HHsearch alignment for GI: 254780271 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=97.43 E-value=0.00027 Score=50.66 Aligned_cols=143 Identities=25% Similarity=0.445 Sum_probs=95.6
Q ss_pred CCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHH---HCCCE
Q ss_conf 998789999974203085999999999998658875212101355225683588407332176999999987---18531
Q gi|254780271|r 65 IPNPQEILRVLDEYVIGQGQAKKVLAVAVHNHYKRLAHSSKSSNVELAKSNILLVGPTGCGKTYLAQTLARI---IDVPF 141 (424)
Q Consensus 65 ~~tP~eI~~~Ld~yVIGQ~~AKkavAvAv~nh~rR~~~~~~~~~~ei~~~NILliGPTGvGKTelAr~LAk~---l~~PF 141 (424)
T Consensus 200 ~~~~~~~~~~~~~~i~G~Spam~~v~~~~----~~vA---~------~nSTVLlRGESGTGKEl~A~AIH~~SpR~~~PF 266 (574)
T TIGR01817 200 EPEAARRRSGKEDGIVGKSPAMRQVVDQI----KVVA---R------SNSTVLLRGESGTGKELIAKAIHELSPRAKRPF 266 (574)
T ss_pred CCCHHHHHCCCCCCCCCCCHHHHHHHHHH----HHHC---C------CCCEEEEECCCCCCHHHHHHHHCCCCCCCCCCC
T ss_conf 55412331234474012478999999886----5201---3------176678505657443344423404664557885
Q ss_pred EEHHHHHHHHH----HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHC-
Q ss_conf 31012211111----1035563303577887654227765422333223332002333333443210256898875310-
Q gi|254780271|r 142 TMADATTLTEA----GYVGEDVENIILKLLQAADYNVERAQRGIVYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIM- 216 (424)
Q Consensus 142 ~~vdaT~~TE~----GYvG~Dvesii~~L~~~a~~~v~~a~~~iv~iDEidKi~~~~~~~~~~~dvs~~gvq~~LLkil- 216 (424)
T Consensus 267 VK~NCAALse~lLESELFGHEKGA-FTGA~~~RkGRFElAdGGTLFLDEIGEISPa--------------FQAKLLRVLQ 331 (574)
T TIGR01817 267 VKLNCAALSETLLESELFGHEKGA-FTGAVAQRKGRFELADGGTLFLDEIGEISPA--------------FQAKLLRVLQ 331 (574)
T ss_pred EEEECCCCCCCHHHHHHHCCCCHH-HHHHHHHCCCCEEECCCCCCCCCCCCCCCHH--------------HHHHHHHHHH
T ss_conf 450064477611245451343014-6888751777533027883200001467856--------------8889988752
Q ss_pred CCCEEECCCCCCCCCCCCCEEEEECCH
Q ss_conf 587010256556432224302431000
Q gi|254780271|r 217 EGTIASVPPQGGRKHPQQEFLQVDTTN 243 (424)
Q Consensus 217 eg~~~~v~~~~grk~~~~~~~~Idt~n 243 (424)
T Consensus 332 EGEFERV---GG~-----~TlKVdVRl 350 (574)
T TIGR01817 332 EGEFERV---GGN-----RTLKVDVRL 350 (574)
T ss_pred CCCEEEE---CCC-----EEEEEEEEE
T ss_conf 1002532---787-----248873678