HHsearch alignment for GI: 254780270 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=98.16 E-value=9.1e-06 Score=62.48 Aligned_cols=277 Identities=24% Similarity=0.404 Sum_probs=167.5
Q ss_pred HHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHH---CCCEEEEECCCCCC---HHHHCCCCCC-CCCC---
Q ss_conf 999999999984244467359986056565027999999770---88249986188888---8883563200-1456---
Q gi|254780270|r 349 ERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKAT---GRQYVRMSLGGVYD---EADIRGHRRT-YIGS--- 418 (820)
Q Consensus 349 ~rile~lav~~~~~~~~g~il~l~gppgvGKts~~~sia~al---~r~f~~islgg~~d---~~~i~gh~~t-y~ga--- 418 (820)
T Consensus 222 ~~v~~~~--~~vA~~-nS-TVLlRGESGTGKEl~A~AIH~~SpR~~~PFVK~NCAALse~lLESELFGHEKGAFTGA~~~ 297 (574)
T TIGR01817 222 RQVVDQI--KVVARS-NS-TVLLRGESGTGKELIAKAIHELSPRAKRPFVKLNCAALSETLLESELFGHEKGAFTGAVAQ 297 (574)
T ss_pred HHHHHHH--HHHCCC-CC-EEEEECCCCCCHHHHHHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 9999886--520131-76-6785056574433444234046645578854500644776112454513430146888751
Q ss_pred CCHHHHHHHHHCCCCCEEEEEECHHHHHHHCCCCHHHHHHHHC--------------------------CCC---CCCCE
Q ss_conf 7128999998327887399993315542311771155665540--------------------------600---16813
Q gi|254780270|r 419 MPGRIIQSLKRAKRSNPLLLLDEIDKMGSDLRGDPSAALLEVL--------------------------DPA---QNSSF 469 (820)
Q Consensus 419 ~pg~ii~~l~~~~~~npv~~ldeidk~~~~~~gdp~~allevl--------------------------dp~---qn~~f 469 (820)
T Consensus 298 RkGRFE--lAdGGT----LFLDEIGEISPaFQ----AKLLRVLQEGEFERVGG~~TlKVdVRlvaATNrdLE~aV~~GeF 367 (574)
T TIGR01817 298 RKGRFE--LADGGT----LFLDEIGEISPAFQ----AKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGEF 367 (574)
T ss_pred CCCCEE--ECCCCC----CCCCCCCCCCHHHH----HHHHHHHHCCCEEEECCCEEEEEEEEEEECCCCCHHHHHHCCCC
T ss_conf 777533--027883----20000146785688----89988752100253278724887367886137355889727897
Q ss_pred E-EEECCCCCCCCCEEEEEECCCCC-CCHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCHHHHH
Q ss_conf 3-20103523644279999348655-44131172479982587868999899986089899862578131-322899999
Q gi|254780270|r 470 V-DHYLEVEYDLSDVMFIMTANTLN-IPLPLMDRMEIIRIAGYTEEEKLQIAKNHLVKKVLTEHALKQEE-CCISDGVLL 546 (820)
Q Consensus 470 ~-d~y~~~~~dls~v~fi~tan~~~-i~~~l~drme~i~~~~y~~~ek~~i~~~~l~p~~~~~~~~~~~~-~~~~~~~i~ 546 (820)
T Consensus 368 RaDLYY----Rin---------VvPl~lPPLRER~~DIP-----------~LA~~fL~kf~~en~R---~mL~~~~~Ai~ 420 (574)
T TIGR01817 368 RADLYY----RIN---------VVPLILPPLRERREDIP-----------LLAEAFLEKFNRENGR---PMLTLSPSAIR 420 (574)
T ss_pred CCHHHH----HHH---------HHHHHCCCCCCCCCHHH-----------HHHHHHHHHHHHHHCC---CEEEECHHHHH
T ss_conf 302355----442---------22340787778731168-----------9999999987665187---20322678998
Q ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCH--------HHHHHHHCCCC-CC---CCCHHCCCCCCCC
Q ss_conf 997317741023478887999989876542117852012796--------78675305200-03---3200022336500
Q gi|254780270|r 547 DIIRLFTHEAGVRSFERALMKIARKAVTKIVKNSDTTVSINE--------NNLQDYLGVPR-YK---YGKIEGEDQVGIV 614 (820)
Q Consensus 547 ~ii~~Yt~EaGvR~l~r~i~~i~r~~~~~~~~~~~~~~~i~~--------~~l~~~lg~~~-~~---~~~~~~~~~~G~v 614 (820)
T Consensus 421 ~Lm~-c~wPGNVRELENC~e----RtAtLs-~~----~~It~~df~c~~~~c~s~~L~~~~~~~~~~P~~~~~p~~~~~~ 490 (574)
T TIGR01817 421 VLMS-CKWPGNVRELENCVE----RTATLS-RS----GTITRSDFSCQSGQCLSKMLAKSSAYKKVDPAVPDAPLGAVSI 490 (574)
T ss_pred HHHC-CCCCCCCEEHHHHHH----HHHHHC-CC----CCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEC
T ss_conf 9751-789997400443787----787541-68----8516423664278888888888887788778777888886532
Q ss_pred CEEEECCCCCEEEE-E-EEEEECCCCCEEECC---------CHHHHHHH---HHHHHHHHHHHHHHH-CCCCHH----HH
Q ss_conf 00000001680799-9-999974899724432---------56899999---999999999998886-299855----74
Q gi|254780270|r 615 TGLAWTEVGGEILT-V-EGVIMPGKGEITITG---------NLKEIMKE---SILAASSYVRSKATT-FGIIPS----AF 675 (820)
Q Consensus 615 ~GLa~t~~GG~~l~-I-E~~~~~g~g~l~lTG---------~lg~vmkE---S~~~A~s~~k~~~~~-~~~~~~----~~ 675 (820)
T Consensus 491 ~pla~~~~----~PA~~~pa~~~~p~~~~~~gteaCPavA~~l~e--RERli~AlE~aGWVQAKAARlLg~TPRQVgYal 564 (574)
T TIGR01817 491 VPLAETTA----LPAVESPASAALPAEVGLSGTEACPAVAPTLSE--RERLIAALEKAGWVQAKAARLLGLTPRQVGYAL 564 (574)
T ss_pred CCCCCCCC----CCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC--HHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHH
T ss_conf 57301467----752205433467766777875545567887231--789999997515379999997378655899999
Q ss_pred HHCCCEE
Q ss_conf 2078147
Q gi|254780270|r 676 NEINIHV 682 (820)
Q Consensus 676 ~~~diHi 682 (820)
T Consensus 565 r~~~I~~ 571 (574)
T TIGR01817 565 RKLNIEV 571 (574)
T ss_pred HHCCCCC
T ss_conf 8848765