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Conserved domains on  [gi|157823243|ref|NP_001099871|]
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cotranscriptional regulator ARB2A [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Arb2 super family cl10738
Arb2 domain; This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) also ...
 103-271 4.56e-03

Arb2 domain; This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) also known as histone deacetylase clr3 (EC:3.5.1.98). Structure analysis reveals that the Arb2 domain has clear homology to alpha/beta-hydrolases but that it is lacking the catalytic triad of these enzymes. Functional studies show that the Arb2 domain is necessary for centromeric heterochromatin silencing suggesting a model where the Arb2 domain, through residues N562 and Y563, acts as an anchor that connects the HDAC activity of Clr3 to the SHREC complex. SHREC (Snf2/Hdac Repressive) complex in fission yeast drives transcriptional gene silencing in heterochromatin.


The actual alignment was detected with superfamily member pfam09757:

Pssm-ID: 401634  Cd Length: 252  Bit Score: 38.32  E-value: 4.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823243  103 KLMVLIHGSGVVragqWARRLIINEDLDSGTQI------PFIKRAVDEGYGVIVLNPNENYievekqkmhkqsssdgTDE 176
Cdd:pfam09757  48 TLLVIVHDPPEL----WAQPDPITNKLDPHNSWlvdsvlDYIDWAVKQGYGVIDVNIPQHI----------------TET 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823243  177 PAGKRERKDKVSKETKkrrdfyekyrnpqkekemmqlfirengspEEHAVYVWDHFIAQA-AAENVFF--VAHSYGGlaF 253
Cdd:pfam09757 108 PESLEEDDEYNRISES-----------------------------QELLLYLWDNYIELFdSATKIFFigVGDAYSG--I 156

                         170
                  ....*....|....*...
gi 157823243  254 VELMIQReaDVKSKVTAV 271
Cdd:pfam09757 157 VHLLGHR--DCRSRVKGV 172
 
Name Accession Description Interval E-value
Arb2 pfam09757
Arb2 domain; This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) also ...
 103-271 4.56e-03

Arb2 domain; This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) also known as histone deacetylase clr3 (EC:3.5.1.98). Structure analysis reveals that the Arb2 domain has clear homology to alpha/beta-hydrolases but that it is lacking the catalytic triad of these enzymes. Functional studies show that the Arb2 domain is necessary for centromeric heterochromatin silencing suggesting a model where the Arb2 domain, through residues N562 and Y563, acts as an anchor that connects the HDAC activity of Clr3 to the SHREC complex. SHREC (Snf2/Hdac Repressive) complex in fission yeast drives transcriptional gene silencing in heterochromatin.


Pssm-ID: 401634  Cd Length: 252  Bit Score: 38.32  E-value: 4.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823243  103 KLMVLIHGSGVVragqWARRLIINEDLDSGTQI------PFIKRAVDEGYGVIVLNPNENYievekqkmhkqsssdgTDE 176
Cdd:pfam09757  48 TLLVIVHDPPEL----WAQPDPITNKLDPHNSWlvdsvlDYIDWAVKQGYGVIDVNIPQHI----------------TET 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823243  177 PAGKRERKDKVSKETKkrrdfyekyrnpqkekemmqlfirengspEEHAVYVWDHFIAQA-AAENVFF--VAHSYGGlaF 253
Cdd:pfam09757 108 PESLEEDDEYNRISES-----------------------------QELLLYLWDNYIELFdSATKIFFigVGDAYSG--I 156

                         170
                  ....*....|....*...
gi 157823243  254 VELMIQReaDVKSKVTAV 271
Cdd:pfam09757 157 VHLLGHR--DCRSRVKGV 172
 
Name Accession Description Interval E-value
Arb2 pfam09757
Arb2 domain; This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) also ...
 103-271 4.56e-03

Arb2 domain; This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) also known as histone deacetylase clr3 (EC:3.5.1.98). Structure analysis reveals that the Arb2 domain has clear homology to alpha/beta-hydrolases but that it is lacking the catalytic triad of these enzymes. Functional studies show that the Arb2 domain is necessary for centromeric heterochromatin silencing suggesting a model where the Arb2 domain, through residues N562 and Y563, acts as an anchor that connects the HDAC activity of Clr3 to the SHREC complex. SHREC (Snf2/Hdac Repressive) complex in fission yeast drives transcriptional gene silencing in heterochromatin.


Pssm-ID: 401634  Cd Length: 252  Bit Score: 38.32  E-value: 4.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823243  103 KLMVLIHGSGVVragqWARRLIINEDLDSGTQI------PFIKRAVDEGYGVIVLNPNENYievekqkmhkqsssdgTDE 176
Cdd:pfam09757  48 TLLVIVHDPPEL----WAQPDPITNKLDPHNSWlvdsvlDYIDWAVKQGYGVIDVNIPQHI----------------TET 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823243  177 PAGKRERKDKVSKETKkrrdfyekyrnpqkekemmqlfirengspEEHAVYVWDHFIAQA-AAENVFF--VAHSYGGlaF 253
Cdd:pfam09757 108 PESLEEDDEYNRISES-----------------------------QELLLYLWDNYIELFdSATKIFFigVGDAYSG--I 156

                         170
                  ....*....|....*...
gi 157823243  254 VELMIQReaDVKSKVTAV 271
Cdd:pfam09757 157 VHLLGHR--DCRSRVKGV 172
 
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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