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 SOX9
Homo sapiens
 HIF1A
Homo sapiens
 Pax6
Mus musculus
 PAX6
Homo sapiens
 Snai2
Mus musculus
 PPARA
Homo sapiens
 Ppara
Mus musculus
 Thrb
Mus musculus
 SNAI2
Homo sapiens
 Tbr1
Mus musculus
Transcription Factor Encyclopedia  BETA
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Overview
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Structures
About this section
This section contains 3D PDB models of structural predictions for this transcription factor. METHODS: The template selection protocol follows that of Morozov and Siggia, in which templates are selected to optimize similarity of DNA-binding residues (Morozov AV, Siggia ED. PNAS 104(17):7068-73). This has been shown to increase modeling accuracy at the DNA-binding interface. For all solved structures containing DNA, amino acids within 4A of DNA (DNA-binding residues) are stored. Pfam domain hits of each DNA-bound chain are detected by hmmer, and each hit is added to a list mapping domain family name to chain hits. Pfam domain hits of each unsolved structure are detected by HMMER. For each identified Pfam family, the unsolved sequence is aligned to all solved family members (putative templates). Alignments are scored based on similarity of the DNA-binding residues in the template to the aligned residues of the unsolved sequence. For each subsequence of the unsolved protein identified as a DNA-binding domain, the top scoring template is selected. For sequences known to form homodimers, a homodimeric template is selected. The model is constructed from the template using Modeller 9v2. DNA bound to the template is added to the model by superimposition of the solved and modeled structures.
Tbr1 21375 T box 1h6fA
Image 3D Model .PDB File
Family
Beta-Hairpin-Ribbon Group » Transcription Factor T-Domain
 EOMES
Homo sapiens
 Eomes
Mus musculus
T
Homo sapiens
T
Mus musculus
TBPL1
Homo sapiens
 TBR1
Homo sapiens
 Tbr1
Mus musculus
TBX1
Homo sapiens
Tbx1
Mus musculus
TBX19
Homo sapiens
Tbx19
Mus musculus
Tbx2
Mus musculus
TBX20
Homo sapiens
Tbx20
Mus musculus
 TBX21
Homo sapiens
 Tbx21
Mus musculus
Tbx3
Mus musculus
TBX5
Homo sapiens
Tbx5
Mus musculus
TBX6
Homo sapiens
Tbx6
Mus musculus
 
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