outline
34complement(237065..237274)hypothetical protein; XnspCFBP7698_009450.0Showinfo_outline
35complement(237369..238307)hypothetical protein; XnspCFBP7698_009500.0Showinfo_outline
36complement(238317..238541)hypothetical protein; XnspCFBP7698_009550.0Showinfo_outline
37238601..238804hypothetical protein; XnspCFBP7698_009600.0Showinfo_outline
38complement(238963..239760)PHAGE_Plankt_PaV_LD_NC_016564: hypothetical protein; XnspCFBP7698_00965; phage(gi371496230)4.24e-18Showinfo_outline
Xanthomonas sp
Click on a region to see details.
Intact (score > 90)
Questionable (score 70-90)
Incomplete (score < 70)

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Length: 1853199 bps
Phages: 1
Click on a region in the genome above to show details here.
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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