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Conserved domains on  [gi|332003504|gb|AED90887|]
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sequence-specific DNA binding transcription factor [Arabidopsis thaliana]

Protein Classification

myb/SANT-like DNA-binding domain-containing protein( domain architecture ID 10619758)

nyb/SANT (SWI3, ADA2, N-CoR and TFIIIB)-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
PubMed:  8882580
SCOP:  4000317

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Myb_DNA-bind_4 pfam13837
Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb ...
21-104 1.74e-07

Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT-like DNA binding domains. In particular pfam10545 seems most related. This family is greatly expanded in plants and appears in several proteins annotated as transposon proteins.


:

Pssm-ID: 463994  Cd Length: 84  Bit Score: 47.65  E-value: 1.74e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332003504   21 EDWWSEEATATLVEAWGNRYVKLNHGNLRQN--DWKDVADAVNSRhgdnSRKKTDLQCKNRVDTLKKK--YKTEKAKLSP 96
Cdd:pfam13837   1 RNKWTEEETLALIEIWGERLELRFQESKKRNkkLWEEIAEKMAEL----GYNRSPEQCKEKWENLKKKyrKEKEGNNGSG 76

                  ....*...
gi 332003504   97 STWRFYNR 104
Cdd:pfam13837  77 SSWPFFEE 84
SPFH_like super family cl19107
core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; This model ...
190-234 7.79e-03

core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; This model summarizes proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons, and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins. Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease, and in cancer invasion and metastasis. Mutations in the podocin gene give rise to autosomal recessive steroid resistant nephritic syndrome.


The actual alignment was detected with superfamily member cd03406:

Pssm-ID: 473137 [Multi-domain]  Cd Length: 293  Bit Score: 36.89  E-value: 7.79e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 332003504 190 YERIEGKKQQMMIELEKQRMeVTKEVELKRMNMLMEMQLEIEKSK 234
Cdd:cd03406  168 YEAMEAEKTKLLIAEQHQKV-VEKEAETERKRAVIEAEKDAEVAK 211
 
Name Accession Description Interval E-value
Myb_DNA-bind_4 pfam13837
Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb ...
21-104 1.74e-07

Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT-like DNA binding domains. In particular pfam10545 seems most related. This family is greatly expanded in plants and appears in several proteins annotated as transposon proteins.


Pssm-ID: 463994  Cd Length: 84  Bit Score: 47.65  E-value: 1.74e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332003504   21 EDWWSEEATATLVEAWGNRYVKLNHGNLRQN--DWKDVADAVNSRhgdnSRKKTDLQCKNRVDTLKKK--YKTEKAKLSP 96
Cdd:pfam13837   1 RNKWTEEETLALIEIWGERLELRFQESKKRNkkLWEEIAEKMAEL----GYNRSPEQCKEKWENLKKKyrKEKEGNNGSG 76

                  ....*...
gi 332003504   97 STWRFYNR 104
Cdd:pfam13837  77 SSWPFFEE 84
SPFH_like_u3 cd03406
Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; This ...
190-234 7.79e-03

Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; This model summarizes an uncharacterized family of proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins. Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podocin gene give rise to autosomal recessive steroid resistant nephritic syndrome.


Pssm-ID: 259804 [Multi-domain]  Cd Length: 293  Bit Score: 36.89  E-value: 7.79e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 332003504 190 YERIEGKKQQMMIELEKQRMeVTKEVELKRMNMLMEMQLEIEKSK 234
Cdd:cd03406  168 YEAMEAEKTKLLIAEQHQKV-VEKEAETERKRAVIEAEKDAEVAK 211
 
Name Accession Description Interval E-value
Myb_DNA-bind_4 pfam13837
Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb ...
21-104 1.74e-07

Myb/SANT-like DNA-binding domain; This presumed domain appears to be related to other Myb/SANT-like DNA binding domains. In particular pfam10545 seems most related. This family is greatly expanded in plants and appears in several proteins annotated as transposon proteins.


Pssm-ID: 463994  Cd Length: 84  Bit Score: 47.65  E-value: 1.74e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332003504   21 EDWWSEEATATLVEAWGNRYVKLNHGNLRQN--DWKDVADAVNSRhgdnSRKKTDLQCKNRVDTLKKK--YKTEKAKLSP 96
Cdd:pfam13837   1 RNKWTEEETLALIEIWGERLELRFQESKKRNkkLWEEIAEKMAEL----GYNRSPEQCKEKWENLKKKyrKEKEGNNGSG 76

                  ....*...
gi 332003504   97 STWRFYNR 104
Cdd:pfam13837  77 SSWPFFEE 84
SPFH_like_u3 cd03406
Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; This ...
190-234 7.79e-03

Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; This model summarizes an uncharacterized family of proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins. Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podocin gene give rise to autosomal recessive steroid resistant nephritic syndrome.


Pssm-ID: 259804 [Multi-domain]  Cd Length: 293  Bit Score: 36.89  E-value: 7.79e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 332003504 190 YERIEGKKQQMMIELEKQRMeVTKEVELKRMNMLMEMQLEIEKSK 234
Cdd:cd03406  168 YEAMEAEKTKLLIAEQHQKV-VEKEAETERKRAVIEAEKDAEVAK 211
 
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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