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Conserved domains on  [gi|60359866|dbj|BAD90152|]
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mKIAA4013 protein, partial [Mus musculus]

Protein Classification

exosome complex component RRP43( domain architecture ID 10183523)

exosome complex component RRP43 similar to Saccharomyces cerevisiae exosome RRP43 subunit which is involved in pre-rRNA processing and found both in the nucleus and in the cytoplasm.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 38-298 1.08e-163

RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


:

Pssm-ID: 206774 [Multi-domain]  Cd Length: 261  Bit Score: 455.48  E-value: 1.08e-163
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  38 KTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDL 117
Cdd:cd11369   1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 118 PPLCSSRFRTGPPGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 197
Cdd:cd11369  81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 198 PEVTINEETALAEVNLKKKSYLNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 277
Cdd:cd11369 161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                       250       260
                ....*....|....*....|.
gi 60359866 278 AKLQDCMSRAVTRHKEVSKLL 298
Cdd:cd11369 241 AQLQECIELAKKRAKELQKLI 261
 
Name Accession Description Interval E-value
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 38-298 1.08e-163

RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206774 [Multi-domain]  Cd Length: 261  Bit Score: 455.48  E-value: 1.08e-163
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  38 KTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDL 117
Cdd:cd11369   1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 118 PPLCSSRFRTGPPGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 197
Cdd:cd11369  81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 198 PEVTINEETALAEVNLKKKSYLNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 277
Cdd:cd11369 161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                       250       260
                ....*....|....*....|.
gi 60359866 278 AKLQDCMSRAVTRHKEVSKLL 298
Cdd:cd11369 241 AQLQECIELAKKRAKELQKLI 261
PRK04282 PRK04282
exosome complex protein Rrp42;
44-304 3.18e-81

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 246.71  E-value: 3.18e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866   44 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSS 123
Cdd:PRK04282  14 DYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASP 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  124 RFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 197
Cdd:PRK04282  94 TFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  198 PEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 277
Cdd:PRK04282 168 PAVEEGEDG--VVDKLGEDFPLPVNDKPVTVTFAKIGN-YLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTE 244

                        250       260
                 ....*....|....*....|....*..
gi 60359866  278 AKLQDCMSRAVTRHKEVSKLLDEVIQS 304
Cdd:PRK04282 245 EEVDKAIDIALEKAKELREKLKEALGI 271
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 44-299 2.75e-77

Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 441726 [Multi-domain]  Cd Length: 264  Bit Score: 236.62  E-value: 2.75e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  44 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSS 123
Cdd:COG2123  12 DYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLASP 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 124 RFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 197
Cdd:COG2123  92 TFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKV 165

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 198 PEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 277
Cdd:COG2123 166 PKVEVGEDG--VVVDKGEDTPLPVNTLPVSVTMAKIGD-YLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTE 242

                       250       260
                ....*....|....*....|..
gi 60359866 278 AKLQDCMSRAVTRHKEVSKLLD 299
Cdd:COG2123 243 EEIDKAIDIALEKGKELRELLK 264
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 63-198 3.42e-31

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 113.46  E-value: 3.42e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866    63 EFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSSRF-RTGPPGEEAQVTSQFI 141
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERpGEGRPSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 60359866   142 ADVVdnsqvikkEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLP 198
Cdd:pfam01138  81 DRAL--------RPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
 
Name Accession Description Interval E-value
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 38-298 1.08e-163

RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206774 [Multi-domain]  Cd Length: 261  Bit Score: 455.48  E-value: 1.08e-163
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  38 KTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDL 117
Cdd:cd11369   1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 118 PPLCSSRFRTGPPGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 197
Cdd:cd11369  81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 198 PEVTINEETALAEVNLKKKSYLNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 277
Cdd:cd11369 161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                       250       260
                ....*....|....*....|.
gi 60359866 278 AKLQDCMSRAVTRHKEVSKLL 298
Cdd:cd11369 241 AQLQECIELAKKRAKELQKLI 261
PRK04282 PRK04282
exosome complex protein Rrp42;
44-304 3.18e-81

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 246.71  E-value: 3.18e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866   44 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSS 123
Cdd:PRK04282  14 DYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASP 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  124 RFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 197
Cdd:PRK04282  94 TFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  198 PEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 277
Cdd:PRK04282 168 PAVEEGEDG--VVDKLGEDFPLPVNDKPVTVTFAKIGN-YLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTE 244

                        250       260
                 ....*....|....*....|....*..
gi 60359866  278 AKLQDCMSRAVTRHKEVSKLLDEVIQS 304
Cdd:PRK04282 245 EEVDKAIDIALEKAKELREKLKEALGI 271
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 64-294 1.53e-77

RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites.


Pssm-ID: 206766 [Multi-domain]  Cd Length: 218  Bit Score: 235.68  E-value: 1.53e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  64 FRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVD-APDRGYVVPNVDLPPLCSSRFRTGPPGEEAQVTSQFIA 142
Cdd:cd11358   1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLeRPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 143 DVVDNSQVIKKedlciSPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETalaevnlkkKSYLNVR 222
Cdd:cd11358  81 RTIEASVILDK-----STRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVDERS---------PPLLLMK 146

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 60359866 223 TNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEV 294
Cdd:cd11358 147 DLIVAVSVGGISDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAKKRSLHL 218
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 44-299 2.75e-77

Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 441726 [Multi-domain]  Cd Length: 264  Bit Score: 236.62  E-value: 2.75e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  44 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSS 123
Cdd:COG2123  12 DYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLASP 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 124 RFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 197
Cdd:COG2123  92 TFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKV 165

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 198 PEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 277
Cdd:COG2123 166 PKVEVGEDG--VVVDKGEDTPLPVNTLPVSVTMAKIGD-YLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTE 242

                       250       260
                ....*....|....*....|..
gi 60359866 278 AKLQDCMSRAVTRHKEVSKLLD 299
Cdd:COG2123 243 EEIDKAIDIALEKGKELRELLK 264
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 44-297 9.15e-77

RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. It is required for 3' processing of the 5.8S rRNA.


Pssm-ID: 206770 [Multi-domain]  Cd Length: 256  Bit Score: 234.80  E-value: 9.15e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  44 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSS 123
Cdd:cd11365   6 DYILSLLEKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLASP 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 124 RFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 197
Cdd:cd11365  86 TFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKV 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 198 PEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDTlLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 277
Cdd:cd11365 160 PEYEVDENE--VIEVLGEELPLPVNTLPVSVTVAKIGGY-IVVDPTLEEELVMDARITITIDEDGNIVALQKGGGGSFTE 236

                       250       260
                ....*....|....*....|
gi 60359866 278 AKLQDCMSRAVTRHKEVSKL 297
Cdd:cd11365 237 DEIDKAIDIALEKAAELREK 256
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 50-297 1.78e-57

RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206773 [Multi-domain]  Cd Length: 259  Bit Score: 185.81  E-value: 1.78e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  50 LKENCRPDGRELGEFRATTVNIGsisTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSSRFRTGP 129
Cdd:cd11368  13 LKEGLRLDGRGLDEFRPIKITFG---LEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPMASPAFEPGR 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 130 PGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEEtala 209
Cdd:cd11368  90 PSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDVTVDGE---- 165

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 210 EVNLKKKSY-----LNVRTNPVATSFAVFDD-TLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAKLQDC 283
Cdd:cd11368 166 EVTVHSPEErepvpLSIHHIPICVTFAFFDDgEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLSPSQILRC 245

                       250
                ....*....|....
gi 60359866 284 MSRAVTRHKEVSKL 297
Cdd:cd11368 246 VKIAAAKAKELTEL 259
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 50-302 7.55e-54

RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206772 [Multi-domain]  Cd Length: 272  Bit Score: 176.63  E-value: 7.55e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  50 LKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSSRFRTGP 129
Cdd:cd11367  14 VEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDCSPNASPEFEGRG 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 130 PGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETA-L 208
Cdd:cd11367  94 GEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRIPKVEVSEDDEgT 173

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 209 AEVNLKKK----SYLNVRTNPVATSFAVFDDTlLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAKLQDCM 284
Cdd:cd11367 174 KEIELSDDpydvKRLDVSNVPLIVTLSKIGNR-HIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGGSLEPESIIEMI 252

                       250
                ....*....|....*...
gi 60359866 285 SRAVTRHKEVSKLLDEVI 302
Cdd:cd11367 253 ETAKEVGKKLNAALDKAL 270
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 63-198 3.42e-31

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 113.46  E-value: 3.42e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866    63 EFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSSRF-RTGPPGEEAQVTSQFI 141
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERpGEGRPSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 60359866   142 ADVVdnsqvikkEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLP 198
Cdd:pfam01138  81 DRAL--------RPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 225-287 5.77e-17

3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 427466 [Multi-domain]  Cd Length: 67  Bit Score: 73.76  E-value: 5.77e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 60359866   225 PVATSFAVFDDTLlIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAKLQDCMSRA 287
Cdd:pfam03725   3 VAAVTVGKIDGQL-VVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELA 64
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 65-289 9.54e-08

RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206777 [Multi-domain]  Cd Length: 199  Bit Score: 51.41  E-value: 9.54e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  65 RATTVNIGSISTADGSALVKLGNTTVICGVKAefaapPVDA------PDRGYVvpNVDLPPlcssrfRTGPPGEEAQVTS 138
Cdd:cd11372   2 RPLSCELGLLSRADGSARFSQGDTSVLAAVYG-----PIEVklrkelPDRATL--EVIVRP------KSGLPGVKEKLLE 68

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 139 QFIADVVDNsqVIKKED---LCISpgklawvlycdLIC--LDYDGNILDACTFALLAALKNvqlpevtineetalAEVNL 213
Cdd:cd11372  69 LLLRSTLEP--IILLHLhprTLIS-----------VVLqvLQDDGSLLACAINAACLALLD--------------AGVPM 121

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 60359866 214 KkksylnvrTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTD--EDGKLCCLHKPGgsGLTGAKLQDCMSRAVT 289
Cdd:cd11372 122 K--------GLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDsgEEKNLVLSESEG--SFTEEELFACLELAQA 189
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 49-94 2.25e-06

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 48.09  E-value: 2.25e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 60359866   49 FLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGV 94
Cdd:PRK03983   9 ILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAV 54
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
55-92 4.57e-06

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 46.95  E-value: 4.57e-06
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 60359866  55 RPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVIC 92
Cdd:COG0689   2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLC 39
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 55-95 5.20e-06

RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206775 [Multi-domain]  Cd Length: 226  Bit Score: 46.77  E-value: 5.20e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 60359866  55 RPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVK 95
Cdd:cd11370   3 RLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVY 43
rph PRK00173
ribonuclease PH; Reviewed
 55-102 8.03e-06

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 46.26  E-value: 8.03e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 60359866   55 RPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPP 102
Cdd:PRK00173   2 RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPR 49
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 64-256 2.39e-05

MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206776 [Multi-domain]  Cd Length: 210  Bit Score: 44.48  E-value: 2.39e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  64 FRATTVNIGSISTADGSALVKLGNTTVICGV--------KAEFAappvdapDRGYVVPNVDLPPLCSSRFRTGPPGEEAQ 135
Cdd:cd11371   1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVygprpipgRTEFS-------DRGRLNCEVKFAPFATPGRRRHGQDSEER 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866 136 VTSQFIADVVD---------NSQVikkeDLCISpgklawvlycdliCLDYDGNILDACTFALLAALKNVQLPEVTIneet 206
Cdd:cd11371  74 ELSSLLHQALEpavrlekypKSQI----DVFVT-------------VLESDGSVLAAAITAASLALADAGIEMYDL---- 132

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 60359866 207 alaevnlkkksylnvrtnpVATSFAVFDDTLLIVDPTGEEEHLSTGTLTV 256
Cdd:cd11371 133 -------------------VTACSAALIGDELLLDPTREEEEASSGGVML 163
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 63-129 1.22e-03

RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA.


Pssm-ID: 206771 [Multi-domain]  Cd Length: 214  Bit Score: 39.24  E-value: 1.22e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60359866  63 EFRATTVNIGSISTADGSALVKLGNTTVICGV--KAEFAAPPVDAPDRGYVVPNVDLPPLC-SSRFRTGP 129
Cdd:cd11366   1 ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVygPREVHPRHLQLPDRAVIRVRYNMAPFSvDERKRPGP 70
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 63-102 4.05e-03

Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Structurally all members of this family form hexameric rings (trimers of dimers). Bacterial RNase PH forms a homohexameric ring, and removes nucleotide residues following the -CCA terminus of tRNA.


Pssm-ID: 206767 [Multi-domain]  Cd Length: 227  Bit Score: 37.98  E-value: 4.05e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 60359866  63 EFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPP 102
Cdd:cd11362   1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPP 40
 
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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