DNA Binding Motif

						

			
Accessions: 7khi_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: Escherichia coli RNA polymerase and rrnBP1 promoter complex with DksA/ppGpp
Length: 24
Consensus: Agnnwnnnnnnnnnnnnnnacaag
Weblogo: 
PSSM: P0      A      C      G      T
01     96      0      0      0      A
02     14     16     52     14      g
03     24     24     24     24      n
04     24     24     24     24      n
05     27     22     22     25      w
06     24     24     24     24      n
07     24     24     24     24      n
08     24     24     24     24      n
09     24     24     24     24      n
10     24     24     24     24      n
11     24     24     24     24      n
12     24     24     24     24      n
13     24     24     24     24      n
14     24     24     24     24      n
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     33     21     21     21      a
21     12     60     12     12      c
22     38     20     19     19      a
23     63     10     13     10      a
24     13     10     63     10      g
Binding TFs: 7khi_F (Sigma-70 factor, region 1.2, Sigma-70 factor, region 1.1, Sigma-70 region 3, Sigma-70 region 2 , Sigma-70, region 4, Sigma-70, non-essential region)
Binding Sites: 7khi_X
7khi_Y
			
Publications: Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS. Structural basis of ribosomal RNA transcription regulation. Nat Commun 12:528 (2021). [Pubmed]

	
			


			

				

				
				
				
				

			

			

		

	
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