NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2796073736|ref|WP_372833286|]
View 

hypothetical protein, partial [Puniceibacterium confluentis]

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
RNase_Zc3h12a super family cl46280
Zc3h12a-like Ribonuclease NYN domain; This domain is found in the Zc3h12a protein which has ...
 60-169 1.22e-10

Zc3h12a-like Ribonuclease NYN domain; This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes. It has been suggested that this domain belongs to the PIN domain superfamily. This domain has also been identified as part of the NYN domain family.


The actual alignment was detected with superfamily member pfam11977:

Pssm-ID: 403256  Cd Length: 154  Bit Score: 56.95  E-value: 1.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796073736  60 VVVDGSNVMYW--KDETPSLATVRKVVQHLRSEGLACRVFFDANVGYLVSGRYLNDRDLSRLlgVRRNRITVVPKGTPA- 136
Cdd:pfam11977   5 IVIDGSNVAMShgRQKKFSVRGLAIAVDYFVKRGHEEITVFVPQWRKEADEKITDQHELLEL--ERLGLIVFTPSRTLDg 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2796073736 137 -------DPEILSEARKLGARVITNDRYRDWITAHPEIRT 169
Cdd:pfam11977  83 krivsydDRFILKLAEETDGVIVSNDNFRDLADENPEWID 122
 
Name Accession Description Interval E-value
RNase_Zc3h12a pfam11977
Zc3h12a-like Ribonuclease NYN domain; This domain is found in the Zc3h12a protein which has ...
 60-169 1.22e-10

Zc3h12a-like Ribonuclease NYN domain; This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes. It has been suggested that this domain belongs to the PIN domain superfamily. This domain has also been identified as part of the NYN domain family.


Pssm-ID: 403256  Cd Length: 154  Bit Score: 56.95  E-value: 1.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796073736  60 VVVDGSNVMYW--KDETPSLATVRKVVQHLRSEGLACRVFFDANVGYLVSGRYLNDRDLSRLlgVRRNRITVVPKGTPA- 136
Cdd:pfam11977   5 IVIDGSNVAMShgRQKKFSVRGLAIAVDYFVKRGHEEITVFVPQWRKEADEKITDQHELLEL--ERLGLIVFTPSRTLDg 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2796073736 137 -------DPEILSEARKLGARVITNDRYRDWITAHPEIRT 169
Cdd:pfam11977  83 krivsydDRFILKLAEETDGVIVSNDNFRDLADENPEWID 122
PIN_Zc3h12a-N4BP1-like cd18719
PRORP-like PIN domain of ribonuclease Zc3h12a, NEDD4-binding partner-1, and related proteins; ...
 60-168 6.35e-04

PRORP-like PIN domain of ribonuclease Zc3h12a, NEDD4-binding partner-1, and related proteins; Zc3h12a (zinc finger CCCH-type containing 12A, also known as MCPIP1/MCP induced protein 1 and Regnase-1) is a critical regulator of inflammatory response, with additional roles in defense against viruses and various stresses, cellular differentiation, and apoptosis. This subfamily also includes Caenorhabditis elegans REGE-1 (REGnasE-1), which also functions as a cytoplasmic endonuclease. Additionally, it includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4, as well as N4BP1 (NEDD4-binding partner-1), NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. This subfamily belongs to the PRORP-Zc3h12a-like PIN family which in addition includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350286  Cd Length: 127  Bit Score: 37.95  E-value: 6.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796073736  60 VVVDGSNV-MYW-KDETPSLATVRKVVQHLRSEGLACRVFFDanVGYLVSGRYlNDRDLSRLLGVRRNRITVVpkgTPA- 136
Cdd:cd18719     1 VVIDGSNVaMSHgNGKVFSCKGIQICVRYFLERGHEVTAFVP--QFRLESPNP-NSTDQDILEELERLGILVF---TPSr 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2796073736 137 -----------DPEILSEARKLGARVITNDRYRDWITAHPEIR 168
Cdd:cd18719    75 rvpgkrissydDRFILQLAEETDGVIVSNDNFRDLLNENPDWR 117
 
Name Accession Description Interval E-value
RNase_Zc3h12a pfam11977
Zc3h12a-like Ribonuclease NYN domain; This domain is found in the Zc3h12a protein which has ...
 60-169 1.22e-10

Zc3h12a-like Ribonuclease NYN domain; This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes. It has been suggested that this domain belongs to the PIN domain superfamily. This domain has also been identified as part of the NYN domain family.


Pssm-ID: 403256  Cd Length: 154  Bit Score: 56.95  E-value: 1.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796073736  60 VVVDGSNVMYW--KDETPSLATVRKVVQHLRSEGLACRVFFDANVGYLVSGRYLNDRDLSRLlgVRRNRITVVPKGTPA- 136
Cdd:pfam11977   5 IVIDGSNVAMShgRQKKFSVRGLAIAVDYFVKRGHEEITVFVPQWRKEADEKITDQHELLEL--ERLGLIVFTPSRTLDg 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2796073736 137 -------DPEILSEARKLGARVITNDRYRDWITAHPEIRT 169
Cdd:pfam11977  83 krivsydDRFILKLAEETDGVIVSNDNFRDLADENPEWID 122
PIN_Zc3h12a-N4BP1-like cd18719
PRORP-like PIN domain of ribonuclease Zc3h12a, NEDD4-binding partner-1, and related proteins; ...
 60-168 6.35e-04

PRORP-like PIN domain of ribonuclease Zc3h12a, NEDD4-binding partner-1, and related proteins; Zc3h12a (zinc finger CCCH-type containing 12A, also known as MCPIP1/MCP induced protein 1 and Regnase-1) is a critical regulator of inflammatory response, with additional roles in defense against viruses and various stresses, cellular differentiation, and apoptosis. This subfamily also includes Caenorhabditis elegans REGE-1 (REGnasE-1), which also functions as a cytoplasmic endonuclease. Additionally, it includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4, as well as N4BP1 (NEDD4-binding partner-1), NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. This subfamily belongs to the PRORP-Zc3h12a-like PIN family which in addition includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350286  Cd Length: 127  Bit Score: 37.95  E-value: 6.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796073736  60 VVVDGSNV-MYW-KDETPSLATVRKVVQHLRSEGLACRVFFDanVGYLVSGRYlNDRDLSRLLGVRRNRITVVpkgTPA- 136
Cdd:cd18719     1 VVIDGSNVaMSHgNGKVFSCKGIQICVRYFLERGHEVTAFVP--QFRLESPNP-NSTDQDILEELERLGILVF---TPSr 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2796073736 137 -----------DPEILSEARKLGARVITNDRYRDWITAHPEIR 168
Cdd:cd18719    75 rvpgkrissydDRFILQLAEETDGVIVSNDNFRDLLNENPDWR 117
 
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