HHsearch alignment for GI: 254780548 and conserved domain: pfam02239

>pfam02239 Cytochrom_D1 Cytochrome D1 heme domain. Cytochrome cd1 (nitrite reductase) catalyses the conversion of nitrite to nitric oxide in the nitrogen cycle. This family represents the d1 heme binding domain of cytochrome cd1, in which His/Tyr side chains ligate the d1 heme iron of the active site in the oxidized state.
Probab=98.39  E-value=0.00019  Score=46.79  Aligned_cols=194  Identities=13%  Similarity=0.136  Sum_probs=98.1

Q ss_pred             CCCCCEEEEEEECCCCCCCCCEEEECCCCCE--EEEECCCCCEEEEEECCCCCEEEEEECCCCCEEEEEEECCCCCCCCC
Q ss_conf             6899848998503467644303771179717--99743798524445515895567741378730389984047741100
Q gi|254780548|r  220 SPNQQKVAYATYDDEDILRVYLMDTRIDRAP--KRIGNFRSMILAPRFSSNGKRALISVQKDEAMDIYSVDLQSNATERL  297 (447)
Q Consensus       220 SpDG~~Iay~s~~~~~~~~i~~~~~~~g~~~--~~~~~~~~~~~~p~wSPDG~~la~~~s~~g~~~I~~~d~~~~~~~~l  297 (447)
T Consensus       136 s~~~~~fvv~l---kdtgeIw~Vdy~d~~~~~~~~i-~~~~~lhD~~~d~~~Ryfl~aa~~~n--ki~vvd~~~~k~v~l  209 (369)
T pfam02239       136 SPGRPEFVVNL---KDTGEIWLVDYSDGKNLKTTFI-GAAKFLHDGGFDPDGRYFLAAANASD--KIAVWDTKRGKLVAL  209 (369)
T ss_pred             CCCCCEEEEEE---EECCEEEEEECCCCCCCCCEEE-CCCCCCCCCCCCCCCCEEEEECCCCC--CEEEEECCCCEEEEE
T ss_conf             58998699997---3289799997876887401586-65445646664798879987425887--065895588808997


Q ss_pred             ------------CCCCCCCCCEEEECCCCEEEEEECCCCCCCEEEEEECC-CCCCEEEEECCCCEEEEEECCCCCEEEEE
Q ss_conf             ------------25776432025521674789972377653315764025-67411122035300004687768889999
Q gi|254780548|r  298 ------------TNTLFINISASYSPDSSQIVFESDREGKEQLYVMQSNG-SDQKRISQDKEASYFDPVWSPQGDLIAFT  364 (447)
Q Consensus       298 ------------T~~~~~d~~p~~spDG~~I~f~Sdr~G~~qiy~~~~~g-~~~~rlT~~~~~~~~~p~wSPdG~~Iaf~  364 (447)
T Consensus       210 ~d~gk~~~p~~~~n~pH~~~G~vW~~~~~g~~~ip~i-g~~~v~v~d~~~WkvVk~I~~~G~g-~-FvkthP~s~~lwvD  286 (369)
T pfam02239       210 LDTGKTPHPGPGANMPHLEGGPVWTTSHLGDFVTPLI-GTDPVLVHDLQNWKQVKEIDVAGGG-L-FVKTHPDSRYLWVD  286 (369)
T ss_pred             ECCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEEC-CCCCCCCCCCCCCEEEEEEECCCCC-E-EEECCCCCCCEEEE
T ss_conf             3368654888748996888763078568784444314-6797776775344697898158984-7-98769899638986


Q ss_pred             E-CCCCCEEEEEEECCCCCE-EEEEC--CCCCCCCEECCCCCEEEEEEEECCCCCEEEEEEECCC
Q ss_conf             7-149915799998899967-99662--7875543788789989999950898733799998899
Q gi|254780548|r  365 K-FSGEKFAIGVMKKDGSQE-RLLVE--DSNLQAPTWSPSGRSLIFSRKKDGDTGSKLYSIDLNG  425 (447)
Q Consensus       365 ~-~~~~~~~i~~~~~~g~~~-~~lt~--~~~~e~P~wSPDG~~i~f~~~~~g~~~~~l~~~~~~G  425 (447)
T Consensus       287 ~~~~p~~~~v~viD~~tl~vv~~l~~~~gk~v~H~Ef~~~G~evwvSv-w~~~~--aivVyD~~T  348 (369)
T pfam02239       287 TFLNPDNDSVAVIDSETLEIILPLAPWPGLVVVHMEFNKRGDEVWLSV-WDGKG--ALVVYDDKT  348 (369)
T ss_pred             CCCCCCCCEEEEEECCCCCEEECCCCCCCCCEECCEECCCCCEEEEEE-ECCCC--EEEEEECCC
T ss_conf             677999887999988875277703304898388541999999999998-67999--699998988