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