HHsearch alignment for GI: 254780567 and conserved domain: TIGR01817

>TIGR01817 nifA Nif-specific regulatory protein; InterPro: IPR010113 This entry represents NifA, a DNA-binding regulatory protein for nitrogen fixation. Not included in this group are: the homologue in Aquifex aeolicus (which lacks nitrogenase), transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms. In diazotrophic proteobacteria, the sigma54-dependent activator NifA activates transcription of the nif (nitrogen fixation) genes by a conserved mechanism common to members of the enhancer binding protein family. Although NifA proteins have similar domain structures, both transcriptional regulation of nifA expression and posttranslational regulation of NifA activity by oxygen and fixed nitrogen vary significantly from one organism to another. In Klebsiella pneumoniae and Azotobacter vinelandii, nifA is co-ordinately transcribed with a second gene, nifL, whose product inhibits NifA activity in response to oxygen and fixed nitrogen .; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0009399 nitrogen fixation.
Probab=97.00  E-value=0.0085  Score=37.10  Aligned_cols=197  Identities=19%  Similarity=0.205  Sum_probs=126.8

Q ss_pred             CCCCCCCCCCEEECCCHH--HHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHH-----CCCCHHHHHHHHHH---
Q ss_conf             877668845416536189--99999985101678849998787778688999999862-----76201356764445---
Q gi|254780567|r   33 PRCLGISRDDLLVHSAIE--QAVRLIDSWPSWPSRVVILVGPSGSGKSCLANIWSDKS-----RSTRFSNIAKSLDS---  102 (246)
Q Consensus        33 ~~~~~~~~dnFiv~~~N~--~A~~~i~~~~~~~~~~l~i~G~~GsGKTHLl~a~~~~~-----~~~~~~~~~~~~~~---  102 (246)
T Consensus       203 ~~~~~~~~~~~i~G~Spam~~v~~~~~~vA~~-nSTVLlRGESGTGKEl~A~AIH~~SpR~~~PFVK~NCAALse~lLES  281 (574)
T TIGR01817       203 AARRRSGKEDGIVGKSPAMRQVVDQIKVVARS-NSTVLLRGESGTGKELIAKAIHELSPRAKRPFVKLNCAALSETLLES  281 (574)
T ss_pred             HHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCC-CCEEEEECCCCCCHHHHHHHHCCCCCCCCCCCEEEECCCCCCCHHHH
T ss_conf             12331234474012478999999886520131-76678505657443344423404664557885450064477611245


Q ss_pred             -HHHHHH-------------------HHHHHHHHHCCCCC-CHHHHHHHHH----------HHCCCCCEEEEECCCCCC-
Q ss_conf             -466666-------------------65334332100376-1033545554----------311234215640354320-
Q gi|254780567|r  103 -ILIDTR-------------------KPVLLEDIDLLDFN-DTQLFHIINS----------IHQYDSSLLMTARTFPVS-  150 (246)
Q Consensus       103 -~~~~~~-------------------~~i~iddi~~~~~~-ee~lf~l~n~----------~~~~~~~iilts~~~p~~-  150 (246)
T Consensus       282 ELFGHEKGAFTGA~~~RkGRFElAdGGTLFLDEIGEISPaFQAKLLRVLQEGEFERVGG~~TlKVdVRlvaATNrdLE~a  361 (574)
T TIGR01817       282 ELFGHEKGAFTGAVAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEA  361 (574)
T ss_pred             HHHCCCCHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEECCCEEEEEEEEEEECCCCCHHHH
T ss_conf             45134301468887517775330278832000014678568889988752100253278724887367886137355889


Q ss_pred             --HHHHHHHHHHHHHHCCEEEECCCC----H--HHHHHHHHHHHH--HCC-CCCCHHHHHHHHHC-CCCCHHHHHHHHHH
Q ss_conf             --022345667885212224507889----7--899999999866--628-97988999999940-66798999999999
Q gi|254780567|r  151 --WGVCLPDLCSRLKAATVVKISLPD----D--DFLEKVIVKMFA--DRQ-IFIDKKLAAYIVQR-MERSLVFAEKLVDK  218 (246)
Q Consensus       151 --~~~~l~DL~SRl~~g~~~~I~~pd----d--e~~~~il~k~~~--~r~-i~l~~~v~~yl~~r-~~Rs~~~l~~~l~~  218 (246)
T Consensus       362 V~~GeFRaDLYYRinVv-Pl~lPPLRER~~DIP~LA~~fL~kf~~en~R~mL~~~~~Ai~~Lm~c~wPGNVRELENC~eR  440 (574)
T TIGR01817       362 VAKGEFRADLYYRINVV-PLILPPLRERREDIPLLAEAFLEKFNRENGRPMLTLSPSAIRVLMSCKWPGNVRELENCVER  440 (574)
T ss_pred             HHCCCCCCHHHHHHHHH-HHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEECHHHHHHHHCCCCCCCCEEHHHHHHH
T ss_conf             72789730235544222-34078777873116899999999876651872032267899897517899974004437877


Q ss_pred             HHHHHHHHCCCCCHH
Q ss_conf             999999847787889
Q gi|254780567|r  219 MDNLALSRGMGITRS  233 (246)
Q Consensus       219 Ld~~sl~~kr~ITi~  233 (246)
T Consensus       441 --tAtLs~~~~It~~  453 (574)
T TIGR01817       441 --TATLSRSGTITRS  453 (574)
T ss_pred             --HHHHCCCCCCCCC
T ss_conf             --8754168851642