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Conserved domains on  [gi|856759201|gb|AKO16440|]
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HNH endonuclease [Xanthomonas oryzae pv. oryzicola]

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];
103-166 2.71e-22

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


:

Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 86.19  E-value: 2.71e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 856759201 103 RALDPTPTLSNTALFARDAQLCMYCGQHFSRPHLTRDHVMPVSKGGRDSWENVVTACFQCNSRK 166
Cdd:COG1403    1 RRPGREWPALRRAVLKRDNGRCQYCGRPFSGDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
 
Name Accession Description Interval E-value
McrA COG1403
5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];
103-166 2.71e-22

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


Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 86.19  E-value: 2.71e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 856759201 103 RALDPTPTLSNTALFARDAQLCMYCGQHFSRPHLTRDHVMPVSKGGRDSWENVVTACFQCNSRK 166
Cdd:COG1403    1 RRPGREWPALRRAVLKRDNGRCQYCGRPFSGDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
HNH_5 pfam14279
HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. ...
 124-179 2.55e-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: 67.75  E-value: 2.55e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 856759201  124 CMYCGQHFSRPHLTRDHVMPVSKGGRDSWENVVTACFQCNSRKANRTPQQAHMPLL 179
Cdd:pfam14279   1 CIYCGKEFPEKNLTIEHIIPESLGGKNKISNLQTLCKKCNSKKGHDVDAALSRHFL 56
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 115-166 2.21e-11

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: 57.48  E-value: 2.21e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 856759201 115 ALFARDAqLCMYCGQHFSRPHLTRDHVMPVSKGGRDSWENVVTACFQCNSRK 166
Cdd:cd00085    6 VLLARDG-LCPYCGKPGGTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKK 56
HNHc smart00507
HNH nucleases;
115-164 9.10e-07

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 44.76  E-value: 9.10e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 856759201   115 ALFARDAqLCMYCGQHFSrPHLTRDHVMPVSKGGRDSWENVVTACFQCNS 164
Cdd:smart00507   5 LLLHRDG-VCAYCGKPAS-EGLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52
cas_Csn1 TIGR01865
CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1; CRISPR loci appear to be mobile ...
 124-174 2.59e-04

CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1; CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only.


Pssm-ID: 273840  Cd Length: 805  Bit Score: 41.64  E-value: 2.59e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 856759201  124 CMYCGQHFSRPHLTR------DHVMPVSKGGRDSWENVVTACFQCNSRKANRTPQQA 174
Cdd:TIGR01865 584 CMYTGKEIDIDDLFDlsyyeiDHILPQSRSFDDSISNKVLVLASENQEKGDQTPYEA 640
 
Name Accession Description Interval E-value
McrA COG1403
5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];
103-166 2.71e-22

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


Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 86.19  E-value: 2.71e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 856759201 103 RALDPTPTLSNTALFARDAQLCMYCGQHFSRPHLTRDHVMPVSKGGRDSWENVVTACFQCNSRK 166
Cdd:COG1403    1 RRPGREWPALRRAVLKRDNGRCQYCGRPFSGDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
HNH_5 pfam14279
HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. ...
 124-179 2.55e-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: 67.75  E-value: 2.55e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 856759201  124 CMYCGQHFSRPHLTRDHVMPVSKGGRDSWENVVTACFQCNSRKANRTPQQAHMPLL 179
Cdd:pfam14279   1 CIYCGKEFPEKNLTIEHIIPESLGGKNKISNLQTLCKKCNSKKGHDVDAALSRHFL 56
HNH pfam01844
HNH endonuclease; His-Asn-His (HNH) proteins are a very common family of small nucleic ...
 124-169 7.70e-15

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: 66.22  E-value: 7.70e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 856759201  124 CMYCGQHFS-RPHLTRDHVMPVSKGGRDSWENVVTACFQCNSRKANR 169
Cdd:pfam01844   1 CQYCGRPFHiSDALTVDHIIPLSDGGADDIENLILLCPSCHNKKHNR 47
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 115-166 2.21e-11

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: 57.48  E-value: 2.21e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 856759201 115 ALFARDAqLCMYCGQHFSRPHLTRDHVMPVSKGGRDSWENVVTACFQCNSRK 166
Cdd:cd00085    6 VLLARDG-LCPYCGKPGGTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKK 56
HNH_4 pfam13395
HNH endonuclease; This HNH nuclease domain is found in CRISPR-related proteins.
 124-171 1.83e-07

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


Pssm-ID: 433172 [Multi-domain]  Cd Length: 55  Bit Score: 46.47  E-value: 1.83e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 856759201  124 CMYCGQHFSRPHLTR------DHVMPVSKGGRDSWENVVTACFQCNSRKANRTP 171
Cdd:pfam13395   1 CPYTGEQISIDDLFSeknydiDHILPYSRSFDDSFSNKVLVLRSANQEKGNRTP 54
HNHc smart00507
HNH nucleases;
115-164 9.10e-07

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 44.76  E-value: 9.10e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 856759201   115 ALFARDAqLCMYCGQHFSrPHLTRDHVMPVSKGGRDSWENVVTACFQCNS 164
Cdd:smart00507   5 LLLHRDG-VCAYCGKPAS-EGLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52
cas_Csn1 TIGR01865
CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1; CRISPR loci appear to be mobile ...
 124-174 2.59e-04

CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1; CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only.


Pssm-ID: 273840  Cd Length: 805  Bit Score: 41.64  E-value: 2.59e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 856759201  124 CMYCGQHFSRPHLTR------DHVMPVSKGGRDSWENVVTACFQCNSRKANRTPQQA 174
Cdd:TIGR01865 584 CMYTGKEIDIDDLFDlsyyeiDHILPQSRSFDDSISNKVLVLASENQEKGDQTPYEA 640
Csn1 cd09643
CRISPR/Cas system-associated protein Cas9; CRISPR (Clustered Regularly Interspaced Short ...
 124-174 2.84e-04

CRISPR/Cas system-associated protein Cas9; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Very large protein containing McrA/HNH-nuclease related domain and a RuvC-like nuclease domain; signature gene for type II


Pssm-ID: 187774 [Multi-domain]  Cd Length: 799  Bit Score: 41.64  E-value: 2.84e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 856759201 124 CMYCGQHFSRPHLTR------DHVMPVSKGGRDSWENVVTACFQCNSRKANRTPQQA 174
Cdd:cd09643  580 CMYTGKEIDIDDLFDlsyyeiDHILPQSRSFDDSISNKVLVLASENQEKGDQTPYEE 636
 
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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