>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family; InterPro: IPR014303 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 and bidirectional best hits, to represent a conserved family. This entry is found in a limited number of bacterial lineages and ncludes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis str. MC2 155, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM 10152.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.

Probab=98.10 E-value=1.6e-05 Score=56.49 Aligned_cols=157 Identities=17% Similarity=0.149 Sum_probs=92.5 Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHH Q ss_conf 94307787565555799998889999998889989862185345689997577899999985320246001102300358 Q gi|254780611|r 55 TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134 (302) Q Consensus 55 ~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~ 134 (302) T Consensus 4 ~~~rplLF~~AYRmLGSv~dAED~VQEtfLrw~~~-d~~~i~~~~AyL~---------------------~~~T----r~ 57 (287) T TIGR02957 4 EALRPLLFSVAYRMLGSVADAEDIVQETFLRWQEA-DRAQIENPKAYLV---------------------KVVT----RR 57 (287) T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-CHHCCCCCCCHHH---------------------HHHH----HH T ss_conf 56723789999997304756877899998978711-4404268640556---------------------8789----74 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHH Q ss_conf 99999999788786624478882467788861898321100000012234335520232345320000012356870565 Q gi|254780611|r 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214 (302) Q Consensus 135 l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~ 214 (302) T Consensus 58 cid~LrSAr~rRE~YvG~WLPEPl~---------------------------------------------~~s~~dP~e~ 92 (287) T TIGR02957 58 CIDVLRSARARRESYVGPWLPEPLL---------------------------------------------TTSSADPAES 92 (287) T ss_pred HHHHHHHCCCCCCCCCCCCCCCCCC---------------------------------------------CCCCCCHHHH T ss_conf 5788885022146310788988888---------------------------------------------8885553889 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH--HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 56666666777999999621999999999998--2788888989999997789999999999999999999997401 Q gi|254780611|r 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289 (302) Q Consensus 215 ~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~r--y~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~ 289 (302) T Consensus 93 ~E---~~eslS~A~L~lLErL~P~ERAVF~LREVF~y~----Y~EIA~~v~kS~ancRQl~~RAr~~lr~~~r~R~~ 162 (287) T TIGR02957 93 VE---LAESLSMAYLLLLERLSPLERAVFLLREVFDYD----YEEIASIVGKSEANCRQLVSRARRHLRAARRPRFE 162 (287) T ss_pred HH---HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCC----CHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 98---875377999998730797899999999874588----26789760689579999999999999752888751

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02957