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