HHsearch alignment for GI: 254780831 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=100.00  E-value=6.6e-42  Score=299.29  Aligned_cols=228  Identities=25%  Similarity=0.285  Sum_probs=169.1

Q ss_pred             CCEECCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCEECCCCCCCCCC--------CCC---CCCCCCCC
Q ss_conf             2010244666542578999989872357750698822467876531000245631123--------344---57663223
Q gi|254780831|r   96 KFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLLKISGKVEISD--------KKF---LKPKENYG  164 (341)
Q Consensus        96 ~iiav~SgKGGVGKSt~s~nLa~ala~~G~~V~liDaDi~~ps~~~~lg~~~~~~~~~--------~~~---i~p~~~~g  164 (341)
T Consensus         2 r~Iai~-GKGGVGKTTtavNLA~aLa~~GkkVlliDaDpq~~~t~~l~g~~~~~~~~~~l~~~~~~~~~~~~~i~~~~~g   80 (270)
T cd02040           2 RQIAIY-GKGGIGKSTTTQNLSAALAEMGKKVMIVGCDPKADSTRLLLGGKAIPTVLDTLREKGEVELELEDVIFEGFGG   80 (270)
T ss_pred             CEEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHCCCCCCCCHHHHHHHCCCCCCCHHHHEECCCCC
T ss_conf             589997-9985778999999999999879949998657998513465299888828998875277765388961337677


Q ss_pred             EEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCHHHH----CCCCCCEEEEECCCCCH
Q ss_conf             03223334355221000134202478999867521377758997455644421000000----02234026742144311
Q gi|254780831|r  165 IKIMSMASLVDENVAMIWRGPMVQSAIMHMLHNVVWGQLDFLLIDMPPGTGDAHLTIAQ----KIPLSGVVIVSTPQDLA  240 (341)
Q Consensus       165 i~~~s~g~l~~~~~~~~~rg~~~~~~l~~~l~~~~w~~~D~liiD~ppG~gd~~lsl~~----~~~~~~~iiVttP~~~s  240 (341)
T Consensus        81 v~~ip~~~~-~~~~~~~gr~~~~~~~ll~~l-~~~~~~~D~iliD~---lg~~~~~~~~~~i~~~~ad~viiv~t~e~~a  155 (270)
T cd02040          81 IKCVESGGP-EPGVGCAGRGVITAINLLEEL-GAYEDDLDFVIYDV---LGDVVCGGFAMPIREGKAQEIYIVTSGEMMA  155 (270)
T ss_pred             CEEEECCCC-CCCCHHCCCCHHHHHHHHHHH-HHHHCCCCEEEEEC---CCCCCCCHHHCHHHHCCCCEEEEECCCCHHH
T ss_conf             064105996-435121240078899999985-43440698899823---5633321232303553388799962881899


Q ss_pred             HHHHH---HHHHHHHCCC-CCHHHHHHHHCCCCCCCCCCEEECCCCCHHHHHHHHHCCCEEEECCCCHHHHHHHCCCCCE
Q ss_conf             34566---6777640012-2114455442024587788665124776589999984797898827998999750288217
Q gi|254780831|r  241 LIDVK---RAISMYQKMN-IPIIGMIENMSYFLASDTGKKYDLFGNGGARFEAEKIGIPFLESVPFDMDVRVLSDLGIPI  316 (341)
Q Consensus       241 ~~da~---r~~~~~~~~~-~~i~GiV~NMs~~~~~~~~~~~~~fg~~~~~~~a~~~~i~~lg~IP~d~~i~~a~~~g~P~  316 (341)
T Consensus       156 l~~~~~l~k~i~~~~~~~~~~l~gvv~~~----------~~~~~~~~~~~~~~~~~~~~~l~~IP~d~~v~EA~~~g~pi  225 (270)
T cd02040         156 LYAANNICKGILKYAKSGGVRLGGLICNS----------RNTDREDELIDAFAKRLGTQMIHFVPRDNVVQRAELRGKTV  225 (270)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEEECC----------CCCCHHHHHHHHHHHHHCCCEEEECCCCHHHHHHHHCCCEE
T ss_conf             99999999999999834697479998378----------66513789999999985995287779971787513429707


Q ss_pred             EEECCCCHHHHHHHHHHHHHHHH
Q ss_conf             99779998999999999999998
Q gi|254780831|r  317 VVHNMNSATSEIYQEISDRIQQF  339 (341)
Q Consensus       317 v~~~p~s~~a~~~~~iA~~i~~~  339 (341)
T Consensus       226 ~~~~P~S~~A~ay~~LA~eii~~  248 (270)
T cd02040         226 IEYDPESKQADEYRELARKIVEN  248 (270)
T ss_pred             EEECCCCHHHHHHHHHHHHHHHC
T ss_conf             99798998999999999999848