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