HHsearch alignment for GI: 254780693 and conserved domain: cd06171
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=97.88 E-value=3.7e-05 Score=55.94 Aligned_cols=46 Identities=43% Similarity=0.481 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
Q ss_conf 449989999999998-7999789999949998899999999999807
Q gi|254780693|r 172 RNLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235)
Q Consensus 172 ~~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235)
T Consensus 9 ~~L~~~~r~vl~l~y~~~~s~~EIa~~lgis~~tVk~~l~rA~~~Lr 55 (55)
T cd06171 9 DKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf 83999998989999980999999999989599999999999998758