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Conserved domains on  [gi|30682222|ref|NP_179964|]
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HNH endonuclease [Arabidopsis thaliana]

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];
166-226 1.75e-22

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


:

Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 88.12  E-value: 1.75e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30682222 166 KRRRVKNSLSRKNILLRDDYTCQYC---SSRENLTIDHVMPVSRGGEWTWQNLVAACSRCNSRK 226
Cdd:COG1403   1 RRPGREWPALRRAVLKRDNGRCQYCgrpFSGDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
Cas9 super family cl34627
CRISPR-Cas system type-II protein Cas9 [Defense mechanisms]; CRISPR-Cas system type-II protein ...
 198-279 1.12e-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


The actual alignment was detected with superfamily member COG3513:

Pssm-ID: 442735 [Multi-domain]  Cd Length: 812  Bit Score: 43.41  E-value: 1.12e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30682222 198 IDHVMPVSRGGEWTWQNLVAACSRCNSRKGQKTADEAHmkllkVPKEPKDYDivaipltnAAIRMLRSNKGMPEEWRQYL 277
Cdd:COG3513 562 IDHILPRSRTLDDSFNNKVLCLADANREKGNRTPYEAL-----GGDEAEKWE--------EILARVENLKLIPQKKKKRF 628


                ..
gi 30682222 278 AK 279
Cdd:COG3513 629 LK 630
 
Name Accession Description Interval E-value
McrA COG1403
5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];
166-226 1.75e-22

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


Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 88.12  E-value: 1.75e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30682222 166 KRRRVKNSLSRKNILLRDDYTCQYC---SSRENLTIDHVMPVSRGGEWTWQNLVAACSRCNSRK 226
Cdd:COG1403   1 RRPGREWPALRRAVLKRDNGRCQYCgrpFSGDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
HNH_5 pfam14279
HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. ...
 187-239 8.79e-16

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: 70.06  E-value: 8.79e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 30682222   187 CQYCSSR---ENLTIDHVMPVSRGGEWTWQNLVAACSRCNSRKGQKTADEAHMKLL 239
Cdd:pfam14279   1 CIYCGKEfpeKNLTIEHIIPESLGGKNKISNLQTLCKKCNSKKGHDVDAALSRHFL 56
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 177-227 7.67e-12

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: 59.41  E-value: 7.67e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30682222 177 KNILLRDDYTCQYC---SSRENLTIDHVMPVSRGGEWTWQNLVAACSRCNSRKG 227
Cdd:cd00085   4 RLVLLARDGLCPYCgkpGGTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKKH 57
guided_IscB NF040563
RNA-guided endonuclease IscB;
176-246 1.53e-10

RNA-guided endonuclease IscB;


Pssm-ID: 468538 [Multi-domain]  Cd Length: 315  Bit Score: 60.64  E-value: 1.53e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30682222  176 RKNILLRDDYTCQYCSSREN-LTIDHVMPVSRGGEWTWQNLVAACSRCNSRKGQKTADEahmkLLKVPKEPK 246
Cdd:NF040563 185 REYLLERDGRTCQYCGAKDVpLEVHHIVPRSKGGSDRVSNLILACEPCNQKKGNQPVEE----FLKGPELLK 252
HNHc smart00507
HNH nucleases;
177-224 1.10e-09

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 53.23  E-value: 1.10e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 30682222    177 KNILLRDDYTCQYCSSREN--LTIDHVMPVSRGGEWTWQNLVAACSRCNS 224
Cdd:smart00507   3 RRLLLHRDGVCAYCGKPASegLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52
Cas9 COG3513
CRISPR-Cas system type-II protein Cas9 [Defense mechanisms]; CRISPR-Cas system type-II protein ...
 198-279 1.12e-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: 43.41  E-value: 1.12e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30682222 198 IDHVMPVSRGGEWTWQNLVAACSRCNSRKGQKTADEAHmkllkVPKEPKDYDivaipltnAAIRMLRSNKGMPEEWRQYL 277
Cdd:COG3513 562 IDHILPRSRTLDDSFNNKVLCLADANREKGNRTPYEAL-----GGDEAEKWE--------EILARVENLKLIPQKKKKRF 628


                ..
gi 30682222 278 AK 279
Cdd:COG3513 629 LK 630
 
Name Accession Description Interval E-value
McrA COG1403
5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];
166-226 1.75e-22

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


Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 88.12  E-value: 1.75e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30682222 166 KRRRVKNSLSRKNILLRDDYTCQYC---SSRENLTIDHVMPVSRGGEWTWQNLVAACSRCNSRK 226
Cdd:COG1403   1 RRPGREWPALRRAVLKRDNGRCQYCgrpFSGDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
HNH_5 pfam14279
HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. ...
 187-239 8.79e-16

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: 70.06  E-value: 8.79e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 30682222   187 CQYCSSR---ENLTIDHVMPVSRGGEWTWQNLVAACSRCNSRKGQKTADEAHMKLL 239
Cdd:pfam14279   1 CIYCGKEfpeKNLTIEHIIPESLGGKNKISNLQTLCKKCNSKKGHDVDAALSRHFL 56
HNH pfam01844
HNH endonuclease; His-Asn-His (HNH) proteins are a very common family of small nucleic ...
 187-229 1.25e-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: 61.21  E-value: 1.25e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 30682222   187 CQYCSS----RENLTIDHVMPVSRGGEWTWQNLVAACSRCNSRKGQK 229
Cdd:pfam01844   1 CQYCGRpfhiSDALTVDHIIPLSDGGADDIENLILLCPSCHNKKHNR 47
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 177-227 7.67e-12

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: 59.41  E-value: 7.67e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30682222 177 KNILLRDDYTCQYC---SSRENLTIDHVMPVSRGGEWTWQNLVAACSRCNSRKG 227
Cdd:cd00085   4 RLVLLARDGLCPYCgkpGGTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKKH 57
guided_IscB NF040563
RNA-guided endonuclease IscB;
176-246 1.53e-10

RNA-guided endonuclease IscB;


Pssm-ID: 468538 [Multi-domain]  Cd Length: 315  Bit Score: 60.64  E-value: 1.53e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30682222  176 RKNILLRDDYTCQYCSSREN-LTIDHVMPVSRGGEWTWQNLVAACSRCNSRKGQKTADEahmkLLKVPKEPK 246
Cdd:NF040563 185 REYLLERDGRTCQYCGAKDVpLEVHHIVPRSKGGSDRVSNLILACEPCNQKKGNQPVEE----FLKGPELLK 252
HNHc smart00507
HNH nucleases;
177-224 1.10e-09

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 53.23  E-value: 1.10e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 30682222    177 KNILLRDDYTCQYCSSREN--LTIDHVMPVSRGGEWTWQNLVAACSRCNS 224
Cdd:smart00507   3 RRLLLHRDGVCAYCGKPASegLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52
HNH_4 pfam13395
HNH endonuclease; This HNH nuclease domain is found in CRISPR-related proteins.
 191-231 7.08e-05

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


Pssm-ID: 433172 [Multi-domain]  Cd Length: 55  Bit Score: 39.92  E-value: 7.08e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 30682222   191 SSRENLTIDHVMPVSRGGEWTWQNLVAACSRCNSRKGQKTA 231
Cdd:pfam13395  14 FSEKNYDIDHILPYSRSFDDSFSNKVLVLRSANQEKGNRTP 54
Cas9 COG3513
CRISPR-Cas system type-II protein Cas9 [Defense mechanisms]; CRISPR-Cas system type-II protein ...
 198-279 1.12e-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: 43.41  E-value: 1.12e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30682222 198 IDHVMPVSRGGEWTWQNLVAACSRCNSRKGQKTADEAHmkllkVPKEPKDYDivaipltnAAIRMLRSNKGMPEEWRQYL 277
Cdd:COG3513 562 IDHILPRSRTLDDSFNNKVLCLADANREKGNRTPYEAL-----GGDEAEKWE--------EILARVENLKLIPQKKKKRF 628


                ..
gi 30682222 278 AK 279
Cdd:COG3513 629 LK 630
 
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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