>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; InterPro: IPR014327 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 members of the sigma-70 family and are found primarily in the genus Bacteroides. This appears to have resulted from a lineage-specific expansion as Bacteroides thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037 (Tannerella forsythensis ATCC 43037), Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currently only two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.

Probab=99.25 E-value=4.4e-10 Score=86.95 Aligned_cols=166 Identities=14% Similarity=0.214 Sum_probs=121.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCC Q ss_conf 99999994307787565555799998889999998889989862185345689997577899999985320246001102 Q gi|254780611|r 49 AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128 (302) Q Consensus 49 Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~ 128 (302) T Consensus 2 aF~~ly~~Yy~~l~~fA~~yv~~~e~AEdIVqdvF~~lWe~r~~l~~~~--~~~~YL~~~v~N~~ln~Lr~~~--~~--- 74 (167) T TIGR02985 2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRESLEESE--SIKAYLFTIVKNRCLNYLRHKQ--VE--- 74 (167) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHH--HH--- T ss_conf 4889999987999999999836899999999999999973145256213--5217999999998998998899--99--- Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCC Q ss_conf 30035899999999788786624478882467788861898321100000012234335520232345320000012356 Q gi|254780611|r 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208 (302) Q Consensus 129 ~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~ 208 (302) T Consensus 75 -----------~~~~~~~~---~~~-----------------------------~~~~~~~--------------~~~l~ 97 (167) T TIGR02985 75 -----------EKYQEELS---EIE-----------------------------EDEIELR--------------LQSLE 97 (167) T ss_pred -----------HHHHHHHH---HHH-----------------------------HHHHHHH--------------HHHCC T ss_conf -----------99999999---865-----------------------------5678763--------------10036 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 8705655666666677799999962199999999999827888889899999977899999999999999999999 Q gi|254780611|r 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302) Q Consensus 209 ~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302) T Consensus 98 ~~~~~~~----~~~El~~~i~~~~~~LPe~~R~iF~lsr~--eg~s~~EIA~~L~iS~~TVe~hi~~ALk~LR~~L 167 (167) T TIGR02985 98 ADPEEDI----YSKELEEIIEEAIEKLPEQCREIFILSRF--EGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 167 (167) T ss_pred CCCHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHH--HCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHC T ss_conf 8974578----79999999999987568989999999886--1798678998848988899999999999998739

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02985