HHsearch alignment for GI: 254780487 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=98.65  E-value=2.3e-06  Score=59.24  Aligned_cols=183  Identities=13%  Similarity=0.084  Sum_probs=87.6

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCEECCC------------CCCCHHH--HHHHHHCCCCCCCCC---CC
Q ss_conf             983299983589874799999999998404861201388------------7380689--999985578731144---30
Q gi|254780487|r    1 MKLRLVIVGTDTSVGKTIFASALVHALNAYYWKPIQSGM------------YEETDSK--TIHRIGRIPKSHIIP---EK   63 (217)
Q Consensus         1 M~~~i~I~GT~t~vGKT~vs~~L~~~l~~~~~KPv~~G~------------~~~~D~~--~~~~~~~~~~~~~~~---~~   63 (217)
T Consensus         1 ~r-~Iai~G-KGGVGKTTtavNLA~aLa~~GkkVlliDaDpq~~~t~~l~g~~~~~~~~~~l~~~~~~~~~~~~~i~~~~   78 (270)
T cd02040           1 MR-QIAIYG-KGGIGKSTTTQNLSAALAEMGKKVMIVGCDPKADSTRLLLGGKAIPTVLDTLREKGEVELELEDVIFEGF   78 (270)
T ss_pred             CC-EEEEEC-CCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHCCCCCCCCHHHHHHHCCCCCCCHHHHEECCC
T ss_conf             95-899979-9857789999999999998799499986579985134652998888289988752777653889613376


Q ss_pred             --CCC---CCCHHHHHHHHHH---HCCCHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHCCCEEEEECCCCC
Q ss_conf             --014---5103478899985---02350788642232887999227655566767530899999747944897057765
Q gi|254780487|r   64 --WKL---RTPASPHLAAEID---GVIIDPATINPPDINDSIIIEGIGGLLVPLTTEYLFIDLIERWQFPIILCARTSLG  135 (217)
Q Consensus        64 --~~~---~~~~~~~~~~~~~---~~~i~~~~~~~~~~~D~viIEGagg~~~~~~~~~~~~dla~~l~~~vILV~~~~~g  135 (217)
T Consensus        79 ~gv~~ip~~~~~~~~~~~gr~~~~~~~ll~~l~~~~~~~D~iliD~lg~~~~~----~~~~~i~~~~ad~viiv~t~e~~  154 (270)
T cd02040          79 GGIKCVESGGPEPGVGCAGRGVITAINLLEELGAYEDDLDFVIYDVLGDVVCG----GFAMPIREGKAQEIYIVTSGEMM  154 (270)
T ss_pred             CCCEEEECCCCCCCCHHCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC----HHHCHHHHCCCCEEEEECCCCHH
T ss_conf             77064105996435121240078899999985434406988998235633321----23230355338879996288189


Q ss_pred             HHHH---HHHHHHHHHHC-CCEEEEEEECCCCCCCH---HHHHHHHCCCCEEEEECCCCCC
Q ss_conf             0457---99999999847-99079999769778005---9999986199899994788888
Q gi|254780487|r  136 TINH---SLLSLETLRNR-NINIIGIAFIGDSMPKV---EETIVKIGRIPHLGRLPKIDPI  189 (217)
Q Consensus       136 ~i~~---~~l~~~~~~~~-g~~i~GiIlN~~~~~~~---~~~le~~~~ipvLG~iP~~~~~  189 (217)
T Consensus       155 al~~~~~l~k~i~~~~~~~~~~l~gvv~~~~~~~~~~~~~~~~~~~~~~~~l~~IP~d~~v  215 (270)
T cd02040         155 ALYAANNICKGILKYAKSGGVRLGGLICNSRNTDREDELIDAFAKRLGTQMIHFVPRDNVV  215 (270)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEECCCCHHH
T ss_conf             9999999999999998346974799983786651378999999998599528777997178