NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|543170388|ref|YP_008530456|]
View 

HNH endonuclease [Escherichia phage JES2013]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HNH_3 pfam13392
HNH endonuclease; This is a zinc-binding loop of Fold group 7 as found in ...
 68-116 1.16e-09

HNH endonuclease; This is a zinc-binding loop of Fold group 7 as found in endo-deoxy-ribonucleases and HNH nucleases.


:

Pssm-ID: 433169  Cd Length: 46  Bit Score: 52.59  E-value: 1.16e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 543170388   68 KGAHVIIWEMFNGPVPEGYEVDHIKEIRetggvADNSIQNLQLLEPTDN 116
Cdd:pfam13392   1 KYAHRVAWELHNGPIPDGMVVDHIDGDR-----RNNRPENLRLVTRREN 44
PHA00280 super family cl27633
putative NHN endonuclease
 71-171 3.40e-08

putative NHN endonuclease


The actual alignment was detected with superfamily member PHA00280:

Pssm-ID: 106901 [Multi-domain]  Cd Length: 121  Bit Score: 50.55  E-value: 3.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543170388  71 HVIIWEMFNGPVPEGYEVDHikeirETGGVADNSIQNLQLLEPTDNKKKScKIPRSnNKSGRVGVHYSE----------- 139
Cdd:PHA00280  15 HIQVWEAANGPIPKGYYIDH-----IDGNPLNDALDNLRLALPKENSWNM-KTPKS-NTSGLKGLSWSKeremwrgtvta 87

                         90       100       110
                 ....*....|....*....|....*....|..
gi 543170388 140 EREAWVAQGTDSVGERVWLGQYRTFEEAEWAR 171
Cdd:PHA00280  88 EGKQHNFRSRDLLEVVAWIYRTRRELHGQFAR 119
AP2 pfam00847
AP2 domain; This 60 amino acid residue domain can bind to DNA and is found in transcription ...
 196-238 8.89e-03

AP2 domain; This 60 amino acid residue domain can bind to DNA and is found in transcription factor proteins.


:

Pssm-ID: 425904  Cd Length: 52  Bit Score: 33.76  E-value: 8.89e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 543170388  196 SGVNWDKTHERWVARIYVDGKRKC-------LGYFKNRDDAIAARKNAEK 238
Cdd:pfam00847   3 RGVRYDKKWGRWVAEWSENGKRRKkrfslgkYGTEEAKRAAIEARKKLEG 52
 
Name Accession Description Interval E-value
HNH_3 pfam13392
HNH endonuclease; This is a zinc-binding loop of Fold group 7 as found in ...
 68-116 1.16e-09

HNH endonuclease; This is a zinc-binding loop of Fold group 7 as found in endo-deoxy-ribonucleases and HNH nucleases.


Pssm-ID: 433169  Cd Length: 46  Bit Score: 52.59  E-value: 1.16e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 543170388   68 KGAHVIIWEMFNGPVPEGYEVDHIKEIRetggvADNSIQNLQLLEPTDN 116
Cdd:pfam13392   1 KYAHRVAWELHNGPIPDGMVVDHIDGDR-----RNNRPENLRLVTRREN 44
PHA00280 PHA00280
putative NHN endonuclease
 71-171 3.40e-08

putative NHN endonuclease


Pssm-ID: 106901 [Multi-domain]  Cd Length: 121  Bit Score: 50.55  E-value: 3.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543170388  71 HVIIWEMFNGPVPEGYEVDHikeirETGGVADNSIQNLQLLEPTDNKKKScKIPRSnNKSGRVGVHYSE----------- 139
Cdd:PHA00280  15 HIQVWEAANGPIPKGYYIDH-----IDGNPLNDALDNLRLALPKENSWNM-KTPKS-NTSGLKGLSWSKeremwrgtvta 87

                         90       100       110
                 ....*....|....*....|....*....|..
gi 543170388 140 EREAWVAQGTDSVGERVWLGQYRTFEEAEWAR 171
Cdd:PHA00280  88 EGKQHNFRSRDLLEVVAWIYRTRRELHGQFAR 119
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 83-120 5.57e-04

HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.


Pssm-ID: 238038 [Multi-domain]  Cd Length: 57  Bit Score: 37.07  E-value: 5.57e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 543170388  83 PEGYEVDHIKEIRETGgvaDNSIQNLQLLEPTDNKKKS 120
Cdd:cd00085   23 TEGLEVDHIIPLSDGG---NNDLDNLVLLCRKCHRKKH 57
AP2 pfam00847
AP2 domain; This 60 amino acid residue domain can bind to DNA and is found in transcription ...
 196-238 8.89e-03

AP2 domain; This 60 amino acid residue domain can bind to DNA and is found in transcription factor proteins.


Pssm-ID: 425904  Cd Length: 52  Bit Score: 33.76  E-value: 8.89e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 543170388  196 SGVNWDKTHERWVARIYVDGKRKC-------LGYFKNRDDAIAARKNAEK 238
Cdd:pfam00847   3 RGVRYDKKWGRWVAEWSENGKRRKkrfslgkYGTEEAKRAAIEARKKLEG 52
 
Name Accession Description Interval E-value
HNH_3 pfam13392
HNH endonuclease; This is a zinc-binding loop of Fold group 7 as found in ...
 68-116 1.16e-09

HNH endonuclease; This is a zinc-binding loop of Fold group 7 as found in endo-deoxy-ribonucleases and HNH nucleases.


Pssm-ID: 433169  Cd Length: 46  Bit Score: 52.59  E-value: 1.16e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 543170388   68 KGAHVIIWEMFNGPVPEGYEVDHIKEIRetggvADNSIQNLQLLEPTDN 116
Cdd:pfam13392   1 KYAHRVAWELHNGPIPDGMVVDHIDGDR-----RNNRPENLRLVTRREN 44
PHA00280 PHA00280
putative NHN endonuclease
 71-171 3.40e-08

putative NHN endonuclease


Pssm-ID: 106901 [Multi-domain]  Cd Length: 121  Bit Score: 50.55  E-value: 3.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543170388  71 HVIIWEMFNGPVPEGYEVDHikeirETGGVADNSIQNLQLLEPTDNKKKScKIPRSnNKSGRVGVHYSE----------- 139
Cdd:PHA00280  15 HIQVWEAANGPIPKGYYIDH-----IDGNPLNDALDNLRLALPKENSWNM-KTPKS-NTSGLKGLSWSKeremwrgtvta 87

                         90       100       110
                 ....*....|....*....|....*....|..
gi 543170388 140 EREAWVAQGTDSVGERVWLGQYRTFEEAEWAR 171
Cdd:PHA00280  88 EGKQHNFRSRDLLEVVAWIYRTRRELHGQFAR 119
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 83-120 5.57e-04

HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.


Pssm-ID: 238038 [Multi-domain]  Cd Length: 57  Bit Score: 37.07  E-value: 5.57e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 543170388  83 PEGYEVDHIKEIRETGgvaDNSIQNLQLLEPTDNKKKS 120
Cdd:cd00085   23 TEGLEVDHIIPLSDGG---NNDLDNLVLLCRKCHRKKH 57
AP2 pfam00847
AP2 domain; This 60 amino acid residue domain can bind to DNA and is found in transcription ...
 196-238 8.89e-03

AP2 domain; This 60 amino acid residue domain can bind to DNA and is found in transcription factor proteins.


Pssm-ID: 425904  Cd Length: 52  Bit Score: 33.76  E-value: 8.89e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 543170388  196 SGVNWDKTHERWVARIYVDGKRKC-------LGYFKNRDDAIAARKNAEK 238
Cdd:pfam00847   3 RGVRYDKKWGRWVAEWSENGKRRKkrfslgkYGTEEAKRAAIEARKKLEG 52
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH