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