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