HHsearch alignment for GI: 254780567 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=97.00 E-value=0.0085 Score=37.10 Aligned_cols=197 Identities=19% Similarity=0.205 Sum_probs=126.8
Q ss_pred CCCCCCCCCCEEECCCHH--HHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHH-----CCCCHHHHHHHHHH---
Q ss_conf 877668845416536189--99999985101678849998787778688999999862-----76201356764445---
Q gi|254780567|r 33 PRCLGISRDDLLVHSAIE--QAVRLIDSWPSWPSRVVILVGPSGSGKSCLANIWSDKS-----RSTRFSNIAKSLDS--- 102 (246)
Q Consensus 33 ~~~~~~~~dnFiv~~~N~--~A~~~i~~~~~~~~~~l~i~G~~GsGKTHLl~a~~~~~-----~~~~~~~~~~~~~~--- 102 (246)
T Consensus 203 ~~~~~~~~~~~i~G~Spam~~v~~~~~~vA~~-nSTVLlRGESGTGKEl~A~AIH~~SpR~~~PFVK~NCAALse~lLES 281 (574)
T TIGR01817 203 AARRRSGKEDGIVGKSPAMRQVVDQIKVVARS-NSTVLLRGESGTGKELIAKAIHELSPRAKRPFVKLNCAALSETLLES 281 (574)
T ss_pred HHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCC-CCEEEEECCCCCCHHHHHHHHCCCCCCCCCCCEEEECCCCCCCHHHH
T ss_conf 12331234474012478999999886520131-76678505657443344423404664557885450064477611245
Q ss_pred -HHHHHH-------------------HHHHHHHHHCCCCC-CHHHHHHHHH----------HHCCCCCEEEEECCCCCC-
Q ss_conf -466666-------------------65334332100376-1033545554----------311234215640354320-
Q gi|254780567|r 103 -ILIDTR-------------------KPVLLEDIDLLDFN-DTQLFHIINS----------IHQYDSSLLMTARTFPVS- 150 (246)
Q Consensus 103 -~~~~~~-------------------~~i~iddi~~~~~~-ee~lf~l~n~----------~~~~~~~iilts~~~p~~- 150 (246)
T Consensus 282 ELFGHEKGAFTGA~~~RkGRFElAdGGTLFLDEIGEISPaFQAKLLRVLQEGEFERVGG~~TlKVdVRlvaATNrdLE~a 361 (574)
T TIGR01817 282 ELFGHEKGAFTGAVAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEA 361 (574)
T ss_pred HHHCCCCHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEECCCEEEEEEEEEEECCCCCHHHH
T ss_conf 45134301468887517775330278832000014678568889988752100253278724887367886137355889
Q ss_pred --HHHHHHHHHHHHHHCCEEEECCCC----H--HHHHHHHHHHHH--HCC-CCCCHHHHHHHHHC-CCCCHHHHHHHHHH
Q ss_conf --022345667885212224507889----7--899999999866--628-97988999999940-66798999999999
Q gi|254780567|r 151 --WGVCLPDLCSRLKAATVVKISLPD----D--DFLEKVIVKMFA--DRQ-IFIDKKLAAYIVQR-MERSLVFAEKLVDK 218 (246)
Q Consensus 151 --~~~~l~DL~SRl~~g~~~~I~~pd----d--e~~~~il~k~~~--~r~-i~l~~~v~~yl~~r-~~Rs~~~l~~~l~~ 218 (246)
T Consensus 362 V~~GeFRaDLYYRinVv-Pl~lPPLRER~~DIP~LA~~fL~kf~~en~R~mL~~~~~Ai~~Lm~c~wPGNVRELENC~eR 440 (574)
T TIGR01817 362 VAKGEFRADLYYRINVV-PLILPPLRERREDIPLLAEAFLEKFNRENGRPMLTLSPSAIRVLMSCKWPGNVRELENCVER 440 (574)
T ss_pred HHCCCCCCHHHHHHHHH-HHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEECHHHHHHHHCCCCCCCCEEHHHHHHH
T ss_conf 72789730235544222-34078777873116899999999876651872032267899897517899974004437877
Q ss_pred HHHHHHHHCCCCCHH
Q ss_conf 999999847787889
Q gi|254780567|r 219 MDNLALSRGMGITRS 233 (246)
Q Consensus 219 Ld~~sl~~kr~ITi~ 233 (246)
T Consensus 441 --tAtLs~~~~It~~ 453 (574)
T TIGR01817 441 --TATLSRSGTITRS 453 (574)
T ss_pred --HHHHCCCCCCCCC
T ss_conf --8754168851642