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