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Conserved domains on  [gi|2055716377|ref|WP_216596320|]
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HNH endonuclease [Bifidobacterium pseudocatenulatum]

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];
95-155 1.56e-24

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


:

Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 90.04  E-value: 1.56e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2055716377  95 RSREPISKKLRKAVYERDHYRCVECGA---ADHLSLDHIIPWSLGGEDTMENLQTMCRSCNSRK 155
Cdd:COG1403     1 RRPGREWPALRRAVLKRDNGRCQYCGRpfsGDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
 
Name Accession Description Interval E-value
McrA COG1403
5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];
95-155 1.56e-24

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


Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 90.04  E-value: 1.56e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2055716377  95 RSREPISKKLRKAVYERDHYRCVECGA---ADHLSLDHIIPWSLGGEDTMENLQTMCRSCNSRK 155
Cdd:COG1403     1 RRPGREWPALRRAVLKRDNGRCQYCGRpfsGDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 102-156 1.24e-13

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: 61.72  E-value: 1.24e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2055716377 102 KKLRKAVYERDHyRCVECGA---ADHLSLDHIIPWSLGGEDTMENLQTMCRSCNSRKG 156
Cdd:cd00085     1 RSHRLVLLARDG-LCPYCGKpggTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKKH 57
HNH_5 pfam14279
HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. ...
 116-160 3.66e-13

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: 60.43  E-value: 3.66e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2055716377 116 CVECG---AADHLSLDHIIPWSLGGEDTMENLQTMCRSCNSRKGNRLD 160
Cdd:pfam14279   1 CIYCGkefPEKNLTIEHIIPESLGGKNKISNLQTLCKKCNSKKGHDVD 48
HNHc smart00507
HNH nucleases;
103-153 4.22e-11

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 55.16  E-value: 4.22e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2055716377  103 KLRKAVYERDHyRCVECG--AADHLSLDHIIPWSLGGEDTMENLQTMCRSCNS 153
Cdd:smart00507   1 KLRRLLLHRDG-VCAYCGkpASEGLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52
cas_Csn1 TIGR01865
CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1; CRISPR loci appear to be mobile ...
 98-158 6.38e-03

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: 36.25  E-value: 6.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2055716377  98 EPISKK-LRKAVYERDHYRCVECG---AADHLS------LDHIIPWSLGGEDTMENLQTMCRSCNSRKGNR 158
Cdd:TIGR01865 565 ENSSKNiLKLRLYYQQNGKCMYTGkeiDIDDLFdlsyyeIDHILPQSRSFDDSISNKVLVLASENQEKGDQ 635
 
Name Accession Description Interval E-value
McrA COG1403
5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];
95-155 1.56e-24

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


Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 90.04  E-value: 1.56e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2055716377  95 RSREPISKKLRKAVYERDHYRCVECGA---ADHLSLDHIIPWSLGGEDTMENLQTMCRSCNSRK 155
Cdd:COG1403     1 RRPGREWPALRRAVLKRDNGRCQYCGRpfsGDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 102-156 1.24e-13

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: 61.72  E-value: 1.24e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2055716377 102 KKLRKAVYERDHyRCVECGA---ADHLSLDHIIPWSLGGEDTMENLQTMCRSCNSRKG 156
Cdd:cd00085     1 RSHRLVLLARDG-LCPYCGKpggTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKKH 57
HNH_5 pfam14279
HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. ...
 116-160 3.66e-13

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: 60.43  E-value: 3.66e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2055716377 116 CVECG---AADHLSLDHIIPWSLGGEDTMENLQTMCRSCNSRKGNRLD 160
Cdd:pfam14279   1 CIYCGkefPEKNLTIEHIIPESLGGKNKISNLQTLCKKCNSKKGHDVD 48
HNH pfam01844
HNH endonuclease; His-Asn-His (HNH) proteins are a very common family of small nucleic ...
 116-158 1.22e-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: 1.22e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2055716377 116 CVECGAADHLS----LDHIIPWSLGGEDTMENLQTMCRSCNSRKGNR 158
Cdd:pfam01844   1 CQYCGRPFHISdaltVDHIIPLSDGGADDIENLILLCPSCHNKKHNR 47
HNHc smart00507
HNH nucleases;
103-153 4.22e-11

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 55.16  E-value: 4.22e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2055716377  103 KLRKAVYERDHyRCVECG--AADHLSLDHIIPWSLGGEDTMENLQTMCRSCNS 153
Cdd:smart00507   1 KLRRLLLHRDG-VCAYCGkpASEGLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52
Cas9 COG3513
CRISPR-Cas system type-II protein Cas9 [Defense mechanisms]; CRISPR-Cas system type-II protein ...
 109-159 8.46e-08

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: 50.35  E-value: 8.46e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2055716377 109 YERDHYRCVECGAADHLS--------LDHIIPWSLGGEDTMENLQTMCRSCNSRKGNRL 159
Cdd:COG3513   536 WEEQNGRCPYTGKPISISdlldgsveIDHILPRSRTLDDSFNNKVLCLADANREKGNRT 594
HNH_4 pfam13395
HNH endonuclease; This HNH nuclease domain is found in CRISPR-related proteins.
 123-159 1.90e-05

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


Pssm-ID: 433172 [Multi-domain]  Cd Length: 55  Bit Score: 40.30  E-value: 1.90e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2055716377 123 DHLSLDHIIPWSLGGEDTMENLQTMCRSCNSRKGNRL 159
Cdd:pfam13395  17 KNYDIDHILPYSRSFDDSFSNKVLVLRSANQEKGNRT 53
cas_Csn1 TIGR01865
CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1; CRISPR loci appear to be mobile ...
 98-158 6.38e-03

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: 36.25  E-value: 6.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2055716377  98 EPISKK-LRKAVYERDHYRCVECG---AADHLS------LDHIIPWSLGGEDTMENLQTMCRSCNSRKGNR 158
Cdd:TIGR01865 565 ENSSKNiLKLRLYYQQNGKCMYTGkeiDIDDLFdlsyyeIDHILPQSRSFDDSISNKVLVLASENQEKGDQ 635
 
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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