HHsearch alignment for GI: 254780289 and conserved domain: TIGR02393
>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=100.00 E-value=0 Score=831.21 Aligned_cols=238 Identities=65% Similarity=1.022 Sum_probs=236.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC
Q ss_conf 68999875557899988752235677788754436799998874385457312010289899999999972287046142
Q gi|254780289|r 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523 (682)
Q Consensus 444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~ 523 (682)
T Consensus 1 Ak~~l~~sNLRLVvSIAKkY~nRGL~F~DLIQEGn~GL~KAv~KFdy~kGyKFSTYATWWIRQAITRAIADQARtIRiPV 80 (240)
T TIGR02393 1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (240)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCH
T ss_conf 93568873014666676663047863343676523578988776213578865511578999999998875137201103
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH
Q ss_conf 05889899999999987760889997899987099989999999860898755363588998604756238988998999
Q gi|254780289|r 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603 (682)
Q Consensus 524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~ 603 (682)
T Consensus 81 Hm~ETINk~~~~~R~l~Q~~Gr~Pt~EelAe~~g~~~~Kv~~i~~~~~~PiSLe~piG~e~dS~l~DFi~D~~~~~P~~~ 160 (240)
T TIGR02393 81 HMVETINKLIKAERKLLQELGREPTDEELAERMGLPVEKVREIKKIAQEPISLETPIGEEEDSSLGDFIEDESIESPEDA 160 (240)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf 26678889999989999872889987789987089989999999862488656667788777744265257444685899
Q ss_pred HHHHHHHHHHHHHHH-CCCHHHHHHHHHHHCCCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHC
Q ss_conf 999999999999973-2998899999998187986-74688999899667899999999999998329677787566517
Q gi|254780289|r 604 AIQANLRETTTRVLA-SLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681 (682)
Q Consensus 604 ~~~~~~~~~~~~~l~-~l~~re~~v~~~r~g~~~~-~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~~ 681 (682)
T Consensus 161 ~~~~~l~~~l~~vL~~~L~~rE~~Vl~~RyGL~d~~~~~TLEEVG~~f~VTRERIRQIE~KALRKLrhp~r~~~Lk~f~~ 240 (240)
T TIGR02393 161 AAKELLREQLEEVLENTLTERERKVLRMRYGLLDGEKPKTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 240 (240)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 99999999999998601788899999874389988765337888765178711456888999885028436677776419