>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family; InterPro: IPR014300 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 group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This entry is found in certain Bacillus and Clostridium species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.

Probab=90.40 E-value=1.4 Score=23.49 Aligned_cols=162 Identities=19% Similarity=0.259 Sum_probs=110.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHH Q ss_conf 99876533211246899987555789998875223567778875443679999887438545731201028989999999 Q gi|254780289|r 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510 (682) Q Consensus 431 ~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~ 510 (682) T Consensus 7 v~~a~~Gn---~~aF~~Li~~~ke~LYk~Af~Yvkne~DALd~i~EtvyKAY~sI~kL---k~~~Y--F~TW~trILIn~ 78 (173) T TIGR02954 7 VKKAIRGN---KEAFESLIKKNKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIEKL---KHPEY--FNTWLTRILINE 78 (173) T ss_pred HHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHH---CCCCC--CHHHHHHHHHHH T ss_conf 99987249---34789999984366857665440673405899999999999989983---36100--025678999999 Q ss_pred HHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEE Q ss_conf 99722870461420588989999999998776088999789998709998999999986089875536358899860475 Q gi|254780289|r 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590 (682) Q Consensus 511 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~ 590 (682) T Consensus 79 ci~--------------lL~K--------------------------------------~kk~i~~~~~~~~~~~----- 101 (173) T TIGR02954 79 CID--------------LLKK--------------------------------------KKKVILFDKNTKIEKK----- 101 (173) T ss_pred HHH--------------HHHC--------------------------------------CCCEEECCCCCCHHHH----- T ss_conf 999--------------9843--------------------------------------8975306887101223----- Q ss_pred EECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 6238988998999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 591 ~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) T Consensus 102 ----~~~~~~~~~lef----~dLy~Ai~~L~~~~~t~IIL~Y----y~DL~I~eIa~vM~~P~gTvKtyl~Ra~~~lk~ 168 (173) T TIGR02954 102 ----ECEVDADERLEF----EDLYKAIDTLNDKYKTAIILRY----YHDLKIKEIAEVMNKPEGTVKTYLRRAKKKLKK 168 (173) T ss_pred ----HCCCCHHHHHCH----HHHHHHHHHHHHHHHHHHHHHH----CCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHH T ss_conf ----216686886258----6899999731145440264332----179984259985168985178999999999888

HHsearch alignment for GI: 254780289 and conserved domain: TIGR02954