>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=99.00 E-value=4.2e-08 Score=73.72 Aligned_cols=166 Identities=14% Similarity=0.207 Sum_probs=111.3 Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH Q ss_conf 99999999982859999999994307787565555799998889999998889989862185345689997577899999 Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113 (302) Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I 113 (302) T Consensus 3 ~~~Lv~~a~-~Gn~~aF~~Li~~~ke~LYk~Af~Yvkne~DALd~i~EtvyKAY~sI~kLk~~-~Y-F~TW~---trILI 76 (173) T TIGR02954 3 DIELVKKAI-RGNKEAFESLIKKNKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIEKLKHP-EY-FNTWL---TRILI 76 (173) T ss_pred HHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCC-CC-CHHHH---HHHHH T ss_conf 368999987-24934789999984366857665440673405899999999999989983361-00-02567---89999 Q ss_pred H---HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHC Q ss_conf 9---8532024600110230035899999999788786624478882467788861898321100000012234335520 Q gi|254780611|r 114 Q---EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190 (302) Q Consensus 114 ~---~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i 190 (302) T Consensus 77 n~ci~lL~K~kk~i------------------------------------------------------------~~~~~~ 96 (173) T TIGR02954 77 NECIDLLKKKKKVI------------------------------------------------------------LFDKNT 96 (173) T ss_pred HHHHHHHHCCCCEE------------------------------------------------------------ECCCCC T ss_conf 99999984389753------------------------------------------------------------068871 Q ss_pred CCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH- Q ss_conf 2323453200000123568705655666666677799999962199999999999827888889899999977899999- Q gi|254780611|r 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV- 269 (302) Q Consensus 191 ~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV- 269 (302) T Consensus 97 ~~~~~---------~~-~~~----~~~~lef----~dLy~Ai~~L~~~~~t~IIL~Yy~D--L~I~eIa~vM~~P~gTvK 156 (173) T TIGR02954 97 KIEKK---------EC-EVD----ADERLEF----EDLYKAIDTLNDKYKTAIILRYYHD--LKIKEIAEVMNKPEGTVK 156 (173) T ss_pred CHHHH---------HC-CCC----HHHHHCH----HHHHHHHHHHHHHHHHHHHHHHCCC--CCHHHHHHHCCCCCCCHH T ss_conf 01223---------21-668----6886258----6899999731145440264332179--984259985168985178 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 99999999999999997 Q gi|254780611|r 270 RQIEARAFKKVQESIQK 286 (302) Q Consensus 270 rQI~~~AL~kLR~~l~~ 286 (302) T Consensus 157 tyl-~Ra~~~lk~~l~~ 172 (173) T TIGR02954 157 TYL-RRAKKKLKKELEE 172 (173) T ss_pred HHH-HHHHHHHHHHHCC T ss_conf 999-9999998886236

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02954