>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family; InterPro: IPR011517 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 a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.

Probab=98.72 E-value=2.4e-06 Score=62.00 Aligned_cols=159 Identities=19% Similarity=0.285 Sum_probs=98.3 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHC-----CCCCC----------HHHHHHHHHHHHH--HHHHHCCCCC Q ss_conf 99999999828599999999943077875655557-----99998----------8899999988899--8986218534 Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-----GYGLP----------ISEVVSEGNIGLM--QAVKKFDPER 97 (302) Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~-----~~g~~----------~~DLiQeG~iGLi--~Ai~kFDp~k 97 (302) T Consensus 5 t~ll~~~~-~Gd~~A~~~L~~~~Y~~LR~~A~~~~~~~~~~~~Lq~~~~~~ci~stT~LV~EAylrL~~t~~~~~~~-~r 82 (194) T TIGR02999 5 TELLQQWQ-NGDQAARDQLFPALYQELRRIARRELRRERSGQTLQVEVLAVCIDSTTALVHEAYLRLVDTQDEQEWS-DR 82 (194) T ss_pred HHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHCCCCHHHHC-CH T ss_conf 99999883-64588999999999999999999999851036652044677510466788998766421232023222-50 Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCC Q ss_conf 56899975778999999853202460011023003589999999978878662447888246778886189832110000 Q gi|254780611|r 98 GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177 (302) Q Consensus 98 G~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~ 177 (302) T Consensus 83 ~H-F~~~AA----~aMRrIL~D~A------------------R~~-~~--~--KRGg~~~-------------------- 114 (194) T TIGR02999 83 RH-FFAAAA----KAMRRILVDHA------------------RRR-RA--Q--KRGGGAV-------------------- 114 (194) T ss_pred HH-HHHHHH----HHHHHHHHHHH------------------HHH-HH--H--CCCCCCC-------------------- T ss_conf 88-999999----99999999999------------------999-87--4--1367763-------------------- Q ss_pred CCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHH Q ss_conf 00122343355202323453200000123568705655666666677799999962199999999999827888889899 Q gi|254780611|r 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257 (302) Q Consensus 178 ~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~E 257 (302) T Consensus 115 -----~~~l~~~~--------------~~~~~~~~~------~L~~Ld~aL~-~L~~~~Pr~a~~veLr~F~G--l~~~E 166 (194) T TIGR02999 115 -----RVSLDEVL--------------PDAEADADE------ELLDLDDALD-KLAQVDPRQAEVVELRFFAG--LTVEE 166 (194) T ss_pred -----CCCCCCCC--------------CCCCCCCHH------HHHHHHHHHH-HHHHCCHHHHHHHHHHHHCC--CCHHH T ss_conf -----35520000--------------135777403------5999999998-77400678899885311048--89899 Q ss_pred HHHHHCCCHHHHHH Q ss_conf 99997789999999 Q gi|254780611|r 258 LSSEFEVSRERVRQ 271 (302) Q Consensus 258 Ia~~lgiS~eRVrQ 271 (302) T Consensus 167 ~A~~L~~S~~Tv~R 180 (194) T TIGR02999 167 IAELLGVSVRTVER 180 (194) T ss_pred HHHHHCCCHHHHHH T ss_conf 99986888878998

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02999