HHsearch alignment for GI: 254780842 and conserved domain: TIGR01812

>TIGR01812 sdhA_frdA_Gneg succinate dehydrogenase or fumarate reductase, flavoprotein subunit; InterPro: IPR014006 Succinate:quinone oxidoreductase (1.3.5.1 from EC) refers collectively to succinate:quinone reductase (SQR, or Complex II) and quinol:fumarate reductase (QFR) . SQR is found in aerobic organisms, and catalyses the oxidation of succinate to fumarate in the citric acid cycle and donates the electrons to quinone in the membrane. QFR can be found in anaerobic cells respiring with fumarate as terminal electron acceptor. SQR and QFR are very similar in composition and structure, despite catalysing opposite reactions in vivo. They are thought to have evolved from a common ancestor, and in Escherichia coli they are capable of functionally replacing each other . Succinate:quinone oxidoreductases consist of a peripheral domain, exposed to the cytoplasm in bacteria and to the matrix in mitochondria, and a membrane-integral anchor domain that spans the membrane (Fig. 1). The peripheral part, which contains the dicarboxylate binding site, is composed of a flavoprotein subunit, with one covalently bound FAD, and an iron-sulphur protein subunit containing three iron-sulphur clusters. The membrane-integral domain functions to anchor the peripheral domain to the membrane and is required for quinone reduction and oxidation. The anchor domain shows the largest variability in composition and primary sequence, being composed either of one large subunit, or two smaller subunits, which may, or may not, contain protoheme groups. This entry represents the flavoprotein subunit found in both the SQR and QFR enzymes. This subunit contains an N-terminal domain which binds the FAD cofactor, a central catalytic domain with an unsual fold, and a C-terminal domain whose role is unclear , , . The dicarboxylate binding site is located between the FAD and catalytic domains..
Probab=98.39  E-value=2.2e-06  Score=65.80  Aligned_cols=152  Identities=24%  Similarity=0.343  Sum_probs=87.5

Q ss_pred             EEEEECCCHHHHHHHHHHHHCC---CEEEEEECCCCCCC----------------------CC---------EEEE----
Q ss_conf             2999979089999999999789---85999828855557----------------------83---------6888----
Q gi|254780842|r    5 DVIIIGSGLAGSVAAIGAAKKG---FLTALVSPRSFLQD----------------------LR---------TTML----   46 (384)
Q Consensus         5 DV~IvGaG~aGl~lA~~L~~~g---~~v~iiE~~~~~~~----------------------~r---------~~~l----   46 (384)
T Consensus         1 D~vIVGaGgAGlRAA~e~a~~gPp~~~~AvisKvyP~RSHtvAAQGG~~Aal~~n~d~~D~~e~H~yDTVKGsDyLaDQD   80 (636)
T TIGR01812         1 DVVIVGAGGAGLRAAVEAAKAGPPNLNVAVISKVYPTRSHTVAAQGGIAAALANNVDPDDSWEWHAYDTVKGSDYLADQD   80 (636)
T ss_pred             CEEEECCCHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCHHHH
T ss_conf             97888186689999999973577961079995569885201535678999957786432072123041101442132589


Q ss_pred             --------CHHHHHHHHHCCCHHHHHHCCCCCCCEE------EEECCCCCCCCCCCCCCCHHCCCCCC-CCHHH------
Q ss_conf             --------7889999998899478886047123418------99425765545444345022287531-20111------
Q gi|254780842|r   47 --------MGEGIDFLKEINVWDFLQDIAEPVSSFR------LVDITDRLITAPDAIFHSSEIGLDAF-GYNIP------  105 (384)
Q Consensus        47 --------~~~s~~~L~~lGl~~~l~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~-g~~i~------  105 (384)
T Consensus        81 Ave~~~~~AP~~v~eLe~wG~---------PfSR~~kGDRmaiinaqk--ttiteeDfRDG~IaQR~FGG~~~~~Gg~~a  149 (636)
T TIGR01812        81 AVEYMCKEAPKAVLELERWGV---------PFSRLPKGDRMAIINAQK--TTITEEDFRDGRIAQRPFGGASFDYGGAAA  149 (636)
T ss_pred             HHHHHHHHCCHHHHHHHHCCC---------CCCCCCCCCEEEEEECCC--CEECCCCCCCCCEEECCCCCCCCCCCCCHH
T ss_conf             999998515178999973789---------856786776477762454--200201155883534378888865566222


Q ss_pred             -H---------CCHHHHHHHHHHHCCCCCCC-CEEEEEECCC-CE--EE----EEECCCCC--EEEEEEEEEECCCCCCC
Q ss_conf             -0---------00000001236647983234-2056530268-71--78----98302320--12111235303754320
Q gi|254780842|r  106 -N---------HVLMESFAEKISQDPLIHCF-DALANEIQIG-EE--EV----TILLSTGQ--QIVGQFLIGSDGRNSSV  165 (384)
Q Consensus       106 -r---------~~L~~~L~~~~~~~~~~~~~-~~~v~~i~~~-~~--~v----~v~~~dg~--~i~adlvVgADG~~S~v  165 (384)
T Consensus       150 ~RTcyAADkTGh~~LHTLye~~l~~~~V~ff~E~fa~~L~~~~~~GP~~~Gvva~~l~~G~~~~~~AKaVv~ATGG~GR~  229 (636)
T TIGR01812       150 RRTCYAADKTGHALLHTLYEQCLKLDGVEFFNEYFALDLILDQDGGPRVRGVVAYDLKTGEIVFFRAKAVVLATGGYGRV  229 (636)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEEEEECCEEEEECCCHHH
T ss_conf             13420012113147898999985379942753888877887458986799999998058808999607489830651021


Q ss_pred             CC
Q ss_conf             00
Q gi|254780842|r  166 RR  167 (384)
Q Consensus       166 R~  167 (384)
T Consensus       230 Y~  231 (636)
T TIGR01812       230 YK  231 (636)
T ss_pred             HC
T ss_conf             03