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Conserved domains on  [gi|818283826|gb|KKP69226|]
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MAG: hypothetical protein UR66_C0001G0108 [Candidatus Moranbacteria bacterium GW2011_GWE1_35_17]

Protein Classification

NYN domain-containing protein( domain architecture ID 11444475)

NYN domain-containing protein; the NYN domain shares a common protein fold with PIN (PilT N-terminal)-domain nucleases

Gene Ontology:  GO:0004540
PubMed:  17114934

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LabA COG1432
NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction ...
 8-157 5.61e-22

NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction only];


:

Pssm-ID: 441041  Cd Length: 164  Bit Score: 86.49  E-value: 5.61e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818283826   8 VFIDGQNLYMGTAKREygkWRIDLERFRVYLEKKYYVEKAYYFLGCIQKENQDLYEEIQSAGFVLVFREHNTaMLGKKKG 87
Cdd:COG1432    5 VFIDGDNLYAAARDLG---FDIDYEKLLEELAEYGRLVRARAYGDDTDERQQGFIDALRENGFEVILKPLQQ-FRTSGKN 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818283826  88 NVDSDIIFSIMKKLYkKESFNKILLVSGDGDYKQLVDFLIEEKRFGKILFPNKKFASSLyKKLGSEFFDY 157
Cdd:COG1432   81 AVDVELAVDAMELAY-TPNIDTFVLVSGDSDFTPLVERLRERGKRVEVVGVEGKTSDAL-RNAADEFIDL 148
 
Name Accession Description Interval E-value
LabA COG1432
NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction ...
 8-157 5.61e-22

NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction only];


Pssm-ID: 441041  Cd Length: 164  Bit Score: 86.49  E-value: 5.61e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818283826   8 VFIDGQNLYMGTAKREygkWRIDLERFRVYLEKKYYVEKAYYFLGCIQKENQDLYEEIQSAGFVLVFREHNTaMLGKKKG 87
Cdd:COG1432    5 VFIDGDNLYAAARDLG---FDIDYEKLLEELAEYGRLVRARAYGDDTDERQQGFIDALRENGFEVILKPLQQ-FRTSGKN 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818283826  88 NVDSDIIFSIMKKLYkKESFNKILLVSGDGDYKQLVDFLIEEKRFGKILFPNKKFASSLyKKLGSEFFDY 157
Cdd:COG1432   81 AVDVELAVDAMELAY-TPNIDTFVLVSGDSDFTPLVERLRERGKRVEVVGVEGKTSDAL-RNAADEFIDL 148
PIN_LabA cd10911
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 4-134 3.67e-20

PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; This subfamily contains Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. This subfamily belongs to the LabA-like domain family which includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Also included in the LabA-like domain family are human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously Pseudomonas putida S16 NicB , which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like family. 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: 350235  Cd Length: 154  Bit Score: 81.38  E-value: 3.67e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818283826   4 GKNCVFIDGQNLYMGTakREYGkWRIDLERFRVYLEKKYYVEKAYYFLGCIQKEN---QDLYEEIQSAGFVLVF---REH 77
Cdd:cd10911    1 ERVAVFIDGANLYYAA--KKLG-WKIDYEKLLKYLVGGRELVRAYYYTAVDDEEDekqQKFLDALRKIGYEVVTkplKEF 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 818283826  78 NTAMLGKKKGNVDSDIIFSIMKKLYKkesFNKILLVSGDGDYKQLVDFLieeKRFGK 134
Cdd:cd10911   78 RDEGGGSVKGNVDVEIAVDMLRLADK---YDTAILVSGDGDFAPLVEYL---QRKGK 128
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 7-146 1.21e-12

NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.


Pssm-ID: 426520  Cd Length: 137  Bit Score: 61.53  E-value: 1.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818283826    7 CVFIDGQNLYMGtakreygkWRIDLERFRVYLEKKYYVEKAYYFLGCIQKENQDLYEEIQSAGFVLVFREhntamLGKKK 86
Cdd:pfam01936   3 AVFIDGENCPLP--------DGVDYRKVLEEIRSGGEVVRARAYGNWGDPDLRKFPDALSSTGIPVQHKP-----LTKGK 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818283826   87 GNVDSDIIFSIMKKLYKKEsFNKILLVSGDGDYKQLVDFLieeKRFGK----ILFPNKKFASSL 146
Cdd:pfam01936  70 NAVDVGLAVDALELAYDNN-PDTFVLVSGDGDFAPLLERL---RERGKrvevLGAEEPSTSDAL 129
 
Name Accession Description Interval E-value
LabA COG1432
NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction ...
 8-157 5.61e-22

NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction only];


Pssm-ID: 441041  Cd Length: 164  Bit Score: 86.49  E-value: 5.61e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818283826   8 VFIDGQNLYMGTAKREygkWRIDLERFRVYLEKKYYVEKAYYFLGCIQKENQDLYEEIQSAGFVLVFREHNTaMLGKKKG 87
Cdd:COG1432    5 VFIDGDNLYAAARDLG---FDIDYEKLLEELAEYGRLVRARAYGDDTDERQQGFIDALRENGFEVILKPLQQ-FRTSGKN 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818283826  88 NVDSDIIFSIMKKLYkKESFNKILLVSGDGDYKQLVDFLIEEKRFGKILFPNKKFASSLyKKLGSEFFDY 157
Cdd:COG1432   81 AVDVELAVDAMELAY-TPNIDTFVLVSGDSDFTPLVERLRERGKRVEVVGVEGKTSDAL-RNAADEFIDL 148
PIN_LabA cd10911
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 4-134 3.67e-20

PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; This subfamily contains Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. This subfamily belongs to the LabA-like domain family which includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Also included in the LabA-like domain family are human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously Pseudomonas putida S16 NicB , which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like family. 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: 350235  Cd Length: 154  Bit Score: 81.38  E-value: 3.67e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818283826   4 GKNCVFIDGQNLYMGTakREYGkWRIDLERFRVYLEKKYYVEKAYYFLGCIQKEN---QDLYEEIQSAGFVLVF---REH 77
Cdd:cd10911    1 ERVAVFIDGANLYYAA--KKLG-WKIDYEKLLKYLVGGRELVRAYYYTAVDDEEDekqQKFLDALRKIGYEVVTkplKEF 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 818283826  78 NTAMLGKKKGNVDSDIIFSIMKKLYKkesFNKILLVSGDGDYKQLVDFLieeKRFGK 134
Cdd:cd10911   78 RDEGGGSVKGNVDVEIAVDMLRLADK---YDTAILVSGDGDFAPLVEYL---QRKGK 128
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 7-146 1.21e-12

NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.


Pssm-ID: 426520  Cd Length: 137  Bit Score: 61.53  E-value: 1.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818283826    7 CVFIDGQNLYMGtakreygkWRIDLERFRVYLEKKYYVEKAYYFLGCIQKENQDLYEEIQSAGFVLVFREhntamLGKKK 86
Cdd:pfam01936   3 AVFIDGENCPLP--------DGVDYRKVLEEIRSGGEVVRARAYGNWGDPDLRKFPDALSSTGIPVQHKP-----LTKGK 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818283826   87 GNVDSDIIFSIMKKLYKKEsFNKILLVSGDGDYKQLVDFLieeKRFGK----ILFPNKKFASSL 146
Cdd:pfam01936  70 NAVDVGLAVDALELAYDNN-PDTFVLVSGDGDFAPLLERL---RERGKrvevLGAEEPSTSDAL 129
PIN_NicB-like cd18722
LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins; Curiously NicB from ...
 8-118 2.89e-05

LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins; Curiously NicB from Pseudomonas putida S16 is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine. This subfamily also includes the uncharacterized CPP15 (plasmid) protein from Campylobacter jejuni. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. 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: 350289  Cd Length: 117  Bit Score: 41.39  E-value: 2.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818283826   8 VFIDGQNLYmgtakreYG-KWRIDLERFRVYlekkYYVEKAYYFLGCIQKENQDLYEEIQsagfvlVFREHNTAMLGKKK 86
Cdd:cd18722    4 VYVDGFNLY-------YGlKAREELKLYRYY----WLDLPPLAKNLLLPDPSQELLERVK------YFTARVNSSPKEEK 66

                         90       100       110
                 ....*....|....*....|....*....|..
gi 818283826  87 GnVDSDIIFSIMKKLYKKEsFNKILLVSGDGD 118
Cdd:cd18722   67 G-VDVNIALDILSDAYKKQ-VDQAVLVSGDSD 96
 
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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