HHsearch alignment for GI: 254780163 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=98.87 E-value=9.3e-08 Score=74.90 Aligned_cols=233 Identities=21% Similarity=0.338 Sum_probs=173.8
Q ss_pred CHHHHHHHCHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHC---CCCEEEEEHHHHHCCCCC
Q ss_conf 00246653458999999999877520445657874068861432003889999987304---773377206886124653
Q gi|254780163|r 473 KNLGTVVYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL---GVQLLRFDMSEYMERHAV 549 (798)
Q Consensus 473 ~~l~~~v~GQ~~ai~~v~~~i~~~~~gl~~~~rP~g~flf~GptGvGKTelak~la~~~---~~~lir~dmsey~e~~~v 549 (798)
T Consensus 208 ~~~~~~i~G~Spam~~v~~~~~~v----A~~n---STVLlRGESGTGKEl~A~AIH~~SpR~~~PFVK~NCAALse~lLE 280 (574)
T TIGR01817 208 SGKEDGIVGKSPAMRQVVDQIKVV----ARSN---STVLLRGESGTGKELIAKAIHELSPRAKRPFVKLNCAALSETLLE 280 (574)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHH----CCCC---CEEEEECCCCCCHHHHHHHHCCCCCCCCCCCEEEECCCCCCCHHH
T ss_conf 234474012478999999886520----1317---667850565744334442340466455788545006447761124
Q ss_pred CHHCCCCCHHCCCCCCCCCCHHHHHCCC-------EEEEECCHHHCCHHHHHHHHHHHHHHHCC---CCCCCEECCCCEE
Q ss_conf 0110478000256444310035551585-------17774044550289999999987775021---7799776125429
Q gi|254780163|r 550 SRLIGAPPGYVGFGQGGILADSVDQNPY-------SVVLLDEIEKSHPDVLNILLQIMDYGILT---DQSGKKISFRNVI 619 (798)
Q Consensus 550 s~LiGappGYvG~~egg~Lte~vr~~P~-------sVvl~DEiEKAh~~v~~~llqild~G~lt---d~~Gr~vdf~n~i 619 (798)
T Consensus 281 SELFG-------HEK-GAFTGA~~~RkGRFElAdGGTLFLDEIGEISPaFQAKLLRVLQEGEFERVGG~~TlKVd---VR 349 (574)
T TIGR01817 281 SELFG-------HEK-GAFTGAVAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVD---VR 349 (574)
T ss_pred HHHHC-------CCC-HHHHHHHHHCCCCEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEECCCEEEEEE---EE
T ss_conf 54513-------430-14688875177753302788320000146785688899887521002532787248873---67
Q ss_pred EEEECCCCHHHHHHCCCCCCCCCCHHHHHHHH-HHHCCHHHHCCCCEEEECC-CC--CHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99942421455330368988211148899999-8728878817768289628-89--99999999999999999999866
Q gi|254780163|r 620 LIMTTNAGALEMSKARIGFGSSRNDDADKEAL-RNFLSPEFLNRLDSIIPFF-PL--SSDIIRQVVHKFIMKLELQLQEK 695 (798)
Q Consensus 620 ii~TsN~G~~~~~~~~~g~~~~~~~~~~~~~l-~~~f~peflnRid~ii~F~-~l--~~~~~~~i~~~~l~~l~~~l~~~ 695 (798)
T Consensus 350 lvaATN-------------------rdLE~aV~~GeFRaDLYYRinVvPl~lPPLRER~~DIP~LA~~fL~kf~---~en 407 (574)
T TIGR01817 350 LVAATN-------------------RDLEEAVAKGEFRADLYYRINVVPLILPPLRERREDIPLLAEAFLEKFN---REN 407 (574)
T ss_pred EEECCC-------------------CCHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH---HHH
T ss_conf 886137-------------------3558897278973023554422234078777873116899999999876---651
Q ss_pred CCE-EEECHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECC
Q ss_conf 988-999889999999718981015326799999862359999996296768884899996078
Q gi|254780163|r 696 GIS-FHFSEEVINWLVSHGYDVKMGARPLERIIKEHVKVPLADEILFGKLKKGGGVVKVSLNPD 758 (798)
Q Consensus 696 ~i~-l~~~~~~~~~l~~~~~~~~~GAR~l~r~i~~~i~~~la~~il~~~~~~g~~~~~v~~~~~ 758 (798)
T Consensus 408 ~R~mL~~~~~Ai~~Lm~-c~wPGN-VRELENC~eRtA-------tLs----~~~~It~~df~c~ 458 (574)
T TIGR01817 408 GRPMLTLSPSAIRVLMS-CKWPGN-VRELENCVERTA-------TLS----RSGTITRSDFSCQ 458 (574)
T ss_pred CCCEEEECHHHHHHHHC-CCCCCC-CEEHHHHHHHHH-------HHC----CCCCCCCCEEEEC
T ss_conf 87203226789989751-789997-400443787787-------541----6885164236642