>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD; InterPro: IPR012760 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime , . The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation , . Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.

Probab=96.69  E-value=0.0013  Score=47.57  Aligned_cols=190  Identities=11%  Similarity=0.052  Sum_probs=117.2

Q ss_pred             CHHHHHH---HHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHH
Q ss_conf             2389999---9999873117103678764210135433333334333332110001110001000000001221000011
Q gi|254780289|r  161 PLTFQAL---IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS  237 (682)
Q Consensus       161 P~ti~~i---l~~~e~i~~ge~~LrdIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~  237 (682)
T Consensus        15 SIAKkY~nRGL~F~DLIQEGn~GL~KAv~KFdy~kGyKFSTYATWWIRQAITRAIADQARtIRiPVHm~ETINk~~~~~R   94 (240)
T TIGR02393        15 SIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIKAER   94 (240)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             67666304786334367652357898877621357886551157899999999887513720110326678889999989


Q ss_pred             HHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHH
Q ss_conf             11101356666530344310002223345555644421023479876689999999999999875210120007999999
Q gi|254780289|r  238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL  317 (682)
Q Consensus       238 ~~~~~~~~~~~~e~e~~~~~~e~e~de~~~sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl  317 (682)
T Consensus        95 ~l~Q~~Gr~Pt~EelAe~~g~~~~Kv~~i~~~~~~PiSLe~piG~e~dS~l~DFi~D~--------~~~~P~~~~~~~~l  166 (240)
T TIGR02393        95 KLLQELGREPTDEELAERMGLPVEKVREIKKIAQEPISLETPIGEEEDSSLGDFIEDE--------SIESPEDAAAKELL  166 (240)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC--------CCCCHHHHHHHHHH
T ss_conf             9998728899877899870899899999998624886566677887777442652574--------44685899999999


Q ss_pred             HHHHHHHHH-HH---------------HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999998-62---------------10-0577887899999999999999999999
Q gi|254780289|r  318 KEKLVKLVG-SL---------------SL-NQSRIDLLVEQLYDISKRIMHNEGELLR  358 (682)
Q Consensus       318 ~~eL~e~~~-~l---------------kl-~~k~iE~L~~~l~~~~k~Ir~~Er~L~r  358 (682)
T Consensus       167 ~~~l~~vL~~~L~~rE~~Vl~~RyGL~d~~~~~TLEEVG~~f~VTRERIRQIE~KALR  224 (240)
T TIGR02393       167 REQLEEVLENTLTERERKVLRMRYGLLDGEKPKTLEEVGKEFNVTRERIRQIESKALR  224 (240)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             9999999860178889999987438998876533788876517871145688899988