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Conserved domains on  [gi|293352609|ref|XP_341093|]
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sin3 histone deacetylase corepressor complex component SDS3 isoform X1 [Rattus norvegicus]

Protein Classification

suppressor of defective silencing 3( domain architecture ID 230097)

suppressor of defective silencing 3 (SUDS3, formerly SDS3) is an integral component of Sin3/HDAC complex and is required for HDAC activity.

Gene Ontology:  GO:0000122|GO:0006338|GO:0070822|GO:0042826

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sds3 super family cl21737
Sds3-like; Repression of gene transcription is mediated by histone deacetylases containing ...
 62-174 7.41e-14

Sds3-like; Repression of gene transcription is mediated by histone deacetylases containing repressor-co-repressor complexes, which are recruited to promoters of target genes via interactions with sequence-specific transcription factors. The co-repressor complex contains a core of at least seven proteins. This family represents the conserved region found in Sds3, Dep1 and BRMS1-homolog p40 proteins.


The actual alignment was detected with superfamily member pfam08598:

Pssm-ID: 430099  Cd Length: 218  Bit Score: 69.69  E-value: 7.41e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293352609   62 EEDYVEMKEQMYQDKLASLKRQLQQLQEGTLQEYQKRMKKLDQQYRERIRNAELFLQLETEQVERNYIKEKKAAVKEFED 141
Cdd:pfam08598   9 EASFAELRDKLYRNKLTALQTELQLLHQGSHPELLQYYRDLEEERDAELKRLRLREEYQLKRIDIETKADRTAAHQEFKK 88

                          90       100       110
                  ....*....|....*....|....*....|...
gi 293352609  142 KKVELKENLIAELEEKKKMIENEKLTMELTGDS 174
Cdd:pfam08598  89 LVKLLKEKLYDETTQKIYRLNEERRLLDLANTN 121
 
Name Accession Description Interval E-value
Sds3 pfam08598
Sds3-like; Repression of gene transcription is mediated by histone deacetylases containing ...
 62-174 7.41e-14

Sds3-like; Repression of gene transcription is mediated by histone deacetylases containing repressor-co-repressor complexes, which are recruited to promoters of target genes via interactions with sequence-specific transcription factors. The co-repressor complex contains a core of at least seven proteins. This family represents the conserved region found in Sds3, Dep1 and BRMS1-homolog p40 proteins.


Pssm-ID: 430099  Cd Length: 218  Bit Score: 69.69  E-value: 7.41e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293352609   62 EEDYVEMKEQMYQDKLASLKRQLQQLQEGTLQEYQKRMKKLDQQYRERIRNAELFLQLETEQVERNYIKEKKAAVKEFED 141
Cdd:pfam08598   9 EASFAELRDKLYRNKLTALQTELQLLHQGSHPELLQYYRDLEEERDAELKRLRLREEYQLKRIDIETKADRTAAHQEFKK 88

                          90       100       110
                  ....*....|....*....|....*....|...
gi 293352609  142 KKVELKENLIAELEEKKKMIENEKLTMELTGDS 174
Cdd:pfam08598  89 LVKLLKEKLYDETTQKIYRLNEERRLLDLANTN 121
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 27-169 1.04e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.81  E-value: 1.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293352609    27 DEELESVEDDERSCRGRESDEDTE-DASETDLAKHDEEDY-VEMKEQMYQDKLASLKRQLQQLqEGTLQEYQKRMKKLDQ 104
Cdd:TIGR02168  238 REELEELQEELKEAEEELEELTAElQELEEKLEELRLEVSeLEEEIEELQKELYALANEISRL-EQQKQILRERLANLER 316

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 293352609   105 QYrerirnAELFLQLETEQVERNYIKEKKAAVKEFEDKKVELKENLIAELEEKKKMIENEKLTME 169
Cdd:TIGR02168  317 QL------EELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLE 375
 
Name Accession Description Interval E-value
Sds3 pfam08598
Sds3-like; Repression of gene transcription is mediated by histone deacetylases containing ...
 62-174 7.41e-14

Sds3-like; Repression of gene transcription is mediated by histone deacetylases containing repressor-co-repressor complexes, which are recruited to promoters of target genes via interactions with sequence-specific transcription factors. The co-repressor complex contains a core of at least seven proteins. This family represents the conserved region found in Sds3, Dep1 and BRMS1-homolog p40 proteins.


Pssm-ID: 430099  Cd Length: 218  Bit Score: 69.69  E-value: 7.41e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293352609   62 EEDYVEMKEQMYQDKLASLKRQLQQLQEGTLQEYQKRMKKLDQQYRERIRNAELFLQLETEQVERNYIKEKKAAVKEFED 141
Cdd:pfam08598   9 EASFAELRDKLYRNKLTALQTELQLLHQGSHPELLQYYRDLEEERDAELKRLRLREEYQLKRIDIETKADRTAAHQEFKK 88

                          90       100       110
                  ....*....|....*....|....*....|...
gi 293352609  142 KKVELKENLIAELEEKKKMIENEKLTMELTGDS 174
Cdd:pfam08598  89 LVKLLKEKLYDETTQKIYRLNEERRLLDLANTN 121
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 27-169 1.04e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.81  E-value: 1.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293352609    27 DEELESVEDDERSCRGRESDEDTE-DASETDLAKHDEEDY-VEMKEQMYQDKLASLKRQLQQLqEGTLQEYQKRMKKLDQ 104
Cdd:TIGR02168  238 REELEELQEELKEAEEELEELTAElQELEEKLEELRLEVSeLEEEIEELQKELYALANEISRL-EQQKQILRERLANLER 316

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 293352609   105 QYrerirnAELFLQLETEQVERNYIKEKKAAVKEFEDKKVELKENLIAELEEKKKMIENEKLTME 169
Cdd:TIGR02168  317 QL------EELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLE 375
 
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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