HHsearch alignment for GI: 254780545 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=97.05  E-value=0.00034  Score=49.30  Aligned_cols=212  Identities=28%  Similarity=0.361  Sum_probs=116.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHCC---CCCCEECCCHHHH
Q ss_conf             2422569889852889999999998743356766420123331100378742588899997424---6997020585788
Q gi|254780545|r  141 NVGSVTFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGE---ANVPFFTISGSDF  217 (647)
Q Consensus       141 ~~~~v~f~dv~g~~~~k~~~~~~v~~l~~~~~~~~~g~~~p~g~ll~GppGtGKTlla~a~a~e---~~~~f~~~~~s~~  217 (647)
T Consensus       205 ~~~~~~~~~i~G~Spam---~~v~~~~~~-------vA~~nSTVLlRGESGTGKEl~A~AIH~~SpR~~~PFVK~NCAAL  274 (574)
T TIGR01817       205 RRRSGKEDGIVGKSPAM---RQVVDQIKV-------VARSNSTVLLRGESGTGKELIAKAIHELSPRAKRPFVKLNCAAL  274 (574)
T ss_pred             HHHCCCCCCCCCCCHHH---HHHHHHHHH-------HCCCCCEEEEECCCCCCHHHHHHHHCCCCCCCCCCCEEEECCCC
T ss_conf             33123447401247899---999988652-------01317667850565744334442340466455788545006447


Q ss_pred             H------HHHHHC-----CHHHHHH-HHHHHHHHCCHHEEHHHHHHHHCCCCCCCCCCCHHHHHH-HHHHHH--HHCCCC
Q ss_conf             6------444203-----3245999-999998737801206323564144557898862688988-998998--530323
Q gi|254780545|r  218 V------ELFVGV-----GASRVRD-MFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQT-LNQLLV--EMDGFE  282 (647)
Q Consensus       218 ~------~~~~g~-----g~~~vr~-lf~~a~~~~p~iifiDeida~~~~r~~~~~~~~~e~~~~-ln~ll~--~mdg~~  282 (647)
T Consensus       275 se~lLESELFGHEKGAFTGA~~~RkGRFElAd---GGTLFLDEIGEISPa------------FQAKLLRVLQEGEFERVG  339 (574)
T TIGR01817       275 SETLLESELFGHEKGAFTGAVAQRKGRFELAD---GGTLFLDEIGEISPA------------FQAKLLRVLQEGEFERVG  339 (574)
T ss_pred             CCCHHHHHHHCCCCHHHHHHHHHCCCCEEECC---CCCCCCCCCCCCCHH------------HHHHHHHHHHCCCEEEEC
T ss_conf             76112454513430146888751777533027---883200001467856------------888998875210025327


Q ss_pred             CCC----CEEEEEECCCCCCCCHHHCCCCCCC-------CEEEECHHHHHHHH-HH---HHHHHCCCCCCCC---CCHHH
Q ss_conf             577----8299996298100883331656423-------14100013478899-99---9998548877732---11024
Q gi|254780545|r  283 SSE----GVILIAATNRPDVLDAALLRPGRFD-------RQITVPNPDIVGRE-HI---LMVHSRNVPLAPN---VILKT  344 (647)
Q Consensus       283 ~~~----~v~vi~aTn~~~~lD~al~RpgRfd-------~~i~~~~P~~~~r~-~i---~~~~~~~~~~~~~---~d~~~  344 (647)
T Consensus       340 G~~TlKVdVRlvaATNr--dLE~aV~~-GeFRaDLYYRinVvPl~lPPLRER~~DIP~LA~~fL~kf~~en~R~mL~~~~  416 (574)
T TIGR01817       340 GNRTLKVDVRLVAATNR--DLEEAVAK-GEFRADLYYRINVVPLILPPLRERREDIPLLAEAFLEKFNRENGRPMLTLSP  416 (574)
T ss_pred             CCEEEEEEEEEEECCCC--CHHHHHHC-CCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEECH
T ss_conf             87248873678861373--55889727-8973023554422234078777873116899999999876651872032267


Q ss_pred             HH--HH-HHCCCH--HHHHHHHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf             54--41-203798--99999999987645532024210456899
Q gi|254780545|r  345 IA--RG-TPGFSG--ADLRNLVNEAALMAARRNRRLVTMQEFED  383 (647)
Q Consensus       345 la--~~-t~g~sg--Adi~~~~~eAa~~a~r~~~~~i~~~dl~~  383 (647)
T Consensus       417 ~Ai~~Lm~c~wPGNVRELENC~eRtAtLs~---~~~It~~df~c  457 (574)
T TIGR01817       417 SAIRVLMSCKWPGNVRELENCVERTATLSR---SGTITRSDFSC  457 (574)
T ss_pred             HHHHHHHCCCCCCCCEEHHHHHHHHHHHCC---CCCCCCCEEEE
T ss_conf             899897517899974004437877875416---88516423664