HHsearch alignment for GI: 254780627 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=95.78 E-value=0.051 Score=34.36 Aligned_cols=301 Identities=16% Similarity=0.187 Sum_probs=171.5
Q ss_pred HHHHHHHHHCCHHH--HHHHCC-CEE-EEEEECCEEEEEE----CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf 99999998669788--974302-405-7885399898983----898999999998999999999986277665078972
Q gi|254780627|r 41 IVSSRLKNQVGPDV--YASWFQ-RLK-FHSVLHNIVHLSV----PTNFLKAWIKNRYLETITKLFQEEHSRIQGVEILVR 112 (502)
Q Consensus 41 ~il~~Lk~~l~~~~--F~tWi~-pL~-~i~~e~~~L~L~v----Pn~FikdwIe~~Y~~~I~~al~~~~g~~~~I~i~i~ 112 (502)
T Consensus 101 lF~d~~~~~l~~~~e~~~~FIgVPi~~~d~~~~GvL~~~r~~~g~~~~~~~~-~vRFL~mVANL~gQtvRL~r~~~~-~~ 178 (574)
T TIGR01817 101 LFLDRLSEVLSDPGEIPVPFIGVPIKNADSETIGVLAIDRIKEGASRERLEE-EVRFLEMVANLIGQTVRLHRLVAA-RR 178 (574)
T ss_pred HHHHHHHHHHCCCCCEECCEEECCCCCCCCCCCEEEEEEECCCCCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHHH-HH
T ss_conf 4577645540588743111340226677777112267720688884134614-543799999999878887445654-20
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCHHHH--HHHHHHHHHCCCCC
Q ss_conf 1455555555566554444753322322212355444454344557644788763288614789--99999998241001
Q gi|254780627|r 113 SVALPSVEKTASSPSITKLSPINTNISKSPIILGKQTISPVFGSPLDSRFVFSTFIEGSSNRVA--LTAAQSIAEVDSHG 190 (502)
Q Consensus 113 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~s~LNpryTFDnFVVG~sN~lA--~aAAkaVAe~pg~~ 190 (502)
T Consensus 179 ------~~~~~e~~~-~~~----~~---------~~~~sGa~~~~~~~~~~~~~~i~G~Spam~~v~~~~~~vA~~n--- 235 (574)
T TIGR01817 179 ------ERLIAEAAQ-LSK----QL---------RDKKSGAEPEAARRRSGKEDGIVGKSPAMRQVVDQIKVVARSN--- 235 (574)
T ss_pred ------HHHHHHHHH-HHH----HH---------CCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCC---
T ss_conf ------110556777-887----52---------1400156554123312344740124789999998865201317---
Q ss_pred CCCCCCCEEEEECCCCCCHHHHHHHHHHHH--HHHCCCCCEEE-------EEHHHHHHH---HHHHHHCCCHHHHHHHHH
Q ss_conf 365555548986278888579999999999--86306881686-------469888999---999986198899999974
Q gi|254780627|r 191 YTTVRLNPLFIHASVGLGKTHLLQAIANAS--IKRQPNLRVVY-------LTAEYFMWR---FASAIRDNCALNLKDSLR 258 (502)
Q Consensus 191 ~~~~~~NPLfi~G~~GlGKTHLl~ai~~~~--~~~~~~~~v~y-------~~~e~F~~~---~~~a~~~~~~~~fr~~~r 258 (502)
T Consensus 236 ------STVLlRGESGTGKEl~A~AI-H~~SpR~~~PFVK~NCAALse~lLESELFGHEKGAFTGA~~~Rk-----GRFE 303 (574)
T TIGR01817 236 ------STVLLRGESGTGKELIAKAI-HELSPRAKRPFVKLNCAALSETLLESELFGHEKGAFTGAVAQRK-----GRFE 303 (574)
T ss_pred ------CEEEEECCCCCCHHHHHHHH-CCCCCCCCCCCEEEECCCCCCCHHHHHHHCCCCHHHHHHHHHCC-----CCEE
T ss_conf ------66785056574433444234-04664557885450064477611245451343014688875177-----7533
Q ss_pred HC--CHHHHHHHHHH----CCC--C-HHHHHHHHHHHHHHC--------CCEEEEECCCCHHHH---CCCCHHHHHHHHC
Q ss_conf 03--10205444453----175--0-699999999998856--------987999648756761---3630345765302
Q gi|254780627|r 259 NI--DLLLIDDMQFL----QGK--L-IQHEFCHLLNSLLDS--------AKQVVAAADRPPSEL---ESLDPRIRSRLQG 318 (502)
Q Consensus 259 ~~--DvLliDDiqfl----~gk--~-tqee~f~~~n~l~~~--------gkqiv~tsd~~P~~l---~~l~~rL~SR~~~ 318 (502)
T Consensus 304 lAdGGTLFLDEIGEISPaFQAKLLRVLQE------GEFERVGG~~TlKVdVRlvaATNrdLE~aV~~GeFRaDLYYRin- 376 (574)
T TIGR01817 304 LADGGTLFLDEIGEISPAFQAKLLRVLQE------GEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYYRIN- 376 (574)
T ss_pred ECCCCCCCCCCCCCCCHHHHHHHHHHHHC------CCEEEECCCEEEEEEEEEEECCCCCHHHHHHCCCCCCHHHHHHH-
T ss_conf 02788320000146785688899887521------00253278724887367886137355889727897302355442-
Q ss_pred CEEEEECCC-------CHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 115775158-------8899999999999886431168-9789899999985-027888999999999999863024687
Q gi|254780627|r 319 GVSVPLGLH-------DYEMRFSILKNRLAISQKEDPK-LNINEEVLMHVAR-TVTTSGRELDGAFNQLVFRHSFAPILT 389 (502)
Q Consensus 319 Gl~~~i~~P-------d~e~r~~Il~~k~~~~~~~~~~-~~l~~~v~~~la~-~~~~~vR~Legal~~l~~~~~~~~~~~ 389 (502)
T Consensus 377 --VvPl~lPPLRER~~DIP~LA~~fL~kf~~e--n~R~mL~~~~~Ai~~Lm~c~wPGNVRELENC~eRtAtLs~-~~~It 451 (574)
T TIGR01817 377 --VVPLILPPLRERREDIPLLAEAFLEKFNRE--NGRPMLTLSPSAIRVLMSCKWPGNVRELENCVERTATLSR-SGTIT 451 (574)
T ss_pred --HHHHHCCCCCCCCCHHHHHHHHHHHHHHHH--HCCCEEEECHHHHHHHHCCCCCCCCEEHHHHHHHHHHHCC-CCCCC
T ss_conf --223407877787311689999999987665--1872032267899897517899974004437877875416-88516
Q ss_pred H
Q ss_conf 7
Q gi|254780627|r 390 A 390 (502)
Q Consensus 390 ~ 390 (502)
T Consensus 452 ~ 452 (574)
T TIGR01817 452 R 452 (574)
T ss_pred C
T ss_conf 4