DNA Binding Motif

Accessions: 4ylo_F (3D-footprint 20231221)
Names: RNA polymerase sigma factor RpoD
Organisms: Escherichia coli, strain K12
Libraries: 3D-footprint 20231221 1
1 Contreras-Moreira B. 3D-footprint: a database for the structural analysis of protein-DNA complexes. Nucleic acids research 38:D91-7 (2010). [Pubmed]
Description: E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA
Length: 32
Consensus: AGGATTATAGCAnAnnnnnnnnnnnTGTCnnG
Weblogo:
PSSM: P0 A C G T
01 96 0 0 0 A
02 3 6 84 3 G
03 0 0 96 0 G
04 96 0 0 0 A
05 0 0 0 96 T
06 3 6 3 84 T
07 96 0 0 0 A
08 0 0 0 96 T
09 96 0 0 0 A
10 0 0 96 0 G
11 3 84 3 6 C
12 81 7 8 0 A
13 24 24 24 24 n
14 84 3 6 3 A
15 24 24 24 24 n
16 24 24 24 24 n
17 24 24 24 24 n
18 24 24 24 24 n
19 24 24 24 24 n
20 24 24 24 24 n
21 24 24 24 24 n
22 24 24 24 24 n
23 24 24 24 24 n
24 24 24 24 24 n
25 24 24 24 24 n
26 5 7 7 77 T
27 0 3 88 5 G
28 0 0 0 96 T
29 0 96 0 0 C
30 24 24 24 24 n
31 24 24 24 24 n
32 6 3 84 3 G
Binding TFs: 4ylo_F (Sigma-70 factor, region 1.2, Sigma-70 region 3, Sigma-70 region 2 , Sigma-70, region 4, Sigma-70, non-essential region)
Binding Sites: 4ylo_1
4ylo_2
Publications: Zuo Y, Steitz T.A. Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble. Molecular cell 58:534-40 (2015). [Pubmed]

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