HHsearch alignment for GI: 254780611 and conserved domain: TIGR02947

>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family; InterPro: IPR014293 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 (IPR014284 from INTERPRO). They and appear by homology, tree building, bidirectional best hits and (with one exception, a paralog in Thermobifida fusca strain YX) their one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor (see IPR014295 from INTERPRO) in an apparent operon.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=90.59  E-value=1.3  Score=23.51  Aligned_cols=177  Identities=15%  Similarity=0.150  Sum_probs=89.8

Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH-H
Q ss_conf             999999999982859999999994307787565555799998889999998889989862185345689997577899-9
Q gi|254780611|r   33 EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK-A  111 (302)
Q Consensus        33 ee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr-~  111 (302)
T Consensus         5 ~~~~~~~rfe-rdal~~~dqly~aalrm--------~rnPadaed~vqe~y~kaf~~f~~~~~Gtn--l~aWlyriltnt   73 (193)
T TIGR02947         5 TEEQRAQRFE-RDALEYLDQLYGAALRM--------TRNPADAEDLVQEAYVKAFSAFKQFKPGTN--LKAWLYRILTNT   73 (193)
T ss_pred             HHHHHHHHHH-HHHHHHHHHHHHHHHHH--------HCCCCCHHHHHHHHHHHHHHHHHHHCCCCH--HHHHHHHHHHHH
T ss_conf             2689998776-77999999999999876--------238654788999999999998874137742--899999999999


Q ss_pred             HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC
Q ss_conf             99985320246001102300358999999997887866244788824677888618983211000000122343355202
Q gi|254780611|r  112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN  191 (302)
Q Consensus       112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~  191 (302)
T Consensus        74 yin~yrk~q----r~P~~~~~----------------------~~~~dWq~a~~---------------~~h~s~--Glr  110 (193)
T TIGR02947        74 YINSYRKKQ----REPAQSDS----------------------DEIEDWQLAKA---------------ASHTSS--GLR  110 (193)
T ss_pred             HHHHHHHHH----CCCCCCCC----------------------CHHHHHHHHHH---------------HHHHHC--CCH
T ss_conf             999888752----27655652----------------------01468888765---------------311001--204


Q ss_pred             CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             32345320000012356870565566666667779999996219999999999982788888989999997789999999
Q gi|254780611|r  192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ  271 (302)
Q Consensus       192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ  271 (302)
T Consensus       111 ---sae~eald~lPd-------------------~~~~~al~~~~~efr~~v~~--adveGf~ykei~~im~tP~Gtvms  166 (193)
T TIGR02947       111 ---SAEVEALDALPD-------------------DDIKAALQELPEEFRLAVYF--ADVEGFAYKEIAEIMGTPIGTVMS  166 (193)
T ss_pred             ---HHHHHHHHCCCH-------------------HHHHHHHHHHHHHHHHHHHH--HHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf             ---777888752884-------------------89999998737999898887--620353157799885474779999


Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999999999974
Q gi|254780611|r  272 IEARAFKKVQESIQKQ  287 (302)
Q Consensus       272 I~~~AL~kLR~~l~~~  287 (302)
T Consensus       167 rl~r~rk~l~~~l~d~  182 (193)
T TIGR02947       167 RLHRGRKQLRDLLADV  182 (193)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9899999999999988