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