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Conserved domains on  [gi|17555992|ref|NP_499416|]
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Exosome complex component CSL4 homolog [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 70-162 1.51e-16

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05791:

Pssm-ID: 471952  Cd Length: 92  Bit Score: 71.51  E-value: 1.51e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992  70 LLPFHGAIVTAKVMAVGLRFAKCDIISIGDKVYKKRFSALLPKKKLRPLEPELSEPFKNFvRPNDYILAKVCEDAEIKdK 149
Cdd:cd05791   2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCF-RPGDIVRAKVISLGDAS-S 79

                        90
                ....*....|...
gi 17555992 150 FVLSIAEDELGVV 162
Cdd:cd05791  80 YYLSTAENELGVV 92
PRK09521 super family cl35849
exosome complex RNA-binding protein Csl4; Provisional
 6-194 1.43e-11

exosome complex RNA-binding protein Csl4; Provisional


The actual alignment was detected with superfamily member PRK09521:

Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 60.76  E-value: 1.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992    6 LVAPGDKvLDAIGEYRMGKGLYEANRRIFASVAGFVnvygFRDKSDNLVQVIEVRrsedqlDNELLPFHGAIVTAKVMAV 85
Cdd:PRK09521   7 LVLPGDY-LAVIEEYLPGEGTYEDNGEVYASVVGKV----FIDDINRKISVIPFK------KTPPLLKKGDIVYGRVVDV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992   86 GLRFAKCDIISIgdkvykkrfsallpKKKLRPLEPELS-------------EPFKNFVRPNDYILAKVcedAEIKDKFVL 152
Cdd:PRK09521  76 KEQRALVRIVSI--------------EGSERELATSKLayihisqvsdgyvESLTDAFKIGDIVRAKV---ISYTDPLQL 138

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 17555992  153 SIAEDELGVV--LCrGRFGEPMQKVDWNTVVSTRTGKTEPRKMA 194
Cdd:PRK09521 139 STKGKDLGVIyaMC-SRCRTPLVKKGENELKCPNCGNIETRKLS 181
 
Name Accession Description Interval E-value
S1_CSL4 cd05791
S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 70-162 1.51e-16

S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240217  Cd Length: 92  Bit Score: 71.51  E-value: 1.51e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992  70 LLPFHGAIVTAKVMAVGLRFAKCDIISIGDKVYKKRFSALLPKKKLRPLEPELSEPFKNFvRPNDYILAKVCEDAEIKdK 149
Cdd:cd05791   2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCF-RPGDIVRAKVISLGDAS-S 79

                        90
                ....*....|...
gi 17555992 150 FVLSIAEDELGVV 162
Cdd:cd05791  80 YYLSTAENELGVV 92
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 6-194 1.43e-11

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 60.76  E-value: 1.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992    6 LVAPGDKvLDAIGEYRMGKGLYEANRRIFASVAGFVnvygFRDKSDNLVQVIEVRrsedqlDNELLPFHGAIVTAKVMAV 85
Cdd:PRK09521   7 LVLPGDY-LAVIEEYLPGEGTYEDNGEVYASVVGKV----FIDDINRKISVIPFK------KTPPLLKKGDIVYGRVVDV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992   86 GLRFAKCDIISIgdkvykkrfsallpKKKLRPLEPELS-------------EPFKNFVRPNDYILAKVcedAEIKDKFVL 152
Cdd:PRK09521  76 KEQRALVRIVSI--------------EGSERELATSKLayihisqvsdgyvESLTDAFKIGDIVRAKV---ISYTDPLQL 138

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 17555992  153 SIAEDELGVV--LCrGRFGEPMQKVDWNTVVSTRTGKTEPRKMA 194
Cdd:PRK09521 139 STKGKDLGVIyaMC-SRCRTPLVKKGENELKCPNCGNIETRKLS 181
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 6-43 1.73e-07

Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.


Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 45.81  E-value: 1.73e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 17555992     6 LVAPGDkVLDAIGEYRMGKGLYEANRRIFASVAGFVNV 43
Cdd:pfam14382   1 IVLPGE-RLGSDEEYMPGHGTYVRDGNIYASVAGTVEI 37
PRK04163 PRK04163
exosome complex protein Rrp4;
6-160 3.14e-06

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 46.42  E-value: 3.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992    6 LVAPGDKVldAIGEYRMGKGLYEANRRIFASVAGFVNVygfrdkSDNLVQVIEvrrsedqLDNELLPFHGAIVTAKVMAV 85
Cdd:PRK04163  10 IVVPGDLL--AEGEFKAGRGTYKENGKIYSTVVGLVDI------KDDKVRVIP-------LEGKYIPKVGDLVIGKVTDV 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17555992   86 GLRFAKCDIISigdkvykkRFSALLPKKKL--RPLEPElSEPFKNFVRPNDYILAKVcEDAEIKDKFVLSIAEDELG 160
Cdd:PRK04163  75 TFSGWEVDINS--------PYKAYLPVSEVlgRPVNVE-GTDLRKYLDIGDYIIAKV-KDVDRTRDVVLTLKGKGLG 141
 
Name Accession Description Interval E-value
S1_CSL4 cd05791
S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 70-162 1.51e-16

S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240217  Cd Length: 92  Bit Score: 71.51  E-value: 1.51e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992  70 LLPFHGAIVTAKVMAVGLRFAKCDIISIGDKVYKKRFSALLPKKKLRPLEPELSEPFKNFvRPNDYILAKVCEDAEIKdK 149
Cdd:cd05791   2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCF-RPGDIVRAKVISLGDAS-S 79

                        90
                ....*....|...
gi 17555992 150 FVLSIAEDELGVV 162
Cdd:cd05791  80 YYLSTAENELGVV 92
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 6-194 1.43e-11

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 60.76  E-value: 1.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992    6 LVAPGDKvLDAIGEYRMGKGLYEANRRIFASVAGFVnvygFRDKSDNLVQVIEVRrsedqlDNELLPFHGAIVTAKVMAV 85
Cdd:PRK09521   7 LVLPGDY-LAVIEEYLPGEGTYEDNGEVYASVVGKV----FIDDINRKISVIPFK------KTPPLLKKGDIVYGRVVDV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992   86 GLRFAKCDIISIgdkvykkrfsallpKKKLRPLEPELS-------------EPFKNFVRPNDYILAKVcedAEIKDKFVL 152
Cdd:PRK09521  76 KEQRALVRIVSI--------------EGSERELATSKLayihisqvsdgyvESLTDAFKIGDIVRAKV---ISYTDPLQL 138

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 17555992  153 SIAEDELGVV--LCrGRFGEPMQKVDWNTVVSTRTGKTEPRKMA 194
Cdd:PRK09521 139 STKGKDLGVIyaMC-SRCRTPLVKKGENELKCPNCGNIETRKLS 181
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 6-43 1.73e-07

Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.


Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 45.81  E-value: 1.73e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 17555992     6 LVAPGDkVLDAIGEYRMGKGLYEANRRIFASVAGFVNV 43
Cdd:pfam14382   1 IVLPGE-RLGSDEEYMPGHGTYVRDGNIYASVAGTVEI 37
PRK04163 PRK04163
exosome complex protein Rrp4;
6-160 3.14e-06

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 46.42  E-value: 3.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992    6 LVAPGDKVldAIGEYRMGKGLYEANRRIFASVAGFVNVygfrdkSDNLVQVIEvrrsedqLDNELLPFHGAIVTAKVMAV 85
Cdd:PRK04163  10 IVVPGDLL--AEGEFKAGRGTYKENGKIYSTVVGLVDI------KDDKVRVIP-------LEGKYIPKVGDLVIGKVTDV 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17555992   86 GLRFAKCDIISigdkvykkRFSALLPKKKL--RPLEPElSEPFKNFVRPNDYILAKVcEDAEIKDKFVLSIAEDELG 160
Cdd:PRK04163  75 TFSGWEVDINS--------PYKAYLPVSEVlgRPVNVE-GTDLRKYLDIGDYIIAKV-KDVDRTRDVVLTLKGKGLG 141
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 70-162 2.03e-05

S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 239901 [Multi-domain]  Cd Length: 82  Bit Score: 41.38  E-value: 2.03e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555992  70 LLPFHGAIVTAKVMAVGLRFAKCDIISIGDKVYKKRFSALLPKKKLRPlepelsepfknFVRPNDYILAKVcEDAEIKDK 149
Cdd:cd04454   2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRK-----------SLQPGDLILAKV-ISLGDDMN 69

                        90
                ....*....|...
gi 17555992 150 FVLSIAEDELGVV 162
Cdd:cd04454  70 VLLTTADNELGVI 82
 
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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