HHsearch alignment for GI: 254780808 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=98.84  E-value=3.5e-09  Score=84.72  Aligned_cols=389  Identities=22%  Similarity=0.288  Sum_probs=205.3

Q ss_pred             CEEEECCCHHHHHHHHHHHHCC---CCEEEEE--------------------C-CH-----------HH-----------
Q ss_conf             7889889426899999998589---9899998--------------------0-76-----------26-----------
Q gi|254780808|r    7 DVIVIGGGHAGCEAAAVAAKLG---ASTALIT--------------------H-KT-----------ST-----------   40 (626)
Q Consensus         7 dViVIGaG~AG~EAA~~~Ar~G---~~v~L~~--------------------~-~~-----------~~-----------   40 (626)
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             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHCCCC---------------------------CCCC
Q ss_conf             012466700221122489999986303999999--88631488730787---------------------------8555
Q gi|254780808|r   41 IGSMSCNPAIGGLGKGHLVREIDALDGLMGRVA--DAAGIQFRVLNVKK---------------------------GPAV   91 (626)
Q Consensus        41 ~ael~Cnps~gg~akg~L~~Ei~aLgg~m~~~a--D~~~i~~r~ln~sk---------------------------GpAv   91 (626)
T Consensus        81 Ave~~~~~AP------~~v~eLe~wG~PfSR~~kGDRmai----inaqkttiteeDfRDG~IaQR~FGG~~~~~Gg~~a~  150 (636)
T TIGR01812        81 AVEYMCKEAP------KAVLELERWGVPFSRLPKGDRMAI----INAQKTTITEEDFRDGRIAQRPFGGASFDYGGAAAR  150 (636)
T ss_pred             HHHHHHHHCC------HHHHHHHHCCCCCCCCCCCCEEEE----EECCCCEECCCCCCCCCEEECCCCCCCCCCCCCHHH
T ss_conf             9999985151------789999737898567867764777----624542002011558835343788888655662221


Q ss_pred             CCHHHHHHHHHHHH--HHHHHHHCCCCCEEEHH-HHCCCCCC-CC--CEEEEE-----ECCCCCCCCCCCCCCCCCCCHH
Q ss_conf             34678784999999--99999970899689800-10112025-88--113222-----0358633445433346643101
Q gi|254780808|r   92 RGPRTQADRELYRL--AMQREILSQENLDVIQG-EVAGFNTE-KN--IISSIV-----MQDNSMIRCSTVVLTTGTFLRG  160 (626)
Q Consensus        92 ~alraqvDR~~fs~--~vt~~l~~~pni~i~~~-eV~~l~~~-~~--~~~~v~-----~~~g~~~~~~~viiatGtfl~g  160 (626)
T Consensus       151 RTc-yAADkTGh~~LHTLye~~l~~~~V~ff~E~fa~~L~~~~~~GP~~~Gvva~~l~~G~~~~~~AKaVv~ATGG~---  226 (636)
T TIGR01812       151 RTC-YAADKTGHALLHTLYEQCLKLDGVEFFNEYFALDLILDQDGGPRVRGVVAYDLKTGEIVFFRAKAVVLATGGY---  226 (636)
T ss_pred             HHH-HHHCCCCHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEEEEECCEEEEECCC---
T ss_conf             342-0012113147898999985379942753888877887458986799999998058808999607489830651---


Q ss_pred             HHHHHHCCCCCCCCCC-CCCCCCCCHHHHHHHHCCCCCCCCCCHHHHCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             3444320233222475-111331000010112005444454410110000134432114787668777435657800000
Q gi|254780808|r  161 VIHIGKLKIPAGRMGD-SPSNSLFNSFMKFDFDTGRLKTGTPARLDGKTIIWDKTEKQFADERLIPFSFMTDKITNRQIE  239 (626)
Q Consensus       161 ~~~~g~~~~~~gr~~~-~~s~~ls~~l~~~~~~~~r~ktgtppri~~~sidf~~~e~q~~d~~~~~~s~~~~~~~~~q~~  239 (626)
T Consensus       227 -----------GR~Y~~~tTNa~~~TG------------------DG~A~AlraG~PqL~D-----MEFvQFHPTGL---  269 (636)
T TIGR01812       227 -----------GRVYKFTTTNAHINTG------------------DGLAMALRAGVPQLKD-----MEFVQFHPTGL---  269 (636)
T ss_pred             -----------HHHHCCCCCCCEEECC------------------CHHHHHHHHCCCCCCC-----CCCEECCCCCC---
T ss_conf             -----------0210304454422354------------------0688888734643168-----44050367455---


Q ss_pred             CCCCCCCCCHHHHHHHCCCC---CCCCCCCCCCCCCC--CCCCCCCCCC-------------------CCCCCCC-CCCE
Q ss_conf             00012320014777640245---75414432356422--2553212335-------------------6764334-5201
Q gi|254780808|r  240 CGITRTNLETHRIIMENIKH---SAIYSGDIKSYGPR--YCPSIEDKIV-------------------RFGERNG-HQIF  294 (626)
Q Consensus       240 ~~~~~t~~~~~~~~~~~~~~---~~~~~g~~~~~gpr--ycPsie~k~~-------------------~~~~~p~-h~Vq  294 (626)
T Consensus       270 --------~~sGiL~tEgcRGEGGyL~N~~GeRFM~ryGYAPetP~k~eLApRDvVSRa~~~EireGRGv~~~~~k~~v~  341 (636)
T TIGR01812       270 --------APSGILITEGCRGEGGYLINKEGERFMERYGYAPETPEKMELAPRDVVSRAMVTEIREGRGVGSGPGKDYVY  341 (636)
T ss_pred             --------CCCCEEEEEEEECCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCEEE
T ss_conf             --------667717740133276168678753103446888788750004787699999999998448889887887788


Q ss_pred             E--EECCCCCCEEEECCCCCCCCHHHHHH--------HHHH-HHHHHHCCEEEECCHHHHCCC-CHHH-----HHH-HHH
Q ss_conf             3--01578776454347766689889999--------9987-543400100110001211023-5456-----567-765
Q gi|254780808|r  295 L--EPEGLNTDVVYPNGISTALPEEIQHQ--------FIRT-IPGLEKVNIIRPGYAIEYDYI-NPKE-----LFP-TLE  356 (626)
Q Consensus       295 L--rpE~~~~~~~n~vGFqTsL~~~~Q~r--------v~r~-IPGLEnAef~R~Gy~ieyd~~-~P~~-----L~~-tLe  356 (626)
T Consensus       342 LDLrHLGee~-------i~~RLP~i~E~A~~f~GVDPv~~pWiP-------VrPt--~HY~MGGI~T~~~G~~~~~D~~~  405 (636)
T TIGR01812       342 LDLRHLGEEK-------IEERLPQIRELAKTFAGVDPVKEPWIP-------VRPT--AHYSMGGIDTNYRGQVIGEDAKN  405 (636)
T ss_pred             EEHHHCCHHH-------HHHCCHHHHHHHHHHCCCCCCCCCCCC-------CCCC--CCCCCCCEEECCCCEEECCCCCC
T ss_conf             7640134788-------852075689999970488830057626-------4564--44118278445842487016788


Q ss_pred             HH-CCCEEEEEEEEECCC----------HHHHHHHHHHHHHHHHHHHCC-CCCC--CC---CCCCCCHHHHHHHHHHCCC
Q ss_conf             40-334156621330433----------466666677899999874203-3456--54---6532107999999886078
Q gi|254780808|r  357 TK-KISGLFLAGQINGTT----------GYEEAAAQGLVAGINSARKSN-KLDC--IC---FSRTDSYIGVMIDDLTSKG  419 (626)
Q Consensus       357 ~k-~~~~LffAGQI~Gte----------GYeEAAAqGl~AGiNa~~~~~-~~~p--~~---l~R~eaYiGVlIDDLitkg  419 (626)
T Consensus       406 ~~~iv~GLfAaGE~ACVSVHGANRLGsNSLle~vVFGr~aG~~~ae~~~~~~~~neL~~~~~~~~~~~~~~~~~~~~~~~  485 (636)
T TIGR01812       406 NDSIVKGLFAAGECACVSVHGANRLGSNSLLELVVFGRIAGEAAAEYLAKTGVDNELAADLEEEEVKKEEALIDLLKEEG  485 (636)
T ss_pred             CCCCCCCEEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             88621010220102220341213060567999999979999999999860688631133454458999999999730367


Q ss_pred             CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH-HCCCCC
Q ss_conf             774024420001221211578713668887877378838999999999999999999876-336883
Q gi|254780808|r  420 VLEPYRMFTSRAEYRISLRPDNADNRLTPIGMKLGCIGERRQKRFAKYIQEYNFLRSLLK-SLVLTS  485 (626)
Q Consensus       420 ~~EPYRMfTSRAEyRL~LR~DNAd~RLt~~g~~~GLv~~~r~~~~~~k~~~~~~~~~~l~-~~~~~p  485 (626)
T Consensus       486 ~~-~~~~a~ir~~l~~~M~~~~gvFR--------------~~~~l~~a~~~i~eL~eR~~~~v~i~D  537 (636)
T TIGR01812       486 NG-GERVAQIREELQETMEANVGVFR--------------TEELLKKAVDEIEELRERRYKNVKIND  537 (636)
T ss_pred             CC-CCCHHHHHHHHHHHHHCCCEEEE--------------CCHHHHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             88-73579999999888665857987--------------732278899999998610016456740