HHsearch alignment for GI: 254780709 and conserved domain: cd02040

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.
Probab=98.51  E-value=5.3e-06  Score=62.44  Aligned_cols=165  Identities=18%  Similarity=0.232  Sum_probs=84.7

Q ss_pred             CEEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHHH------------HHHHHHHHH------------HHCC
Q ss_conf             1231135444442478999999985226742677434512456------------889999975------------3035
Q gi|254780709|r  112 HVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAA------------IDQLKIWAD------------RTSA  167 (321)
Q Consensus       112 ~vil~vG~nG~GKTTT~aKLA~~~~~~g~kV~lva~DtfR~aA------------~eQL~~~a~------------~~~v  167 (321)
T Consensus         2 r~Iai~GKGGVGKTTtavNLA~aLa~~GkkVlliDaDpq~~~t~~l~g~~~~~~~~~~l~~~~~~~~~~~~~i~~~~~gv   81 (270)
T cd02040           2 RQIAIYGKGGIGKSTTTQNLSAALAEMGKKVMIVGCDPKADSTRLLLGGKAIPTVLDTLREKGEVELELEDVIFEGFGGI   81 (270)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHCCCCCCCCHHHHHHHCCCCCCCHHHHEECCCCCC
T ss_conf             58999799857789999999999998799499986579985134652998888289988752777653889613376770


Q ss_pred             CCCCCCCCCCCH-H-----H--HHHHHHH--HHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf             321223586612-4-----5--4228999--9651487599865433321157789999899876302223430112310
Q gi|254780709|r  168 DFVCSEIGSDAA-A-----L--AYEAFKQ--AQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQVL  237 (321)
Q Consensus       168 ~~~~~~~~~dp~-~-----v--~~~a~~~--a~~~~~DvvliDTAGR~~~~~~lm~EL~ki~~v~~~~~~~~p~~~~lVl  237 (321)
T Consensus        82 ~~ip~~~-~~~~~~~~gr~~~~~~~ll~~l~~~~~~~D~iliD~lg~~~~~~~~~-~i---~-------~~~ad~viiv~  149 (270)
T cd02040          82 KCVESGG-PEPGVGCAGRGVITAINLLEELGAYEDDLDFVIYDVLGDVVCGGFAM-PI---R-------EGKAQEIYIVT  149 (270)
T ss_pred             EEEECCC-CCCCCHHCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHC-HH---H-------HCCCCEEEEEC
T ss_conf             6410599-64351212400788999999854344069889982356333212323-03---5-------53388799962


Q ss_pred             CC----CCCH-HHHHHHHHHHHH--CCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEE
Q ss_conf             23----3522-577899987643--58976999654578706999999999769889997
Q gi|254780709|r  238 DA----TTGQ-NALRQVEMFHAV--AGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLG  290 (321)
Q Consensus       238 da----~~gq-~~~~~a~~F~~~--~~~~g~I~TKlD~ta~~G~~ls~~~~~~~Pi~fig  290 (321)
T Consensus       150 t~e~~al~~~~~l~k~i~~~~~~~~~~l~gvv~~~~~~~~~~~~~~~~~~~~~~~--~l~  207 (270)
T cd02040         150 SGEMMALYAANNICKGILKYAKSGGVRLGGLICNSRNTDREDELIDAFAKRLGTQ--MIH  207 (270)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCC--EEE
T ss_conf             8818999999999999999983469747999837866513789999999985995--287