HHsearch alignment for GI: 254780829 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=96.50  E-value=0.0035  Score=40.01  Aligned_cols=90  Identities=22%  Similarity=0.325  Sum_probs=62.9

Q ss_pred             HHHHHHHHHHCEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHH---CCCEEEEE
Q ss_conf             899999862030486899999999998778864086444466566866996798886899999999970---78779714
Q gi|254780829|r    9 PREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLA---GAPFIKVE   85 (437)
Q Consensus         9 P~~i~~~Ld~~VvGQ~~AKk~lavav~nhy~R~~~~~~~~~e~~psNiLLiGPtGtGKTlLAktLA~~l---~VPF~~~d   85 (437)
T Consensus       203 ~~~~~~~~~~~i~G~Spam~~v~~~~~------~vA~~n------STVLlRGESGTGKEl~A~AIH~~SpR~~~PFVK~N  270 (574)
T TIGR01817       203 AARRRSGKEDGIVGKSPAMRQVVDQIK------VVARSN------STVLLRGESGTGKELIAKAIHELSPRAKRPFVKLN  270 (574)
T ss_pred             HHHHHCCCCCCCCCCCHHHHHHHHHHH------HHCCCC------CEEEEECCCCCCHHHHHHHHCCCCCCCCCCCEEEE
T ss_conf             123312344740124789999998865------201317------66785056574433444234046645578854500


Q ss_pred             CCCEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3410121223431013467888765212789985654
Q gi|254780829|r   86 VTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEV  122 (437)
Q Consensus        86 aT~ftE~gyvG~DVes~i~~l~~~a~~~~~~a~~~i~  122 (437)
T Consensus       271 CAALse~l------------LESELFGHEKGAFTGA~  295 (574)
T TIGR01817       271 CAALSETL------------LESELFGHEKGAFTGAV  295 (574)
T ss_pred             CCCCCCCH------------HHHHHHCCCCHHHHHHH
T ss_conf             64477611------------24545134301468887