HHsearch alignment for GI: 255764497 and conserved domain: TIGR01253

>TIGR01253 thiP thiamine/thiamine pyrophosphate ABC transporter, permease protein; InterPro: IPR005947 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents thiamine ABC transporter, permease protein in bacteria, believed to be involved in the specific translocation of thiamine and its phosphoesters across the inner membrane. The protein belongs to the larger ABC transport system. It has been experimentally demonstrated that mutants in the various steps in the de novo synthesis of thiamine and its biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP). Thiamine pyrophosphate (TPP)1 is a required cofactor synthesized de novo in Salmonella typhimurium. The primary role for TPP is in central metabolism as an electron carrier and nucleophile for such enzymes as pyruvate dehydrogenase (1.2.4.1 from EC), acetolactate synthase (4.1.3.18 from EC), and -ketoglutarate dehydrogenase (1.2.4.2 from EC). Despite its importance in cellular physiology, neither the de novo biosynthetic pathway nor the salvage systems for thiamine are fully understood in any organism.; GO: 0005215 transporter activity, 0006810 transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=99.89  E-value=2.7e-16  Score=134.69  Aligned_cols=449  Identities=12%  Similarity=0.029  Sum_probs=315.4

Q ss_pred             HCCCCCCCCCHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH-HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             102331352036687074068999999999999999999999999999997150267-8999999999743289999999
Q gi|255764497|r   41 ETTVPRDIVDIVPITLDVHSLPQYASRTTLRMLSAMVISLLFTFVYATLAAKSRRLG-MVLVPILDIMQSIPILGFLTFT  119 (587)
Q Consensus        41 ~~~~~~~~~~~~~~~~~~~~l~~~~~~Tl~~~~~~~~~~~~ig~~~a~~~~~~~~~~-~~~~~~l~~~~~iP~~~~~~~~  119 (587)
T Consensus        28 ~~~~~~~~W~A~---~~D~YL~H~~~FSF~QAlLS~~LS~~~~~lLARALy~~~F~G~~~LL~L~~lTl~LP~LV~~FG~  104 (519)
T TIGR01253        28 FALAGELDWVAV---FTDDYLQHLVLFSFGQALLSALLSVIFALLLARALYRKRFLGKKALLKLMALTLVLPVLVVVFGL  104 (519)
T ss_pred             HHHCCCCCEEEE---EECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             873786560677---62407899999998999999999999999999997406884268999999999999999999977


Q ss_pred             HHHHHCCC------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             99984014------------554210479999999998535999999999972998999999962888201236555262
Q gi|255764497|r  120 VVYFMNLY------------PGKVIGAELAAIFAIFTSQVWNMTFSMYQSLCNIPRDLEEVSRSFRLSGWQKFWYLGVPF  187 (587)
Q Consensus       120 ~~~f~~~~------------~~~~~~~~~~~i~~~~~~~~~~i~~~~~~~l~~i~~~l~eaa~~~Ga~~~~~f~~v~lP~  187 (587)
T Consensus       105 ~~~YG~~GWLA~L~~~lGl~W~~~~YGL~GIL~AH~FFN~PlA~~LlLQ~L~~IP~~QRQLAAQL~l~~W~F~~lVEWP~  184 (519)
T TIGR01253       105 LSVYGRSGWLATLANLLGLEWTFSIYGLSGILLAHLFFNLPLAARLLLQALESIPYEQRQLAAQLNLRSWQFVKLVEWPV  184 (519)
T ss_pred             HHHCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCEEEEEEECHH
T ss_conf             76405753799999871875034334157999999996156999999998741781577999971677530566630512


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             15789999999999998998999997354442036788999999863113256999999999999999999998987544
Q gi|255764497|r  188 SMPGLVWNMMMSMSGGWFFVVASEMIVVGDTVIPLPGIGSYIALAIKEQDLLAILYAMLTMLGVIFLYDQLLFRPMIVWS  267 (587)
Q Consensus       188 ~~P~i~~~~~l~~~~~~~~~~~~~~~g~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  267 (587)
T Consensus       185 lR~Q~~P~~~LIFMLCF~SF~~VL~LGGGPQ~TT~E~AIYQA~~--y~yD~~~AAllAlLQ~V~CL~L~~L~~R------  256 (519)
T TIGR01253       185 LRRQILPVAALIFMLCFASFAVVLSLGGGPQATTLELAIYQALL--YDYDLAKAALLALLQFVFCLILVLLSSR------  256 (519)
T ss_pred             HHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHHHHHHHHHH------
T ss_conf             33211258999999998889998735898406899999999987--3168468999999999999999999887------


Q ss_pred             HHHHHHHHCCCCCCCHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH
Q ss_conf             4321222100112102456-555778998888878889999999999987665654200023445544321012231358
Q gi|255764497|r  268 NKFRLERTTGIYPADSWVL-YLFRKTNFLRFIGYSSWNFFSPLSNNVKKLCRTLGVIRFHFPENFLQLCSNQRVSYMLDI  346 (587)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  346 (587)
T Consensus       257 --lS~~~~~G~~~~~~W~~P~~~~~~~I~~~-~~~~~~~llLl~P~L~~~~~~~~s~~----------------------  311 (519)
T TIGR01253       257 --LSKAIANGLSLLNIWFDPDDKLAVKIFDI-LLLLLALLLLLSPLLAVLVDALSSRN----------------------  311 (519)
T ss_pred             --HHHHCCCCCCHHCCCCCCCCCHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH----------------------
T ss_conf             --87640577520114558875227899999-99999999986479999997531234----------------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHCH-----HHHHHHHHH
Q ss_conf             998778889999987543210000000006889999999999999999997310000112454366-----789998544
Q gi|255764497|r  347 FWFCVVCGVAIGIAWQSIGYIVNHFTYQDVLYVIWLGCITMFRVVVLIIIASIIWIPVGIWIGFRP-----HISSKIQPF  421 (587)
Q Consensus       347 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~tl~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~~~~  421 (587)
T Consensus       312 -----------------------L~~V~~~~~LW~AL~~SL~IA~~~~~L~~~l~~~LL~~SR~L~~~~~~~~~Q~~~~~  368 (519)
T TIGR01253       312 -----------------------LLEVLANSVLWRALGYSLRIALLAALLALVLAIALLLLSRRLRALQKQKISQVLINA  368 (519)
T ss_pred             -----------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             -----------------------688873247899998899999999999999999999875889999878898899984


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             66775444699999999983155665---047999999999999999999999973998999999974988789989998
Q gi|255764497|r  422 AQLLAAFPANVFFPLVVSCVSYYHLN---PNLWLSLLMIFGTQWYILFNVIAGASAFPNDFKEVASSFHITGWRWWRYII  498 (587)
Q Consensus       422 ~~~~~~ip~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~gl~~i~~~l~eaa~~lGa~~~~~~~~V~  498 (587)
T Consensus       369 GM~ILA~P~~VLA~GlFLLL~~~~~~~~~~~~IV~F~NAL~A~Py~L~~L~~P~~~~~~~Y~~LC~SLGI~GW~Rl~~~E  448 (519)
T TIGR01253       369 GMLILAIPILVLATGLFLLLNDRIFLNIDLDIIVVFTNALSAIPYVLKVLEAPFRDITARYENLCNSLGIVGWSRLKLVE  448 (519)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             28999977999999899986134677754201013454777635999984051578899998755321733004778887


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCH
Q ss_conf             574577899999999999999999999850556442237837999999973497
Q gi|255764497|r  499 LPGIFPYYVTGAITACGGAWNASIVSEVASWGHIHLRTTGLGAYIAESTEKGSF  552 (587)
Q Consensus       499 LPl~~P~i~~g~~~a~~~a~~~~~~ae~~~~~~~~~~~~GlG~~i~~~~~~~~~  552 (587)
T Consensus       449 ~~~L~~PL~~AlAl~~~LS~GDF~~~ALFGN--~--~F~~LP~~LYQQ~G~YR~  498 (519)
T TIGR01253       449 LKALKAPLAYALALALVLSLGDFTVVALFGN--D--DFRSLPFLLYQQLGSYRS  498 (519)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHEEEECC--C--CCCHHHHHHHHHHCCCCC
T ss_conf             9998779999999999985211562001037--5--321137899987235336