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Conserved domains on  [gi|6320606|ref|NP_010686|]
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Utp5p [Saccharomyces cerevisiae S288C]

Protein Classification

WD40 repeat and Utp12 domain-containing protein( domain architecture ID 13236691)

WD40 repeat and Utp12 domain-containing protein similar to Saccharomyces cerevisiae U3 small nucleolar RNA-associated protein 5 (UTP5) that is involved in nucleolar processing of pre-18S ribosomal RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Utp12 pfam04003
Dip2/Utp12 Family; This domain is found at the C-terminus of proteins containing WD40 repeats. ...
 448-548 4.10e-30

Dip2/Utp12 Family; This domain is found at the C-terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein the yeast protein is called Utp12 or DIP2.


:

Pssm-ID: 461125  Cd Length: 106  Bit Score: 114.18  E-value: 4.10e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606    448 NDHSLLETVLNNRDERVIRDTIFRLKPALAVILLERLAERIARQTHRQGPLNVWVKWCLIIHGGYLVSIPNLMSTLSSLH 527
Cdd:pfam04003   1 NDEYLLESVLEKIPPSDIELTLLRLPFSYVLRLLKFLAERLAERSPHLELLLRWLKFLLRTHGGYLVSNPDLRPVLRSLQ 80

                          90       100
                  ....*....|....*....|..
gi 6320606    528 STLKRRSDLLPRLLAL-DARLD 548
Cdd:pfam04003  81 KLLRRRLKELKDLLGLnLGALD 102
WD40 super family cl29593
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 3-256 6.49e-06

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


The actual alignment was detected with superfamily member cd00200:

Pssm-ID: 475233 [Multi-domain]  Cd Length: 289  Bit Score: 48.49  E-value: 6.49e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606    3 SPVLQSAYDPSGQYLcyVTVALDKQ-RVgvqptqratssgVDTVWNENFLYLEDSKLKVTCLKWvnlaSSDTVAIILGMN 81
Cdd:cd00200  10 GGVTCVAFSPDGKLL--ATGSGDGTiKV------------WDLETGELLRTLKGHTGPVRDVAA----SADGTYLASGSS 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606   82 NGEIWLYSVLANEVTYKFTtGNSYEIKDIDLMGNQLWCI----DSSDAFyqFDLLQFKLLQHFRINNCvQLNKLTIVPAG 157
Cdd:cd00200  72 DKTIRLWDLETGECVRTLT-GHTSYVSSVAFSPDGRILSsssrDKTIKV--WDVETGKCLTTLRGHTD-WVNSVAFSPDG 147

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606  158 DSVAqllVAS--HSISLIDIEEKKVVMTFPGHVSPVSTLQVI-TNEFFISGAeGDRFLNVYDIHSGMTKCVLVAESD-IK 233
Cdd:cd00200 148 TFVA---SSSqdGTIKLWDLRTGKCVATLTGHTGEVNSVAFSpDGEKLLSSS-SDGTIKLWDLSTGKCLGTLRGHENgVN 223

                       250       260
                ....*....|....*....|...
gi 6320606  234 ELSHSGQADSIAVTTEDGSLEIF 256
Cdd:cd00200 224 SVAFSPDGYLLASGSEDGTIRVW 246
 
Name Accession Description Interval E-value
Utp12 pfam04003
Dip2/Utp12 Family; This domain is found at the C-terminus of proteins containing WD40 repeats. ...
 448-548 4.10e-30

Dip2/Utp12 Family; This domain is found at the C-terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein the yeast protein is called Utp12 or DIP2.


Pssm-ID: 461125  Cd Length: 106  Bit Score: 114.18  E-value: 4.10e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606    448 NDHSLLETVLNNRDERVIRDTIFRLKPALAVILLERLAERIARQTHRQGPLNVWVKWCLIIHGGYLVSIPNLMSTLSSLH 527
Cdd:pfam04003   1 NDEYLLESVLEKIPPSDIELTLLRLPFSYVLRLLKFLAERLAERSPHLELLLRWLKFLLRTHGGYLVSNPDLRPVLRSLQ 80

                          90       100
                  ....*....|....*....|..
gi 6320606    528 STLKRRSDLLPRLLAL-DARLD 548
Cdd:pfam04003  81 KLLRRRLKELKDLLGLnLGALD 102
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 3-256 6.49e-06

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 48.49  E-value: 6.49e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606    3 SPVLQSAYDPSGQYLcyVTVALDKQ-RVgvqptqratssgVDTVWNENFLYLEDSKLKVTCLKWvnlaSSDTVAIILGMN 81
Cdd:cd00200  10 GGVTCVAFSPDGKLL--ATGSGDGTiKV------------WDLETGELLRTLKGHTGPVRDVAA----SADGTYLASGSS 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606   82 NGEIWLYSVLANEVTYKFTtGNSYEIKDIDLMGNQLWCI----DSSDAFyqFDLLQFKLLQHFRINNCvQLNKLTIVPAG 157
Cdd:cd00200  72 DKTIRLWDLETGECVRTLT-GHTSYVSSVAFSPDGRILSsssrDKTIKV--WDVETGKCLTTLRGHTD-WVNSVAFSPDG 147

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606  158 DSVAqllVAS--HSISLIDIEEKKVVMTFPGHVSPVSTLQVI-TNEFFISGAeGDRFLNVYDIHSGMTKCVLVAESD-IK 233
Cdd:cd00200 148 TFVA---SSSqdGTIKLWDLRTGKCVATLTGHTGEVNSVAFSpDGEKLLSSS-SDGTIKLWDLSTGKCLGTLRGHENgVN 223

                       250       260
                ....*....|....*....|...
gi 6320606  234 ELSHSGQADSIAVTTEDGSLEIF 256
Cdd:cd00200 224 SVAFSPDGYLLASGSEDGTIRVW 246
 
Name Accession Description Interval E-value
Utp12 pfam04003
Dip2/Utp12 Family; This domain is found at the C-terminus of proteins containing WD40 repeats. ...
 448-548 4.10e-30

Dip2/Utp12 Family; This domain is found at the C-terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein the yeast protein is called Utp12 or DIP2.


Pssm-ID: 461125  Cd Length: 106  Bit Score: 114.18  E-value: 4.10e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606    448 NDHSLLETVLNNRDERVIRDTIFRLKPALAVILLERLAERIARQTHRQGPLNVWVKWCLIIHGGYLVSIPNLMSTLSSLH 527
Cdd:pfam04003   1 NDEYLLESVLEKIPPSDIELTLLRLPFSYVLRLLKFLAERLAERSPHLELLLRWLKFLLRTHGGYLVSNPDLRPVLRSLQ 80

                          90       100
                  ....*....|....*....|..
gi 6320606    528 STLKRRSDLLPRLLAL-DARLD 548
Cdd:pfam04003  81 KLLRRRLKELKDLLGLnLGALD 102
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 3-256 6.49e-06

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 48.49  E-value: 6.49e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606    3 SPVLQSAYDPSGQYLcyVTVALDKQ-RVgvqptqratssgVDTVWNENFLYLEDSKLKVTCLKWvnlaSSDTVAIILGMN 81
Cdd:cd00200  10 GGVTCVAFSPDGKLL--ATGSGDGTiKV------------WDLETGELLRTLKGHTGPVRDVAA----SADGTYLASGSS 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606   82 NGEIWLYSVLANEVTYKFTtGNSYEIKDIDLMGNQLWCI----DSSDAFyqFDLLQFKLLQHFRINNCvQLNKLTIVPAG 157
Cdd:cd00200  72 DKTIRLWDLETGECVRTLT-GHTSYVSSVAFSPDGRILSsssrDKTIKV--WDVETGKCLTTLRGHTD-WVNSVAFSPDG 147

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606  158 DSVAqllVAS--HSISLIDIEEKKVVMTFPGHVSPVSTLQVI-TNEFFISGAeGDRFLNVYDIHSGMTKCVLVAESD-IK 233
Cdd:cd00200 148 TFVA---SSSqdGTIKLWDLRTGKCVATLTGHTGEVNSVAFSpDGEKLLSSS-SDGTIKLWDLSTGKCLGTLRGHENgVN 223

                       250       260
                ....*....|....*....|...
gi 6320606  234 ELSHSGQADSIAVTTEDGSLEIF 256
Cdd:cd00200 224 SVAFSPDGYLLASGSEDGTIRVW 246
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 129-256 1.06e-05

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 47.71  E-value: 1.06e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320606  129 FDLLQFKLLQHFRINNCvQLNKLTIVPAGdsvAQLLVASH--SISLIDIEEKKVVMTFPGHVSPVSTLQVITNEFFISGA 206
Cdd:cd00200 162 WDLRTGKCVATLTGHTG-EVNSVAFSPDG---EKLLSSSSdgTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASG 237

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 6320606  207 EGDRFLNVYDIHSGMTKCVLVA-ESDIKELSHSGQADSIAVTTEDGSLEIF 256
Cdd:cd00200 238 SEDGTIRVWDLRTGECVQTLSGhTNSVTSLAWSPDGKRLASGSADGTIRIW 288
 
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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