HHsearch alignment for GI: 254781041 and conserved domain: cd00546

>cd00546 QFR_TypeD_subunitC Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type D as they contain two transmembrane subunits (C and D) and no heme groups. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron donor (quinol). The quinone binding site resides in the transmembrane subunits.
Probab=93.03  E-value=0.59  Score=24.58  Aligned_cols=90  Identities=8%  Similarity=0.099  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH--HHHC---CHH
Q ss_conf             99999999999999999999999999851630355467530683169999999999999999989999--9852---123
Q gi|254781041|r   24 FVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYL--IWDV---SLC   98 (129)
Q Consensus        24 ~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL--~wD~---g~g   98 (129)
T Consensus        20 r~YMlRE~T~v~~~~f~lvLl~Gl~~L~~g~~aw~~f~~flqnP~vv~lniiaL~a~L~Ha~TwF~~~Pk~m~i~v~g~~   99 (124)
T cd00546          20 RFYMLREATAVPTVWFSLVLLYGLFALGSGPESWAGFVSFLQNPIVVLLNIIALAAALLHAKTWFEMAPKVMNIIVKGER   99 (124)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCHHEEEEECCEE
T ss_conf             99999888379999999999999999806989999999998385999999999999999999999974230042178867


Q ss_pred             CCHHHHHHHHHHHHH
Q ss_conf             358999999999999
Q gi|254781041|r   99 LDKKIATQMAKINII  113 (129)
Q Consensus        99 ~~~~~~~~s~~~vl~  113 (129)
T Consensus       100 ~~~~~iv~~~wa~~~  114 (124)
T cd00546         100 VPPEAITKALWAVTA  114 (124)
T ss_pred             CCHHHHHHHHHHHHH
T ss_conf             878999999999999