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Conserved domains on  [gi|1232718243|gb|OYZ46586.1|]
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HNH endonuclease [Novosphingobium sp. 16-62-11]

Protein Classification

HNH endonuclease( domain architecture ID 10003646)

HNH endonuclease contains an HNH endonuclease signature motif and may catalyze the hydrolysis of DNA

Gene Ontology:  GO:0004519|GO:0003676|GO:0008270
PubMed:  28211904

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
McrA COG1403
5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];
74-133 2.22e-23

5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];


:

Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 87.73  E-value: 2.22e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1232718243  74 RPSEYPAFTRFNLFLRDSFSCQYCGTH---ENLTFDHIVPRRLGGRTSWENVAAACAPCNLRK 133
Cdd:COG1403     2 RPGREWPALRRAVLKRDNGRCQYCGRPfsgDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
 
Name Accession Description Interval E-value
McrA COG1403
5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];
74-133 2.22e-23

5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];


Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 87.73  E-value: 2.22e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1232718243  74 RPSEYPAFTRFNLFLRDSFSCQYCGTH---ENLTFDHIVPRRLGGRTSWENVAAACAPCNLRK 133
Cdd:COG1403     2 RPGREWPALRRAVLKRDNGRCQYCGRPfsgDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
HNH_5 pfam14279
HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. ...
 94-146 2.71e-15

HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. Suggesting that these proteins have a nucleic acid cleaving function.


Pssm-ID: 464124 [Multi-domain]  Cd Length: 56  Bit Score: 66.59  E-value: 2.71e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1232718243  94 CQYCG---THENLTFDHIVPRRLGGRTSWENVAAACAPCNLRKGGRTPEQARMRLM 146
Cdd:pfam14279   1 CIYCGkefPEKNLTIEHIIPESLGGKNKISNLQTLCKKCNSKKGHDVDAALSRHFL 56
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 86-134 3.69e-10

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: 53.24  E-value: 3.69e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1232718243  86 LFLRDSFSCQYCGTH---ENLTFDHIVPRRLGGRTSWENVAAACAPCNLRKG 134
Cdd:cd00085     6 VLLARDGLCPYCGKPggtEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKKH 57
guided_IscB NF040563
RNA-guided endonuclease IscB;
61-140 6.00e-08

RNA-guided endonuclease IscB;


Pssm-ID: 468538 [Multi-domain]  Cd Length: 315  Bit Score: 51.01  E-value: 6.00e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718243  61 MKLPSVIALRQYVRPSEYPAFTRFNLFLRDSFSCQYCG-THENLTFDHIVPRRLGGRTSWENVAAACAPCNLRKGGRTPE 139
Cdd:NF040563  163 LQNPEIISGVEYQQGELYGYEVREYLLERDGRTCQYCGaKDVPLEVHHIVPRSKGGSDRVSNLILACEPCNQKKGNQPVE 242


                  .
gi 1232718243 140 Q 140
Cdd:NF040563  243 E 243
HNHc smart00507
HNH nucleases;
83-130 7.22e-08

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 47.07  E-value: 7.22e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1232718243   83 RFNLFLRDsFSCQYCGTHENLTF--DHIVPRRLGGRTSWENVAAACAPCN 130
Cdd:smart00507   3 RRLLLHRD-GVCAYCGKPASEGLevDHIIPLSDGGNDDLDNLVLLCPKCH 51
 
Name Accession Description Interval E-value
McrA COG1403
5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];
74-133 2.22e-23

5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];


Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 87.73  E-value: 2.22e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1232718243  74 RPSEYPAFTRFNLFLRDSFSCQYCGTH---ENLTFDHIVPRRLGGRTSWENVAAACAPCNLRK 133
Cdd:COG1403     2 RPGREWPALRRAVLKRDNGRCQYCGRPfsgDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
HNH_5 pfam14279
HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. ...
 94-146 2.71e-15

HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. Suggesting that these proteins have a nucleic acid cleaving function.


Pssm-ID: 464124 [Multi-domain]  Cd Length: 56  Bit Score: 66.59  E-value: 2.71e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1232718243  94 CQYCG---THENLTFDHIVPRRLGGRTSWENVAAACAPCNLRKGGRTPEQARMRLM 146
Cdd:pfam14279   1 CIYCGkefPEKNLTIEHIIPESLGGKNKISNLQTLCKKCNSKKGHDVDAALSRHFL 56
HNH pfam01844
HNH endonuclease; His-Asn-His (HNH) proteins are a very common family of small nucleic ...
 94-136 1.79e-12

HNH endonuclease; His-Asn-His (HNH) proteins are a very common family of small nucleic acid-binding proteins that are generally associated with endonuclease activity.


Pssm-ID: 396422 [Multi-domain]  Cd Length: 47  Bit Score: 58.90  E-value: 1.79e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1232718243  94 CQYCGTH----ENLTFDHIVPRRLGGRTSWENVAAACAPCNLRKGGR 136
Cdd:pfam01844   1 CQYCGRPfhisDALTVDHIIPLSDGGADDIENLILLCPSCHNKKHNR 47
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 86-134 3.69e-10

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: 53.24  E-value: 3.69e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1232718243  86 LFLRDSFSCQYCGTH---ENLTFDHIVPRRLGGRTSWENVAAACAPCNLRKG 134
Cdd:cd00085     6 VLLARDGLCPYCGKPggtEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKKH 57
guided_IscB NF040563
RNA-guided endonuclease IscB;
61-140 6.00e-08

RNA-guided endonuclease IscB;


Pssm-ID: 468538 [Multi-domain]  Cd Length: 315  Bit Score: 51.01  E-value: 6.00e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232718243  61 MKLPSVIALRQYVRPSEYPAFTRFNLFLRDSFSCQYCG-THENLTFDHIVPRRLGGRTSWENVAAACAPCNLRKGGRTPE 139
Cdd:NF040563  163 LQNPEIISGVEYQQGELYGYEVREYLLERDGRTCQYCGaKDVPLEVHHIVPRSKGGSDRVSNLILACEPCNQKKGNQPVE 242


                  .
gi 1232718243 140 Q 140
Cdd:NF040563  243 E 243
HNHc smart00507
HNH nucleases;
83-130 7.22e-08

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 47.07  E-value: 7.22e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1232718243   83 RFNLFLRDsFSCQYCGTHENLTF--DHIVPRRLGGRTSWENVAAACAPCN 130
Cdd:smart00507   3 RRLLLHRD-GVCAYCGKPASEGLevDHIIPLSDGGNDDLDNLVLLCPKCH 51
Cas9 COG3513
CRISPR-Cas system type-II protein Cas9 [Defense mechanisms]; CRISPR-Cas system type-II protein ...
 94-141 3.91e-04

CRISPR-Cas system type-II protein Cas9 [Defense mechanisms]; CRISPR-Cas system type-II protein Cas9 is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442735 [Multi-domain]  Cd Length: 812  Bit Score: 40.33  E-value: 3.91e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1232718243  94 CQYCGT----HENLTF----DHIVPRRLGGRTSWENVAAACAPCNLRKGGRTPEQA 141
Cdd:COG3513   543 CPYTGKpisiSDLLDGsveiDHILPRSRTLDDSFNNKVLCLADANREKGNRTPYEA 598
HNH_4 pfam13395
HNH endonuclease; This HNH nuclease domain is found in CRISPR-related proteins.
 94-138 3.91e-03

HNH endonuclease; This HNH nuclease domain is found in CRISPR-related proteins.


Pssm-ID: 433172 [Multi-domain]  Cd Length: 55  Bit Score: 34.14  E-value: 3.91e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1232718243  94 CQYCGT---------HENLTFDHIVPRRLGGRTSWENVAAACAPCNLRKGGRTP 138
Cdd:pfam13395   1 CPYTGEqisiddlfsEKNYDIDHILPYSRSFDDSFSNKVLVLRSANQEKGNRTP 54
 
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.
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