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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