>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family; InterPro: IPR014289 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 are part of the larger sigma-70 family. From homology, tree building, bidirectional best hits and their one-to-a-genome distribution, they appear to represent a conserved family..

Probab=97.66 E-value=0.0012 Score=43.83 Aligned_cols=158 Identities=18% Similarity=0.260 Sum_probs=103.6 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCC-CCHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 889999998889989862185345689997577899999985320246001102-3003589999999978878662447 Q gi|254780611|r 75 ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFFNLRRLKGHLQAITDNN 153 (302) Q Consensus 75 ~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~-~~~~r~l~~~~rk~~~~~~~~~~~~ 153 (302) T Consensus 30 AEDaVQEtLl~Al~~~~~F~G-~-s~lkTWl~~ILknKiID~LR~~~R~~~v~laT~---------------~d---~e- 88 (194) T TIGR02943 30 AEDAVQETLLAALEHADSFAG-R-SALKTWLFAILKNKIIDVLRAKGREVKVALATD---------------LD---DE- 88 (194) T ss_pred HHHHHHHHHHHHHHCCCCCHH-H-HHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECC---------------HH---HH- T ss_conf 889999999998735776014-8-999999999999999999834675454332010---------------22---01- Q ss_pred CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 88824677888618983211000000122343355202323453200000123568705655666666677799999962 Q gi|254780611|r 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233 (302) Q Consensus 154 ~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~ 233 (302) T Consensus 89 ------------~~-------------dE~d~~~~lF~---~----~GHW~~~~~P~~W~~Pe~~l~~~~Fw~vfeaCl~ 136 (194) T TIGR02943 89 ------------LD-------------DEADEFDALFT---Q----NGHWAEHEKPREWSTPEKQLENKEFWEVFEACLD 136 (194) T ss_pred ------------CC-------------CCHHHHHHCCC---C----CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf ------------26-------------71023243168---5----7661446789998521688875568999999998 Q ss_pred CCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 199999999999827888889899999977899999999999999999999974 Q gi|254780611|r 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 234 ~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 137 ~LP~~~ARVF~MRE~L~--~~~~eIC~~l~is~~N~~VlLyRAR~~LR~CL~~~ 188 (194) T TIGR02943 137 RLPEQTARVFMMREVLG--FESEEICQELEISASNCHVLLYRARLSLRECLSAN 188 (194) T ss_pred HHHHHHCCHHHHHHHHC--CCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 61676401355565424--86688753003137679999999999999998633

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02943