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Conserved domains on  [gi|649123896|gb|AIC55969|]
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EXOSC8, partial [synthetic construct]

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 ...
 6-266 3.21e-168

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: 465.88  E-value: 3.21e-168
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896   6 KTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDL 85
Cdd:cd11369    1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  86 PPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQL 165
Cdd:cd11369   81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 166 PEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTG 245
Cdd:cd11369  161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                        250       260
                 ....*....|....*....|.
gi 649123896 246 AKLQDCMSRAVTRHKEVKKLM 266
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 ...
 6-266 3.21e-168

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: 465.88  E-value: 3.21e-168
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896   6 KTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDL 85
Cdd:cd11369    1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  86 PPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQL 165
Cdd:cd11369   81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 166 PEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTG 245
Cdd:cd11369  161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                        250       260
                 ....*....|....*....|.
gi 649123896 246 AKLQDCMSRAVTRHKEVKKLM 266
Cdd:cd11369  241 AQLQECIELAKKRAKELQKLI 261
PRK04282 PRK04282
exosome complex protein Rrp42;
12-272 2.85e-79

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 240.55  E-value: 2.85e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  12 EYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSS 91
Cdd:PRK04282  14 DYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASP 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  92 RFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTIN 171
Cdd:PRK04282  94 TFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEG 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 172 EETalAEVNLKKKSYLNIRTHPVATSFAVFDDtLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDC 251
Cdd:PRK04282 174 EDG--VVDKLGEDFPLPVNDKPVTVTFAKIGN-YLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTEEEVDKA 250

                        250       260
                 ....*....|....*....|.
gi 649123896 252 MSRAVTRHKEVKKLMDEVIKS 272
Cdd:PRK04282 251 IDIALEKAKELREKLKEALGI 271
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 12-267 7.70e-76

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: 231.61  E-value: 7.70e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  12 EYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSS 91
Cdd:COG2123   12 DYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLASP 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  92 RFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTIN 171
Cdd:COG2123   92 TFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVEVG 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 172 EETalAEVNLKKKSYLNIRTHPVATSFAVFDDtLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDC 251
Cdd:COG2123  172 EDG--VVVDKGEDTPLPVNTLPVSVTMAKIGD-YLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTEEEIDKA 248

                        250
                 ....*....|....*.
gi 649123896 252 MSRAVTRHKEVKKLMD 267
Cdd:COG2123  249 IDIALEKGKELRELLK 264
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-166 5.09e-33

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: 117.31  E-value: 5.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896   31 EFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEfAAPSTDAPD-KGYVVPNVDLPPLCSSRF-RSGPPGEEAQVASQF 108
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGP-IEPKEDRDFaPGRLTVEYELAPFASGERpGEGRPSEREIEISRL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 649123896  109 IADVIENSQIIqkedlcisPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLP 166
Cdd:pfam01138  80 IDRALRPSIPL--------EGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 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 ...
 6-266 3.21e-168

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: 465.88  E-value: 3.21e-168
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896   6 KTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDL 85
Cdd:cd11369    1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  86 PPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQL 165
Cdd:cd11369   81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 166 PEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTG 245
Cdd:cd11369  161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                        250       260
                 ....*....|....*....|.
gi 649123896 246 AKLQDCMSRAVTRHKEVKKLM 266
Cdd:cd11369  241 AQLQECIELAKKRAKELQKLI 261
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 32-262 3.99e-82

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: 246.08  E-value: 3.99e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  32 FRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAP-STDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIA 110
Cdd:cd11358    1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPdKLERPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 111 DVIENSQIIQKedlciSPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETalaevnlkkKSYLNIR 190
Cdd:cd11358   81 RTIEASVILDK-----STRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVDERS---------PPLLLMK 146

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 649123896 191 THPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEV 262
Cdd:cd11358  147 DLIVAVSVGGISDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAKKRSLHL 218
PRK04282 PRK04282
exosome complex protein Rrp42;
12-272 2.85e-79

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 240.55  E-value: 2.85e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  12 EYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSS 91
Cdd:PRK04282  14 DYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASP 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  92 RFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTIN 171
Cdd:PRK04282  94 TFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEG 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 172 EETalAEVNLKKKSYLNIRTHPVATSFAVFDDtLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDC 251
Cdd:PRK04282 174 EDG--VVDKLGEDFPLPVNDKPVTVTFAKIGN-YLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTEEEVDKA 250

                        250       260
                 ....*....|....*....|.
gi 649123896 252 MSRAVTRHKEVKKLMDEVIKS 272
Cdd:PRK04282 251 IDIALEKAKELREKLKEALGI 271
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 12-265 1.25e-76

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: 233.26  E-value: 1.25e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  12 EYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSS 91
Cdd:cd11365    6 DYILSLLEKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLASP 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  92 RFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTIN 171
Cdd:cd11365   86 TFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKVPEYEVD 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 172 EETalAEVNLKKKSYLNIRTHPVATSFAVFDDTlLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDC 251
Cdd:cd11365  166 ENE--VIEVLGEELPLPVNTLPVSVTVAKIGGY-IVVDPTLEEELVMDARITITIDEDGNIVALQKGGGGSFTEDEIDKA 242

                        250
                 ....*....|....
gi 649123896 252 MSRAVTRHKEVKKL 265
Cdd:cd11365  243 IDIALEKAAELREK 256
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 12-267 7.70e-76

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: 231.61  E-value: 7.70e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  12 EYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSS 91
Cdd:COG2123   12 DYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLASP 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  92 RFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTIN 171
Cdd:COG2123   92 TFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVEVG 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 172 EETalAEVNLKKKSYLNIRTHPVATSFAVFDDtLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDC 251
Cdd:COG2123  172 EDG--VVVDKGEDTPLPVNTLPVSVTMAKIGD-YLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTEEEIDKA 248

                        250
                 ....*....|....*.
gi 649123896 252 MSRAVTRHKEVKKLMD 267
Cdd:COG2123  249 IDIALEKGKELRELLK 264
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 18-265 3.80e-64

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: 201.60  E-value: 3.80e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  18 LKENCRPDGRELGEFRTTTVNIGsisTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSSRFRSGP 97
Cdd:cd11368   13 LKEGLRLDGRGLDEFRPIKITFG---LEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPMASPAFEPGR 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  98 PGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEEtala 177
Cdd:cd11368   90 PSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDVTVDGE---- 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 178 EVNLKKKSY-----LNIRTHPVATSFAVFDD-TLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDC 251
Cdd:cd11368  166 EVTVHSPEErepvpLSIHHIPICVTFAFFDDgEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLSPSQILRC 245

                        250
                 ....*....|....
gi 649123896 252 MSRAVTRHKEVKKL 265
Cdd:cd11368  246 VKIAAAKAKELTEL 259
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 18-271 2.98e-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: 2.98e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  18 LKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSSRFRSGP 97
Cdd:cd11367   14 VEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDCSPNASPEFEGRG 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  98 PGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETA-L 176
Cdd:cd11367   94 GEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRIPKVEVSEDDEgT 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 177 AEVNLKKK----SYLNIRTHPVATSFAVFDDTlLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDCM 252
Cdd:cd11367  174 KEIELSDDpydvKRLDVSNVPLIVTLSKIGNR-HIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGGSLEPESIIEMI 252

                        250
                 ....*....|....*....
gi 649123896 253 SRAVTRHKEVKKLMDEVIK 271
Cdd:cd11367  253 ETAKEVGKKLNAALDKALK 271
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-166 5.09e-33

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: 117.31  E-value: 5.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896   31 EFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEfAAPSTDAPD-KGYVVPNVDLPPLCSSRF-RSGPPGEEAQVASQF 108
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGP-IEPKEDRDFaPGRLTVEYELAPFASGERpGEGRPSEREIEISRL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 649123896  109 IADVIENSQIIqkedlcisPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLP 166
Cdd:pfam01138  80 IDRALRPSIPL--------EGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 193-255 5.10e-16

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: 70.68  E-value: 5.10e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 649123896  193 PVATSFAVFDDTLlIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDCMSRA 255
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 ...
 33-257 7.22e-11

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: 60.27  E-value: 7.22e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  33 RTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDA-PDKGYVvpNVDLPPlcssrfRSGPPGEEAQVASQFIAD 111
Cdd:cd11372    2 RPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKElPDRATL--EVIVRP------KSGLPGVKEKLLELLLRS 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 112 VIENsqIIQKED---LCISpgklvwvlycdLIC--LDYDGNILDACTFALLAALKNvqlpevtineetalAEVNLKkksy 186
Cdd:cd11372   74 TLEP--IILLHLhprTLIS-----------VVLqvLQDDGSLLACAINAACLALLD--------------AGVPMK---- 122

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 649123896 187 lnirTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMD--EEGKLCCLHKPGgsGLTGAKLQDCMSRAVT 257
Cdd:cd11372  123 ----GLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDsgEEKNLVLSESEG--SFTEEELFACLELAQA 189
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 32-272 2.89e-07

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: 49.87  E-value: 2.89e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  32 FRTTTVNIGSISTADGSALVKLGNTTVICGV--------KAEFAapstdapDKGYVVPNVDLPPLCSSRFRSGPPGEEAQ 103
Cdd:cd11371    1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVygprpipgRTEFS-------DRGRLNCEVKFAPFATPGRRRHGQDSEER 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 104 VASQFIADVIE---------NSQIiqkeDLCIspgkLVwvlycdlicLDYDGNILDACTFALLAALKNVQLPEVTIneet 174
Cdd:cd11371   74 ELSSLLHQALEpavrlekypKSQI----DVFV----TV---------LESDGSVLAAAITAASLALADAGIEMYDL---- 132

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896 175 alaevnlkkksylnirthpVATSFAVFDDTLLIVDPTGEEEHLATGTLTI-VMDEEGKLCCLHKPGgsGLTGAKLQDCMS 253
Cdd:cd11371  133 -------------------VTACSAALIGDELLLDPTREEEEASSGGVMLaYMPSLNQVTQLWQSG--EMDVDQLEEALD 191

                        250
                 ....*....|....*....
gi 649123896 254 RAVTRHKEVKKLMDEVIKS 272
Cdd:cd11371  192 LCIDGCNRIHPVVRQALLE 210
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 17-62 2.39e-06

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 47.71  E-value: 2.39e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 649123896  17 FLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGV 62
Cdd:PRK03983   9 ILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAV 54
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
23-60 3.47e-06

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 46.95  E-value: 3.47e-06
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 649123896  23 RPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVIC 60
Cdd:COG0689    2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLC 39
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 23-63 3.72e-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: 3.72e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 649123896  23 RPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVK 63
Cdd:cd11370    3 RLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVY 43
rph PRK00173
ribonuclease PH; Reviewed
 23-60 2.12e-05

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 44.71  E-value: 2.12e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 649123896  23 RPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVIC 60
Cdd:PRK00173   2 RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLC 39
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 31-121 1.71e-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: 38.85  E-value: 1.71e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649123896  31 EFRTTTVNIGSISTADGSALVKLGNTTVICGV--KAEFAAPSTDAPDKGYVVPNVDLPPLC-SSRFRSGPPGEEAQVaSQ 107
Cdd:cd11366    1 ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVygPREVHPRHLQLPDRAVIRVRYNMAPFSvDERKRPGPDRREIEI-SK 79

                         90
                 ....*....|....
gi 649123896 108 FIADVIENSQIIQK 121
Cdd:cd11366   80 VIKEALEPAIILEE 93
 
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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