>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor; InterPro: IPR000394 Sigma factors are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. 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. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor , required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognized by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions: A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.

Probab=94.19  E-value=0.02  Score=34.85  Aligned_cols=104  Identities=20%  Similarity=0.174  Sum_probs=72.5

Q ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             99859988999998489999999887799888999999999982899999614532210000232134554677799999
Q gi|254781218|r   40 RKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLK  119 (205)
Q Consensus        40 R~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk  119 (205)
T Consensus       361 ~~LkPL~L~~vA~el~~heSTiSRai~~KYl~T~~G~f~Lk~FFS~~v~~~~~~-------------~~~S~~~ik~~~~  427 (477)
T TIGR02395       361 AALKPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSSGVSTESAE-------------GEASSTAIKALIK  427 (477)
T ss_pred             HCCCCCCHHHHHHHHCCCCCCEEEEECCCEEECCCCCHHHHHHCCHHHCCCCCC-------------HHHHHHHHHHHHH
T ss_conf             006886389999885889872463317735760764033654312012034565-------------0346999999999


Q ss_pred             HH----HHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHH
Q ss_conf             99----9972983899999977------9999999974148899989
Q gi|254781218|r  120 SI----RKDKGMSQIEFGKLLG------MPNSTLSNYEQGRTIPEIK  156 (205)
Q Consensus       120 ~l----R~~~glsq~elA~~lg------is~~tis~~E~g~~~Ps~~  156 (205)
T Consensus       428 ~lI~~E~k~kPLSD~~i~~~L~e~G~i~~ARRTVaKYRe~L~ipss~  474 (477)
T TIGR02395       428 ELIAAEDKRKPLSDQKIAELLKEKGGIKIARRTVAKYREELGIPSSS  474 (477)
T ss_pred             HHHHCCCCCCCCCHHHHHHHHHHCCCEEEEEECHHHHHHHCCCCCCC
T ss_conf             99970178999766899999986298589960228989634889723