HHsearch alignment for GI: 254780725 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=1.3e-37  Score=250.44  Aligned_cols=257  Identities=17%  Similarity=0.211  Sum_probs=192.0

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             37999746988775689999999999626994999978798986033438998789888631845612433765320248
Q gi|254780725|r  162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYA  241 (427)
Q Consensus       162 rvIav~g~KGGvGkTTiA~nLA~~LA~~~~~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~  241 (427)
T Consensus         2 r~Iai~G-KGGVGKTTtavNLA~aLa~-~GkkVlliDaDpq~~~t~~l~g~~~~~~~~~~l~~~~~~~-~~~~~~i~~~~   78 (270)
T cd02040           2 RQIAIYG-KGGIGKSTTTQNLSAALAE-MGKKVMIVGCDPKADSTRLLLGGKAIPTVLDTLREKGEVE-LELEDVIFEGF   78 (270)
T ss_pred             CEEEEEC-CCCCCHHHHHHHHHHHHHH-CCCEEEEECCCCCCCHHHHHCCCCCCCCHHHHHHHCCCCC-CCHHHHEECCC
T ss_conf             5899979-9857789999999999998-7994999865799851346529988882899887527776-53889613376


Q ss_pred             CCEEEEECCCCCCCHH-----CCCHHHHHHHHHHHHHCCCEEEECCCCCCC--HHHHH-HHHHCCCCCCCCCCCHHHHHH
Q ss_conf             9806872487612032-----079999999899985128889973888889--89999-986201254357877688999
Q gi|254780725|r  242 ENLSILTAPAMLSRTY-----DFDEKMIVPVLDILEQIFPLVILDVPHVWN--SWTQE-VLTLSDKVVITTSLDLAGLRN  313 (427)
Q Consensus       242 ~gL~lL~a~~~~~~~~-----~~~~~~l~~ll~~l~~~yd~VIiD~p~~~~--~~~~~-~L~~AD~vviV~~p~~~slr~  313 (427)
T Consensus        79 ~gv~~ip~~~~~~~~~~~gr~~~~~~~ll~~l~~~~~~~D~iliD~lg~~~~~~~~~~i~~~~ad~viiv~t~e~~al~~  158 (270)
T cd02040          79 GGIKCVESGGPEPGVGCAGRGVITAINLLEELGAYEDDLDFVIYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMALYA  158 (270)
T ss_pred             CCCEEEECCCCCCCCHHCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCHHHHCCCCEEEEECCCCHHHHHH
T ss_conf             77064105996435121240078899999985434406988998235633321232303553388799962881899999


Q ss_pred             HHHHHHHHHHCCCC-CCCCE-EEEECCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEECCCCHHHH
Q ss_conf             99999999981987-67538-99956589875200599999984895379906879999998847961898889998999
Q gi|254780725|r  314 SKNLIDVLKKLRPA-DKPPY-LVLNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIAN  391 (427)
Q Consensus       314 a~~ll~~l~~~~~~-~~~~~-iVlNr~~~~~~~~i~~~~~~~~lg~~~~~~IP~D~~~~~~A~~~G~pi~e~~p~s~~a~  391 (427)
T Consensus       159 ~~~l~k~i~~~~~~~~~~l~gvv~~~~~~-~~~~~~~~~~~~~~~~~~l~~IP~d~~-v~EA~~~g~pi~~~~P~S~~A~  236 (270)
T cd02040         159 ANNICKGILKYAKSGGVRLGGLICNSRNT-DREDELIDAFAKRLGTQMIHFVPRDNV-VQRAELRGKTVIEYDPESKQAD  236 (270)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEECCCCC-CHHHHHHHHHHHHHCCCEEEECCCCHH-HHHHHHCCCEEEEECCCCHHHH
T ss_conf             99999999999834697479998378665-137899999999859952877799717-8751342970799798998999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             99999999852212232111058999987423
Q gi|254780725|r  392 LLVDFSRVLMGRVTVSKPQSAMYTKIKKIFNM  423 (427)
Q Consensus       392 ~~~~La~~i~gr~~~~~~k~~~~~~l~~lf~r  423 (427)
T Consensus       237 ay~~LA~eii~~~~~~~p~p~~~~~~~~~~~~  268 (270)
T cd02040         237 EYRELARKIVENKLLVIPTPLEMDELEELLME  268 (270)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
T ss_conf             99999999984899989888997899999996