HHsearch alignment for GI: 254781026 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=99.33 E-value=2e-12 Score=93.66 Aligned_cols=105 Identities=29% Similarity=0.435 Sum_probs=83.7
Q ss_pred CCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCEEECCCCCCCCCCCCCCCEEE-----CCCCCCCHHHCCCCCCCCCHH
Q ss_conf 977786059999999887488989788532300000027888756531112020-----377521001102343456827
Q gi|254781026|r 1 MIGPPGARKSMLASCLPSILLPLSLEESLEVSMIYSISGHSSHEYSFIQNRPFR-----SPHHSVTIAALIGGGLQVLPG 75 (186)
Q Consensus 1 l~GpPG~GKS~lar~l~~iLP~l~~~e~le~~~i~s~~g~~~~~~~~~~~~p~~-----~~~~~~~~~~l~gg~~~~~pG 75 (186)
T Consensus 240 lRGESGTGKEl~A~AIH~~SpR--------------------~------~~PFVK~NCAALse~lLESELFGHEKGAFTG 293 (574)
T TIGR01817 240 LRGESGTGKELIAKAIHELSPR--------------------A------KRPFVKLNCAALSETLLESELFGHEKGAFTG 293 (574)
T ss_pred EECCCCCCHHHHHHHHCCCCCC--------------------C------CCCCEEEECCCCCCCHHHHHHHCCCCHHHHH
T ss_conf 5056574433444234046645--------------------5------7885450064477611245451343014688
Q ss_pred HHH-------HCCCCEEEEECHHHCCHHHHHHHHHHHHCCCEEEHHCCEEEEECCCEEEEEECCC
Q ss_conf 998-------2799889980387859889999999997195230100307898470156752274
Q gi|254781026|r 76 EDS-------LAHNGVLFLDEIPEFSPQTLNALRQPLETGECIIARANRKISYPSRIQLIAAMNP 133 (186)
Q Consensus 76 ~i~-------lAh~GVLflDE~~e~~~~~l~~L~~~le~g~v~i~R~g~~~~~Pa~f~Lvaa~NP 133 (186)
T Consensus 294 A~~~RkGRFElAdGGTLFLDEIGEISPaFQAKLLRVLQEG--EFERVGG~~TlKVdVRlvaATNr 356 (574)
T TIGR01817 294 AVAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEG--EFERVGGNRTLKVDVRLVAATNR 356 (574)
T ss_pred HHHHCCCCEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCC--CEEEECCCEEEEEEEEEEECCCC
T ss_conf 8751777533027883200001467856888998875210--02532787248873678861373