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Conserved domains on  [gi|823253427|ref|XP_012459337|]
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transcription factor SRM1 [Gossypium raimondii]

Protein Classification

SANT/Myb-like DNA-binding domain-containing protein( domain architecture ID 10827525)

SANT (SWI3, ADA2, N-CoR and TFIIIB)/Myb-like DNA-binding domain-containing protein may bind DNA and function as a transcription factor

CATH:  1.20.58.1880
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  8882580|15040448|16877755
SCOP:  4000317

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
myb_SHAQKYF TIGR01557
myb-like DNA-binding domain, SHAQKYF class; This model describes a DNA-binding domain ...
 115-167 2.94e-16

myb-like DNA-binding domain, SHAQKYF class; This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.


:

Pssm-ID: 130620 [Multi-domain]  Cd Length: 57  Bit Score: 71.28  E-value: 2.94e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 823253427  115 RKGIAWTEDEHRLFLLGLDKYGKGDW---RSISRNFVVTR-TPTQVASHAQKYFIRL 167
Cdd:TIGR01557   1 KPRVVWTEDLHDRFLQAVQKLGGPDWatpKRILELMVVDGlTRDQVASHLQKYRLKQ 57
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 11-57 2.10e-09

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


:

Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 52.19  E-value: 2.10e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 823253427  11 KWSREQDKAFENALASYPEDfsdRWEKIAANVPGKTLEEIKEHYELL 57
Cdd:cd00167    1 PWTEEEDELLLEAVKKYGKN---NWEKIAKELPGRTPKQCRERWRNL 44
 
Name Accession Description Interval E-value
myb_SHAQKYF TIGR01557
myb-like DNA-binding domain, SHAQKYF class; This model describes a DNA-binding domain ...
 115-167 2.94e-16

myb-like DNA-binding domain, SHAQKYF class; This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.


Pssm-ID: 130620 [Multi-domain]  Cd Length: 57  Bit Score: 71.28  E-value: 2.94e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 823253427  115 RKGIAWTEDEHRLFLLGLDKYGKGDW---RSISRNFVVTR-TPTQVASHAQKYFIRL 167
Cdd:TIGR01557   1 KPRVVWTEDLHDRFLQAVQKLGGPDWatpKRILELMVVDGlTRDQVASHLQKYRLKQ 57
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
119-166 1.75e-09

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 52.61  E-value: 1.75e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 823253427   119 AWTEDEHRLFLLGLDKYGKGDWRSISRNFvVTRTPTQVASHAQKYFIR 166
Cdd:smart00717   3 EWTEEEDELLIELVKKYGKNNWEKIAKEL-PGRTAEQCRERWRNLLKP 49
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 119-164 1.83e-09

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 52.19  E-value: 1.83e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 823253427 119 AWTEDEHRLFLLGLDKYGKGDWRSISRNfVVTRTPTQVASHAQKYF 164
Cdd:cd00167    1 PWTEEEDELLLEAVKKYGKNNWEKIAKE-LPGRTPKQCRERWRNLL 45
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 11-57 2.10e-09

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 52.19  E-value: 2.10e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 823253427  11 KWSREQDKAFENALASYPEDfsdRWEKIAANVPGKTLEEIKEHYELL 57
Cdd:cd00167    1 PWTEEEDELLLEAVKKYGKN---NWEKIAKELPGRTPKQCRERWRNL 44
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
11-54 1.02e-08

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 50.30  E-value: 1.02e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 823253427    11 KWSREQDKAFENALASYPEDfsdRWEKIAANVPGKTLEEIKEHY 54
Cdd:smart00717   3 EWTEEEDELLIELVKKYGKN---NWEKIAKELPGRTAEQCRERW 43
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 119-164 1.54e-08

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 49.81  E-value: 1.54e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 823253427  119 AWTEDEHRLFLLGLDKYGkGDWRSISRnFVVTRTPTQVASHAQKYF 164
Cdd:pfam00249   3 PWTPEEDELLLEAVEKLG-NRWKKIAK-LLPGRTDNQCKNRWQNYL 46
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 11-54 1.11e-07

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 47.50  E-value: 1.11e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 823253427   11 KWSREQDKAFENALASYPedfsDRWEKIAANVPGKTLEEIKEHY 54
Cdd:pfam00249   3 PWTPEEDELLLEAVEKLG----NRWKKIAKLLPGRTDNQCKNRW 42
COG5114 COG5114
Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics];
120-165 3.17e-03

Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics];


Pssm-ID: 227445 [Multi-domain]  Cd Length: 432  Bit Score: 38.90  E-value: 3.17e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 823253427 120 WTEDEHRLFLLGLDKYGKGDWRSISRnFVVTRTPTQVASHAQKYFI 165
Cdd:COG5114   66 WGADEELLLIECLDTLGLGNWEDIAD-YIGSRAKEEIKSHYLKMYD 110
 
Name Accession Description Interval E-value
myb_SHAQKYF TIGR01557
myb-like DNA-binding domain, SHAQKYF class; This model describes a DNA-binding domain ...
 115-167 2.94e-16

myb-like DNA-binding domain, SHAQKYF class; This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.


Pssm-ID: 130620 [Multi-domain]  Cd Length: 57  Bit Score: 71.28  E-value: 2.94e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 823253427  115 RKGIAWTEDEHRLFLLGLDKYGKGDW---RSISRNFVVTR-TPTQVASHAQKYFIRL 167
Cdd:TIGR01557   1 KPRVVWTEDLHDRFLQAVQKLGGPDWatpKRILELMVVDGlTRDQVASHLQKYRLKQ 57
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
119-166 1.75e-09

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 52.61  E-value: 1.75e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 823253427   119 AWTEDEHRLFLLGLDKYGKGDWRSISRNFvVTRTPTQVASHAQKYFIR 166
Cdd:smart00717   3 EWTEEEDELLIELVKKYGKNNWEKIAKEL-PGRTAEQCRERWRNLLKP 49
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 119-164 1.83e-09

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 52.19  E-value: 1.83e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 823253427 119 AWTEDEHRLFLLGLDKYGKGDWRSISRNfVVTRTPTQVASHAQKYF 164
Cdd:cd00167    1 PWTEEEDELLLEAVKKYGKNNWEKIAKE-LPGRTPKQCRERWRNLL 45
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 11-57 2.10e-09

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 52.19  E-value: 2.10e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 823253427  11 KWSREQDKAFENALASYPEDfsdRWEKIAANVPGKTLEEIKEHYELL 57
Cdd:cd00167    1 PWTEEEDELLLEAVKKYGKN---NWEKIAKELPGRTPKQCRERWRNL 44
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
11-54 1.02e-08

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 50.30  E-value: 1.02e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 823253427    11 KWSREQDKAFENALASYPEDfsdRWEKIAANVPGKTLEEIKEHY 54
Cdd:smart00717   3 EWTEEEDELLIELVKKYGKN---NWEKIAKELPGRTAEQCRERW 43
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 119-164 1.54e-08

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 49.81  E-value: 1.54e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 823253427  119 AWTEDEHRLFLLGLDKYGkGDWRSISRnFVVTRTPTQVASHAQKYF 164
Cdd:pfam00249   3 PWTPEEDELLLEAVEKLG-NRWKKIAK-LLPGRTDNQCKNRWQNYL 46
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 11-54 1.11e-07

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 47.50  E-value: 1.11e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 823253427   11 KWSREQDKAFENALASYPedfsDRWEKIAANVPGKTLEEIKEHY 54
Cdd:pfam00249   3 PWTPEEDELLLEAVEKLG----NRWKKIAKLLPGRTDNQCKNRW 42
SANT_MTA3_like cd11661
Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family ...
 120-156 2.02e-04

Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle. MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis.


Pssm-ID: 212559 [Multi-domain]  Cd Length: 46  Bit Score: 38.36  E-value: 2.02e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 823253427 120 WTEDEHRLFLLGLDKYGKgDWRSISRNFVVTRTPTQV 156
Cdd:cd11661    2 WSESEAKLFEEGLRKYGK-DFHDIRQDFLPWKSVGEL 37
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 120-155 2.78e-04

Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1.


Pssm-ID: 212558 [Multi-domain]  Cd Length: 50  Bit Score: 37.93  E-value: 2.78e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 823253427 120 WTEDEHRLFLLGLDKYGKGDWRSISR--NFVVTRTPTQ 155
Cdd:cd11660    3 WTDEEDEALVEGVEKYGVGNWAKILKdyFFVNNRTSVD 40
COG5114 COG5114
Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics];
120-165 3.17e-03

Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics];


Pssm-ID: 227445 [Multi-domain]  Cd Length: 432  Bit Score: 38.90  E-value: 3.17e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 823253427 120 WTEDEHRLFLLGLDKYGKGDWRSISRnFVVTRTPTQVASHAQKYFI 165
Cdd:COG5114   66 WGADEELLLIECLDTLGLGNWEDIAD-YIGSRAKEEIKSHYLKMYD 110
SANT_MTA3_like cd11661
Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family ...
 11-54 3.19e-03

Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle. MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis.


Pssm-ID: 212559 [Multi-domain]  Cd Length: 46  Bit Score: 34.90  E-value: 3.19e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 823253427  11 KWSREQDKAFENALASYPEDFSD-RWEKiaanVPGKTLEEIKEHY 54
Cdd:cd11661    1 EWSESEAKLFEEGLRKYGKDFHDiRQDF----LPWKSVGELVEFY 41
 
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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