Submission Results

Sequence Name: Not Available

GenBank Accession Number: NC_006552

Download Results: NC_006552.PHASTEST.zip

gi|00000000|ref|NC_000000| Pseudomonas phage F116, complete genome. 65195, gc%: 63.17%

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
165Kbintact15070186-65195 info_outlinePHAGE_Pseudo_F116_NC_006552(70)63.18%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|NC_006552.1| Pseudomonas phage F116, complete genome. 65195, gc%: 63.17%

Download details as .txt file:detail.txt file_download

Hypothetical protein
Phage-like protein
Exonuclease
Regulatory protein
Terminase
Portal protein
Holin
Integrase

intact

Region 1, total 70 CDS

#CDS PositionBLAST HitE-ValueSequence
1186..656PP_00001;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065527.25e-111Show info_outline
2724..1206PP_00002;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065522.63e-114Show info_outline
31188..1610PP_00003;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065524.05e-99Show info_outline
42007..2213PP_00004;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065526.2e-38Show info_outline
52408..3169PP_00005;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
63166..3807PP_00006;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065522.93e-158Show info_outline
73804..4481PP_00007;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065529.48e-166Show info_outline
84478..4906PP_00008;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065522.8e-100Show info_outline
94903..5709PP_00009;DNA adenine methyltransferase;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
105706..7769PP_00010;DNA cytosine methyltransferase;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
117766..8620PP_00011;DNA adenine methyltransferase;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
128762..8971PP_00012;LexA-like protein;phage;PHAGE_Pseudo_F116_NC_0065527.53e-45Show info_outline
138968..10023PP_00013;nucleoid-associated protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
1410050..10973PP_00014;RdgC exonuclease;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
1511002..11505PP_00015;single-stranded DNA-binding protein;phage;PHAGE_Pseudo_F116_NC_0065522.02e-120Show info_outline
1611509..12114PP_00016;exonuclease;phage;PHAGE_Pseudo_F116_NC_0065522.46e-148Show info_outline
1712224..12778PP_00017;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065521.16e-137Show info_outline
1812826..13842PP_00018;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
1913847..14602PP_00019;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
2014599..15072PP_00020;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065529.77e-109Show info_outline
2115232..15453PP_00021;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065522.3e-47Show info_outline
2215437..15586PP_00022;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065525.63e-29Show info_outline
2315583..16053PP_00023;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065526.11e-113Show info_outline
2416229..16600PP_00024;regulatory protein;phage;PHAGE_Pseudo_F116_NC_0065523.81e-84Show info_outline
2516635..16847PP_00025;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065522.25e-45Show info_outline
2616912..17118PP_00026;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065521.11e-45Show info_outline
2717168..17341PP_00027;hypothetical protein;phage;PHAGE_Pseudo_H66_NC_0423421.35e-33Show info_outline
2817753..18019PP_00028;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065521.03e-57Show info_outline
2918056..18853PP_00029;transcriptional regulator;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
3018961..19161PP_00030;Cro-like protein;phage;PHAGE_Pseudo_H66_NC_0423422.4e-41Show info_outline
3119459..19665PP_00031;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065523.2e-39Show info_outline
3219700..20179PP_00032;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065526.3e-115Show info_outline
3320166..21023PP_00033;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
3421016..21567PP_00034;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065529.76e-134Show info_outline
3521567..21887PP_00035;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065521.15e-72Show info_outline
3621884..22231PP_00036;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065521.48e-81Show info_outline
3722231..22725PP_00037;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065522.37e-113Show info_outline
3822851..23666PP_00038;terminase small subunit;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
3923670..25301PP_00039;terminase large subunit;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
4025312..27630PP_00040;portal protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
4127709..28620PP_00041;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
4228782..29912PP_00042;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
4329925..31217PP_00043;virion structural protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
4431276..31755PP_00044;virion structural protein;phage;PHAGE_Pseudo_F116_NC_0065523.85e-108Show info_outline
4531820..32692PP_00045;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
4632689..33366PP_00046;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065524.53e-165Show info_outline
4733363..33569PP_00047;hypothetical protein;phage;PHAGE_Pseudo_H66_NC_0423429.51e-43Show info_outline
4833550..33957PP_00048;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065524.17e-93Show info_outline
4933981..34406PP_00049;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065521.28e-101Show info_outline
5034406..35263PP_00050;virion structural protein;phage;PHAGE_Pseudo_PaMx28_NC_0289319.95e-05Show info_outline
5135266..38229PP_00051;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
5238229..39419PP_00052;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
5339487..40077PP_00053;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065521.8e-139Show info_outline
5440172..42679PP_00054;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
5542672..43022PP_00055;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065522.74e-75Show info_outline
5643229..43834PP_00056;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065522.07e-143Show info_outline
5743834..45648PP_00057;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
5845869..47896PP_00058;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
5947838..54227PP_00059;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
6054250..59199PP_00060;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline
6159294..59551PP_00061;holin;phage;PHAGE_Pseudo_F116_NC_0065522.84e-53Show info_outline
6259535..60068PP_00062;lysozyme;phage;PHAGE_Pseudo_F116_NC_0065525.06e-131Show info_outline
6360065..60583PP_00063;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065523.29e-118Show info_outline
6460594..61187PP_00064;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065521.54e-135Show info_outline
6561207..61626PP_00065;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065524.24e-95Show info_outline
6661799..62065PP_00066;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065522.31e-59Show info_outline
6762047..62733PP_00067;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065521.51e-167Show info_outline
6862743..62835PP_00068;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065521.11e-11Show info_outline
6963024..63539PP_00069;hypothetical protein;phage;PHAGE_Pseudo_F116_NC_0065521.37e-122Show info_outline
7063960..65195PP_00070;integrase;phage;PHAGE_Pseudo_F116_NC_0065520.0Show info_outline

gi|00000000|ref|NC_006552.1| Pseudomonas phage F116, complete genome. 65195, gc%: 63.17%

Download details as .txt file:detail.txt file_download

Bacterial, total 0 CDS

#CDS PositionBLAST HitE-ValueSequence

Phage Genes

Bacterial Genes

Phage Regions

GC Skew

GC Content

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Phage Genes

Bacterial Genes

Phage Regions

GC Skew

GC Content

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Click on a region or gene to view details

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