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Conserved domains on  [gi|616686034|gb|KAE83705|]
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hypothetical protein W632_02198 [Staphylococcus aureus VET0402R]

Protein Classification

NYN domain-containing protein( domain architecture ID 10007840)

uncharacterized YacP-like NYN domain-containing protein may function as a nuclease

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rae1 COG3688
EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN ...
 4-170 9.05e-67

EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN domain [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 442904  Cd Length: 168  Bit Score: 201.24  E-value: 9.05e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034   4 RYLIIDGYNMIGQSPTLSAIAKENLEEARMQLIDAIANYNAVISDEIICVFDAYDQSGVE-REYMYHGVKTIFTKEKETA 82
Cdd:COG3688    1 EILLVDGYNVIGAWPELKELKDDSLEAARDKLIEILANYAAFTGYEVIVVFDAHYVPGSEeKEEKYGGVEVVFTKEGETA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034  83 DSFIERYVYELYDKHTkHITVVTSDMSEQHAIFGSGAYRISSREMWRDLKENEIDVSKSLDDISENKPRTRIPLSSEILA 162
Cdd:COG3688   81 DSYIERLVAELRNRPR-RVTVVTSDRAEQRTVFGRGALRISARELLREVEEAKREIRKKIKKKKPKRNTLKDRLDPEVLE 159


                 ....*...
gi 616686034 163 EFEKIRRG 170
Cdd:COG3688  160 KLEKLRRG 167
 
Name Accession Description Interval E-value
Rae1 COG3688
EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN ...
 4-170 9.05e-67

EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442904  Cd Length: 168  Bit Score: 201.24  E-value: 9.05e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034   4 RYLIIDGYNMIGQSPTLSAIAKENLEEARMQLIDAIANYNAVISDEIICVFDAYDQSGVE-REYMYHGVKTIFTKEKETA 82
Cdd:COG3688    1 EILLVDGYNVIGAWPELKELKDDSLEAARDKLIEILANYAAFTGYEVIVVFDAHYVPGSEeKEEKYGGVEVVFTKEGETA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034  83 DSFIERYVYELYDKHTkHITVVTSDMSEQHAIFGSGAYRISSREMWRDLKENEIDVSKSLDDISENKPRTRIPLSSEILA 162
Cdd:COG3688   81 DSYIERLVAELRNRPR-RVTVVTSDRAEQRTVFGRGALRISARELLREVEEAKREIRKKIKKKKPKRNTLKDRLDPEVLE 159


                 ....*...
gi 616686034 163 EFEKIRRG 170
Cdd:COG3688  160 KLEKLRRG 167
NYN_YacP pfam05991
YacP-like NYN domain; This family consists of bacterial proteins related to YacP. This family ...
 6-169 4.75e-63

YacP-like NYN domain; This family consists of bacterial proteins related to YacP. This family is uncharacterized functionally, but it has been suggested that these proteins are nucleases due to them containing a NYN domain. NYN (for N4BP1, YacP-like Nuclease) domains were discovered by Anantharaman and Aravind. Based on gene neighborhoods it was suggested that the bacterial YacP proteins interact with the Ribonuclease III and TrmH methylase in a processome complex that catalyzes the maturation of rRNA and tRNA.


Pssm-ID: 428711  Cd Length: 165  Bit Score: 191.63  E-value: 4.75e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034    6 LIIDGYNMIGQSPTLSAIA-KENLEEARMQLIDAIANYNAVISDEIICVFDAYDQSGVEREYM-YHGVKTIFTKEKETAD 83
Cdd:pfam05991   1 LLVDGYNVIGAWPELKELKdRGDLEAARDKLIEILANYQAYTGYEVIVVFDAHYVPGPEEKEEkYGGIEVVYTKEGETAD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034   84 SFIERYVYELYDKHtkHITVVTSDMSEQHAIFGSGAYRISSREMWRDLKENEIDVSKSLDDISENKPRTR-IPLSSEILA 162
Cdd:pfam05991  81 SYIERLVAELGRKT--RVTVATSDRAEQQTIFGQGALRLSARELYEEVEAAEKKIKKKVEKRKEKRRNYLeDRLSPEVLE 158


                  ....*..
gi 616686034  163 EFEKIRR 169
Cdd:pfam05991 159 KLEKLRR 165
PIN_YacP-like cd10912
PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also ...
 5-145 8.13e-60

PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also known as Rae1, is an endoribonuclease involved in ribosome-dependent mRNA decay. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350236  Cd Length: 142  Bit Score: 182.37  E-value: 8.13e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034   5 YLIIDGYNMIGQSPTLSAIAKENLEEARMQLIDAIANYNAVISDEIICVFDAYDQ-SGVEREYMYHGVKTIFTKEKETAD 83
Cdd:cd10912    1 ILLVDGYNVIGAWPELKKLKRESLEEARDKLIEELANYQAYKGYEVIVVFDAYYVkGGLEKEEESGGVEVVFTKEGETAD 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 616686034  84 SFIERYVYELYDKHTKhITVVTSDMSEQHAIFGSGAYRISSREMWRDLKENEIDVSKSLDDI 145
Cdd:cd10912   81 SYIERLVASLKRRCKR-VTVATSDRAEQRTVFGQGALRISARELLKEIERAKEEIRRSKRRT 141
 
Name Accession Description Interval E-value
Rae1 COG3688
EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN ...
 4-170 9.05e-67

EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442904  Cd Length: 168  Bit Score: 201.24  E-value: 9.05e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034   4 RYLIIDGYNMIGQSPTLSAIAKENLEEARMQLIDAIANYNAVISDEIICVFDAYDQSGVE-REYMYHGVKTIFTKEKETA 82
Cdd:COG3688    1 EILLVDGYNVIGAWPELKELKDDSLEAARDKLIEILANYAAFTGYEVIVVFDAHYVPGSEeKEEKYGGVEVVFTKEGETA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034  83 DSFIERYVYELYDKHTkHITVVTSDMSEQHAIFGSGAYRISSREMWRDLKENEIDVSKSLDDISENKPRTRIPLSSEILA 162
Cdd:COG3688   81 DSYIERLVAELRNRPR-RVTVVTSDRAEQRTVFGRGALRISARELLREVEEAKREIRKKIKKKKPKRNTLKDRLDPEVLE 159


                 ....*...
gi 616686034 163 EFEKIRRG 170
Cdd:COG3688  160 KLEKLRRG 167
NYN_YacP pfam05991
YacP-like NYN domain; This family consists of bacterial proteins related to YacP. This family ...
 6-169 4.75e-63

YacP-like NYN domain; This family consists of bacterial proteins related to YacP. This family is uncharacterized functionally, but it has been suggested that these proteins are nucleases due to them containing a NYN domain. NYN (for N4BP1, YacP-like Nuclease) domains were discovered by Anantharaman and Aravind. Based on gene neighborhoods it was suggested that the bacterial YacP proteins interact with the Ribonuclease III and TrmH methylase in a processome complex that catalyzes the maturation of rRNA and tRNA.


Pssm-ID: 428711  Cd Length: 165  Bit Score: 191.63  E-value: 4.75e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034    6 LIIDGYNMIGQSPTLSAIA-KENLEEARMQLIDAIANYNAVISDEIICVFDAYDQSGVEREYM-YHGVKTIFTKEKETAD 83
Cdd:pfam05991   1 LLVDGYNVIGAWPELKELKdRGDLEAARDKLIEILANYQAYTGYEVIVVFDAHYVPGPEEKEEkYGGIEVVYTKEGETAD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034   84 SFIERYVYELYDKHtkHITVVTSDMSEQHAIFGSGAYRISSREMWRDLKENEIDVSKSLDDISENKPRTR-IPLSSEILA 162
Cdd:pfam05991  81 SYIERLVAELGRKT--RVTVATSDRAEQQTIFGQGALRLSARELYEEVEAAEKKIKKKVEKRKEKRRNYLeDRLSPEVLE 158


                  ....*..
gi 616686034  163 EFEKIRR 169
Cdd:pfam05991 159 KLEKLRR 165
PIN_YacP-like cd10912
PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also ...
 5-145 8.13e-60

PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also known as Rae1, is an endoribonuclease involved in ribosome-dependent mRNA decay. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350236  Cd Length: 142  Bit Score: 182.37  E-value: 8.13e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 616686034   5 YLIIDGYNMIGQSPTLSAIAKENLEEARMQLIDAIANYNAVISDEIICVFDAYDQ-SGVEREYMYHGVKTIFTKEKETAD 83
Cdd:cd10912    1 ILLVDGYNVIGAWPELKKLKRESLEEARDKLIEELANYQAYKGYEVIVVFDAYYVkGGLEKEEESGGVEVVFTKEGETAD 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 616686034  84 SFIERYVYELYDKHTKhITVVTSDMSEQHAIFGSGAYRISSREMWRDLKENEIDVSKSLDDI 145
Cdd:cd10912   81 SYIERLVASLKRRCKR-VTVATSDRAEQRTVFGQGALRISARELLKEIERAKEEIRRSKRRT 141
 
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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