LAG1, DNA binding; Members of this family are found in various eukaryotic hypothetical ...
780-946
8.29e-63
LAG1, DNA binding; Members of this family are found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding. This domain is also known as RHR-N (Rel-homology region) as it related to Rel domain proteins.
:
Pssm-ID: 462735 Cd Length: 148 Bit Score: 210.63 E-value: 8.29e-63
Beta-trefoil DNA-binding domain; Members of this family of DNA binding domains adopt a ...
1005-1121
4.42e-07
Beta-trefoil DNA-binding domain; Members of this family of DNA binding domains adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and co-repressors (SMRT/N-Cor and CIR).
The actual alignment was detected with superfamily member pfam09270:
Pssm-ID: 462734 Cd Length: 123 Bit Score: 50.02 E-value: 4.42e-07
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
162-541
1.39e-05
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.
The actual alignment was detected with superfamily member pfam09606:
Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 49.62 E-value: 1.39e-05
LAG1, DNA binding; Members of this family are found in various eukaryotic hypothetical ...
780-946
8.29e-63
LAG1, DNA binding; Members of this family are found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding. This domain is also known as RHR-N (Rel-homology region) as it related to Rel domain proteins.
Pssm-ID: 462735 Cd Length: 148 Bit Score: 210.63 E-value: 8.29e-63
IPT domain of the recombination signal Jkappa binding protein (RBP-Jkappa). RBP-J kappa, was ...
1386-1485
6.58e-11
IPT domain of the recombination signal Jkappa binding protein (RBP-Jkappa). RBP-J kappa, was initially considered to be involved in V(D)J recombination because of its DNA binding specificity and structural similarity to site-specific recombinases known as the integrase family. Further studies indicated that RBP-J kappa functions as a repressor of transcription, via destabilization of the general transcription factor IID and recruitment of histone deacetylase complexes.
Pssm-ID: 238581 Cd Length: 97 Bit Score: 60.16 E-value: 6.58e-11
Beta-trefoil DNA-binding domain; Members of this family of DNA binding domains adopt a ...
1005-1121
4.42e-07
Beta-trefoil DNA-binding domain; Members of this family of DNA binding domains adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and co-repressors (SMRT/N-Cor and CIR).
Pssm-ID: 462734 Cd Length: 123 Bit Score: 50.02 E-value: 4.42e-07
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
162-541
1.39e-05
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.
Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 49.62 E-value: 1.39e-05
LAG1, DNA binding; Members of this family are found in various eukaryotic hypothetical ...
780-946
8.29e-63
LAG1, DNA binding; Members of this family are found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding. This domain is also known as RHR-N (Rel-homology region) as it related to Rel domain proteins.
Pssm-ID: 462735 Cd Length: 148 Bit Score: 210.63 E-value: 8.29e-63
IPT domain of the recombination signal Jkappa binding protein (RBP-Jkappa). RBP-J kappa, was ...
1386-1485
6.58e-11
IPT domain of the recombination signal Jkappa binding protein (RBP-Jkappa). RBP-J kappa, was initially considered to be involved in V(D)J recombination because of its DNA binding specificity and structural similarity to site-specific recombinases known as the integrase family. Further studies indicated that RBP-J kappa functions as a repressor of transcription, via destabilization of the general transcription factor IID and recruitment of histone deacetylase complexes.
Pssm-ID: 238581 Cd Length: 97 Bit Score: 60.16 E-value: 6.58e-11
Beta-trefoil DNA-binding domain; Members of this family of DNA binding domains adopt a ...
1005-1121
4.42e-07
Beta-trefoil DNA-binding domain; Members of this family of DNA binding domains adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and co-repressors (SMRT/N-Cor and CIR).
Pssm-ID: 462734 Cd Length: 123 Bit Score: 50.02 E-value: 4.42e-07
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
162-541
1.39e-05
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.
Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 49.62 E-value: 1.39e-05
Ty transposon capsid protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a ...
445-557
2.62e-04
Ty transposon capsid protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles. This entry corresponds to the capsid protein from Ty1 and Ty2 transposons.
Pssm-ID: 425992 Cd Length: 384 Bit Score: 45.33 E-value: 2.62e-04
Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as ...
1419-1485
7.16e-04
Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers.
Pssm-ID: 238050 [Multi-domain] Cd Length: 89 Bit Score: 40.14 E-value: 7.16e-04
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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