HHsearch alignment for GI: 254781042 and conserved domain: cd03497

>cd03497 SQR_TypeB_1_TM Succinate:quinone oxidoreductase (SQR) Type B subfamily 1, transmembrane subunit; composed of proteins similar to Bacillus subtilis SQR. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Bacillus subtilis SQR reduces low potential quinones such as menaquinone. SQR is also called succinate dehydrogenase (Sdh) or Complex II and is part of the citric acid cycle and the aerobic respiratory chain. SQR is 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 B as they contain one transmembrane subunit and two heme groups. The heme and quinone binding sites reside on the transmembrane subunit. The transmembrane subunit of Bacillus subtilis SQR is also called Sdh cytochrome b558 subunit. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers,
Probab=98.34  E-value=4.4e-05  Score=49.55  Aligned_cols=103  Identities=13%  Similarity=0.164  Sum_probs=80.7

Q ss_pred             CHHHH--HHHHHHHHHHHHHHHHHHHHHHHH-------------CCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10899--999999999999999999999996-------------289998999999946259999999999999999840
Q gi|254781042|r   20 DGTGH--FIKQRFTAIANIPFIIFFIAFFIK-------------YGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLG   84 (130)
Q Consensus        20 ~G~~h--W~~QRiSAi~L~~l~i~~i~~~~~-------------~~~~~y~~~~~~~~~~~~~il~~l~~~~~~~Ha~lG   84 (130)
T Consensus        86 ~~~rNw~~~~qr~TGii~l~FIi~Hv~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~Yii~~la~~fHlanG  165 (207)
T cd03497          86 DYFRNWMYTLQRITGIILLVFIAWHVWHTRFAEALGHVDIQTPEAGEANLSAMRNALASPLMLIFYIIGVLAAVFHFANG  165 (207)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             41401999999999999999999999999998860654446676213589999999608099999999999999999988


Q ss_pred             HHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             48899851--277318999999999999999999999999
Q gi|254781042|r   85 MQVIIEDY--IHYRLLKIMFLFMNSCFVLLLIIFCLFSLL  122 (130)
Q Consensus        85 l~~IieDY--I~~~~~k~~~~~~~~~~~~~~~~~~i~~i~  122 (130)
T Consensus       166 lwSf~~twGit~sprsq~~~~~v~~~v~v~l~~~g~~ai~  205 (207)
T cd03497         166 LWTFLITWGITVSPRSQRVSTYVCLLVFVVVSFMGVAAIW  205 (207)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999833068999999999999999999999999998