HHsearch alignment for GI: 254780611 and conserved domain: TIGR02984

>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; InterPro: IPR014326 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) and are apparently found only in the Planctomycetaceae family including the genus s Gemmata and Pirellula, in which seven sequences are found.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=99.55  E-value=7.1e-13  Score=105.60  Aligned_cols=183  Identities=20%  Similarity=0.303  Sum_probs=129.2

Q ss_pred             HCCHHHHHHHHHHHHHHHHHHHHH-----HCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             285999999999430778756555-----579999888999999888998986218534568999757789999998532
Q gi|254780611|r   44 HGDLSAAHRLVTSHLRLVVKIAMG-----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL  118 (302)
Q Consensus        44 ~gd~~Ar~~Li~~nlrlV~~iA~~-----y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~  118 (302)
T Consensus         3 ~GD~eAl~~L~~~Y~~yLr~La~~~L~~~L~~r-~dpSD~VQe~~---l~A~~~~~~fRG~t~~Ef~~W-LR~IL~~~l~   77 (190)
T TIGR02984         3 AGDQEALGELLDRYRNYLRLLARVQLDRRLRRR-VDPSDVVQETL---LEAHRDFDQFRGKTEGEFAGW-LRQILANVLA   77 (190)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHH---HHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHH
T ss_conf             872778988999862499999999760884001-57545899999---999988875328985789999-9999999999


Q ss_pred             CCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCC
Q ss_conf             02460011023003589999999978878662447888246778886189832110000001223433552023234532
Q gi|254780611|r  119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS  198 (302)
Q Consensus       119 ~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~  198 (302)
T Consensus        78 ~------------------~---~~~h~~-~qkRD~--------------------------rrE~~l~~~~~~~~~Ss~  109 (190)
T TIGR02984        78 D------------------A---LRRHLG-AQKRDI--------------------------RREQSLDAGAARVDESSV  109 (190)
T ss_pred             H------------------H---HHHHHH-HHCCCC--------------------------HHCCCCCCCCCCHHHHHH
T ss_conf             9------------------9---998866-420262--------------------------010120124576588799


Q ss_pred             CHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             00000123568705655666666677799999962199999999999827888889899999977899999999999999
Q gi|254780611|r  199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK  278 (302)
Q Consensus       199 ~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~  278 (302)
T Consensus       110 ~L~~~Laa~~~sPS~~a~r~E----~~~~L~~AL~~L~e~~REvi~LR~~EG--LS~~EvA~~Md~~~~av~~l~~Ral~  183 (190)
T TIGR02984       110 RLEAQLAADGPSPSQAAARRE----SAVRLAQALAKLPEDYREVILLRHLEG--LSFAEVAERMDRSEGAVSMLWVRALA  183 (190)
T ss_pred             HHHHHHCCCCCCCHHHHHHHH----HHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             999975189998558999977----999999999647922589999987603--55589998707975898758999999


Q ss_pred             HHHHHHH
Q ss_conf             9999999
Q gi|254780611|r  279 KVQESIQ  285 (302)
Q Consensus       279 kLR~~l~  285 (302)
T Consensus       184 ~Lr~~l~  190 (190)
T TIGR02984       184 RLRQILE  190 (190)
T ss_pred             HHHHHCC
T ss_conf             9987509