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Conserved domains on  [gi|1958802183|ref|XP_038939431|]
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transcriptional-regulating factor 1 isoform X3 [Rattus norvegicus]

Protein Classification

zf-C2H2_6 and ELM2 domain-containing protein( domain architecture ID 12366437)

protein containing domains PRK10263, zf-C2H2_6, ELM2, and SANT

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ELM2 pfam01448
ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown ...
 793-847 4.13e-12

ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in Swiss:O82364. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.


:

Pssm-ID: 460214  Cd Length: 53  Bit Score: 61.86  E-value: 4.13e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802183  793 INIGLRFQAEIPELQDVSAMAQDTHKA--TLVWKPWPELEnqalQQQVENLLNLCCS 847
Cdd:pfam01448    1 IRVGPRYQAEIPELLPPSEEEDRYEEEdeLLVWDPNHNLP----DRKLDEYLVVARS 53
SANT super family cl21498
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 901-945 9.01e-11

'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.


The actual alignment was detected with superfamily member cd11661:

Pssm-ID: 473887 [Multi-domain]  Cd Length: 46  Bit Score: 58.01  E-value: 9.01e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1958802183  901 KWTSLERKLFNKALATYSKDFIFVQK-MVKSKTVAQCVEYYYTWKK 945
Cdd:cd11661      1 EWSESEAKLFEEGLRKYGKDFHDIRQdFLPWKSVGELVEFYYMWKK 46
zf-C2H2_6 pfam13912
C2H2-type zinc finger;
520-540 8.31e-05

C2H2-type zinc finger;


:

Pssm-ID: 433576  Cd Length: 27  Bit Score: 40.69  E-value: 8.31e-05
                           10        20
                   ....*....|....*....|.
gi 1958802183  520 CSICLKEFKSLPALNGHMRSH 540
Cdd:pfam13912    4 CSECGKSFPSYQALGGHKKSH 24
PRK10263 super family cl35903
DNA translocase FtsK; Provisional
 219-390 3.42e-04

DNA translocase FtsK; Provisional


The actual alignment was detected with superfamily member PRK10263:

Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 45.08  E-value: 3.42e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802183  219 PALPVGQHAPQGHLYYDYQQPLAQMS----VQGGQPLQAPQVLSSHMQPLQQHQYYPQPPPQQQQAGLQRLSVQEMQQQQ 294
Cdd:PRK10263   336 PVEPVTQTPPVASVDVPPAQPTVAWQpvpgPQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQP 415

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802183  295 QQQIRPSPPQQQQQQQQQQQQQQLQLQQRQSSLQIPQ--YYQPQPMMQHLQEQQQPSMhlQPPSYHRDP---HQYTPEQA 369
Cdd:PRK10263   416 AQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQqsTFAPQSTYQTEQTYQQPAA--QEPLYQQPQpveQQPVVEPE 493

                          170       180
                   ....*....|....*....|.
gi 1958802183  370 HAVQLIQLGSMPQYYYQEPQQ 390
Cdd:PRK10263   494 PVVEETKPARPPLYYFEEVEE 514
zf-C2H2_6 pfam13912
C2H2-type zinc finger;
1108-1131 6.13e-03

C2H2-type zinc finger;


:

Pssm-ID: 433576  Cd Length: 27  Bit Score: 35.30  E-value: 6.13e-03
                           10        20
                   ....*....|....*....|....
gi 1958802183 1108 IFPCKECGKVFFKIKSRNAHMKTH 1131
Cdd:pfam13912    1 VHECSECGKSFPSYQALGGHKKSH 24
 
Name Accession Description Interval E-value
ELM2 pfam01448
ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown ...
 793-847 4.13e-12

ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in Swiss:O82364. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.


Pssm-ID: 460214  Cd Length: 53  Bit Score: 61.86  E-value: 4.13e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802183  793 INIGLRFQAEIPELQDVSAMAQDTHKA--TLVWKPWPELEnqalQQQVENLLNLCCS 847
Cdd:pfam01448    1 IRVGPRYQAEIPELLPPSEEEDRYEEEdeLLVWDPNHNLP----DRKLDEYLVVARS 53
SANT_MTA3_like cd11661
Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family ...
 901-945 9.01e-11

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: 58.01  E-value: 9.01e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1958802183  901 KWTSLERKLFNKALATYSKDFIFVQK-MVKSKTVAQCVEYYYTWKK 945
Cdd:cd11661      1 EWSESEAKLFEEGLRKYGKDFHDIRQdFLPWKSVGELVEFYYMWKK 46
zf-C2H2_6 pfam13912
C2H2-type zinc finger;
520-540 8.31e-05

C2H2-type zinc finger;


Pssm-ID: 433576  Cd Length: 27  Bit Score: 40.69  E-value: 8.31e-05
                           10        20
                   ....*....|....*....|.
gi 1958802183  520 CSICLKEFKSLPALNGHMRSH 540
Cdd:pfam13912    4 CSECGKSFPSYQALGGHKKSH 24
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 901-944 1.83e-04

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: 40.18  E-value: 1.83e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1958802183  901 KWTSLERKLFNKALATYSKDFIFVQKMVKSKTVAQCVEYYYTWK 944
Cdd:pfam00249    3 PWTPEEDELLLEAVEKLGNRWKKIAKLLPGRTDNQCKNRWQNYL 46
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 219-390 3.42e-04

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 45.08  E-value: 3.42e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802183  219 PALPVGQHAPQGHLYYDYQQPLAQMS----VQGGQPLQAPQVLSSHMQPLQQHQYYPQPPPQQQQAGLQRLSVQEMQQQQ 294
Cdd:PRK10263   336 PVEPVTQTPPVASVDVPPAQPTVAWQpvpgPQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQP 415

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802183  295 QQQIRPSPPQQQQQQQQQQQQQQLQLQQRQSSLQIPQ--YYQPQPMMQHLQEQQQPSMhlQPPSYHRDP---HQYTPEQA 369
Cdd:PRK10263   416 AQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQqsTFAPQSTYQTEQTYQQPAA--QEPLYQQPQpveQQPVVEPE 493

                          170       180
                   ....*....|....*....|.
gi 1958802183  370 HAVQLIQLGSMPQYYYQEPQQ 390
Cdd:PRK10263   494 PVVEETKPARPPLYYFEEVEE 514
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
900-945 5.30e-04

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 38.74  E-value: 5.30e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1958802183   900 DKWTSLERKLFNKALATY-SKDFIFVQKMVKSKTVAQCVEYYYTWKK 945
Cdd:smart00717    2 GEWTEEEDELLIELVKKYgKNNWEKIAKELPGRTAEQCRERWRNLLK 48
zf-C2H2_6 pfam13912
C2H2-type zinc finger;
1108-1131 6.13e-03

C2H2-type zinc finger;


Pssm-ID: 433576  Cd Length: 27  Bit Score: 35.30  E-value: 6.13e-03
                           10        20
                   ....*....|....*....|....
gi 1958802183 1108 IFPCKECGKVFFKIKSRNAHMKTH 1131
Cdd:pfam13912    1 VHECSECGKSFPSYQALGGHKKSH 24
 
Name Accession Description Interval E-value
ELM2 pfam01448
ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown ...
 793-847 4.13e-12

ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in Swiss:O82364. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.


Pssm-ID: 460214  Cd Length: 53  Bit Score: 61.86  E-value: 4.13e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802183  793 INIGLRFQAEIPELQDVSAMAQDTHKA--TLVWKPWPELEnqalQQQVENLLNLCCS 847
Cdd:pfam01448    1 IRVGPRYQAEIPELLPPSEEEDRYEEEdeLLVWDPNHNLP----DRKLDEYLVVARS 53
SANT_MTA3_like cd11661
Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family ...
 901-945 9.01e-11

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: 58.01  E-value: 9.01e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1958802183  901 KWTSLERKLFNKALATYSKDFIFVQK-MVKSKTVAQCVEYYYTWKK 945
Cdd:cd11661      1 EWSESEAKLFEEGLRKYGKDFHDIRQdFLPWKSVGELVEFYYMWKK 46
zf-C2H2_6 pfam13912
C2H2-type zinc finger;
520-540 8.31e-05

C2H2-type zinc finger;


Pssm-ID: 433576  Cd Length: 27  Bit Score: 40.69  E-value: 8.31e-05
                           10        20
                   ....*....|....*....|.
gi 1958802183  520 CSICLKEFKSLPALNGHMRSH 540
Cdd:pfam13912    4 CSECGKSFPSYQALGGHKKSH 24
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 901-944 1.83e-04

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: 40.18  E-value: 1.83e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1958802183  901 KWTSLERKLFNKALATYSKDFIFVQKMVKSKTVAQCVEYYYTWK 944
Cdd:pfam00249    3 PWTPEEDELLLEAVEKLGNRWKKIAKLLPGRTDNQCKNRWQNYL 46
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 219-390 3.42e-04

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 45.08  E-value: 3.42e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802183  219 PALPVGQHAPQGHLYYDYQQPLAQMS----VQGGQPLQAPQVLSSHMQPLQQHQYYPQPPPQQQQAGLQRLSVQEMQQQQ 294
Cdd:PRK10263   336 PVEPVTQTPPVASVDVPPAQPTVAWQpvpgPQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQP 415

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802183  295 QQQIRPSPPQQQQQQQQQQQQQQLQLQQRQSSLQIPQ--YYQPQPMMQHLQEQQQPSMhlQPPSYHRDP---HQYTPEQA 369
Cdd:PRK10263   416 AQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQqsTFAPQSTYQTEQTYQQPAA--QEPLYQQPQpveQQPVVEPE 493

                          170       180
                   ....*....|....*....|.
gi 1958802183  370 HAVQLIQLGSMPQYYYQEPQQ 390
Cdd:PRK10263   494 PVVEETKPARPPLYYFEEVEE 514
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
900-945 5.30e-04

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


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 38.74  E-value: 5.30e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1958802183   900 DKWTSLERKLFNKALATY-SKDFIFVQKMVKSKTVAQCVEYYYTWKK 945
Cdd:smart00717    2 GEWTEEEDELLIELVKKYgKNNWEKIAKELPGRTAEQCRERWRNLLK 48
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 901-944 7.22e-04

'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: 38.33  E-value: 7.22e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1958802183  901 KWTSLERKLFNKALATY-SKDFIFVQKMVKSKTVAQCVEYYYTWK 944
Cdd:cd00167      1 PWTEEEDELLLEAVKKYgKNNWEKIAKELPGRTPKQCRERWRNLL 45
zf-C2H2_6 pfam13912
C2H2-type zinc finger;
1108-1131 6.13e-03

C2H2-type zinc finger;


Pssm-ID: 433576  Cd Length: 27  Bit Score: 35.30  E-value: 6.13e-03
                           10        20
                   ....*....|....*....|....
gi 1958802183 1108 IFPCKECGKVFFKIKSRNAHMKTH 1131
Cdd:pfam13912    1 VHECSECGKSFPSYQALGGHKKSH 24
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 1109-1131 7.03e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 34.97  E-value: 7.03e-03
                           10        20
                   ....*....|....*....|...
gi 1958802183 1109 FPCKECGKVFFKIKSRNAHMKTH 1131
Cdd:pfam00096    1 YKCPDCGKSFSRKSNLKRHLRTH 23
 
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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