HHsearch alignment for GI: 255764501 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=100.00 E-value=0 Score=550.05 Aligned_cols=518 Identities=46% Similarity=0.824 Sum_probs=509.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 10368999999999999999999999741688679999956989999999999999999999999999999999707996
Q gi|255764501|r 8 SIRNALWPGVIISCFLNFIFFLVVYSLWRHMPLISWREFMEDSYLWHVIGFTFWQALLSTLLSVIPSIFLAKSLFRRHFP 87 (535)
Q Consensus 8 li~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~nTl~~a~~s~~~~~~ig~~~A~~~~~~~~~ 87 (535)
T Consensus 1 L~P~~~~~GV~~~~l~~~~~~~Al~~~~~~~~~~~W~A~~~D~YL~H~~~FSF~QAlLS~~LS~~~~~lLARALy~~~F~ 80 (519)
T TIGR01253 1 LIPRHLIGGVVVISLVVLVALAALLALFALAGELDWVAVFTDDYLQHLVLFSFGQALLSALLSVIFALLLARALYRKRFL 80 (519)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 99972133189999999999999999987378656067762407899999998999999999999999999997406884
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf 17999999999998899999999999972278542103315888764333269999999998766548999999850888
Q gi|255764501|r 88 GRILFLRLHTMIFVLPVFVVIMGVFTVYGRTGWIAQLCQWLGIVYQFNLYGIKGILLVHVFFNMPLAIRMLLQALDSISI 167 (535)
Q Consensus 88 ~~~~~~~~~~lp~~~P~~v~~~~~~~~~~~~G~~~~~l~~~g~~~~~~~~~~~~iii~~~~~~~p~~~l~~~~~l~~i~~ 167 (535)
T Consensus 81 G~~~LL~L~~lTl~LP~LV~~FG~~~~YG~~GWLA~L~~~lGl~W~~~~YGL~GIL~AH~FFN~PlA~~LlLQ~L~~IP~ 160 (519)
T TIGR01253 81 GKKALLKLMALTLVLPVLVVVFGLLSVYGRSGWLATLANLLGLEWTFSIYGLSGILLAHLFFNLPLAARLLLQALESIPY 160 (519)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
T ss_conf 26899999999999999999997776405753799999871875034334157999999996156999999998741781
Q ss_pred HHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 99999986214714677544200166402457778777652584156640366554411455567776532000000134
Q gi|255764501|r 168 EQRQLALQLGMNPWYFFRFVEWPYLRRQILPTSSLIFMLCFASFATVLTLGGGPASTTIELAIYQSLSYDFDLNKAAFLS 247 (535)
Q Consensus 168 ~~~eaA~~lGas~~~~f~~v~lP~~~p~i~~~~~l~f~~~~~~f~~~~~lgg~~~~~tl~~~iy~~~~~~~~~~~aa~la 247 (535)
T Consensus 161 ~QRQLAAQL~l~~W~F~~lVEWP~lR~Q~~P~~~LIFMLCF~SF~~VL~LGGGPQ~TT~E~AIYQA~~y~yD~~~AAllA 240 (519)
T TIGR01253 161 EQRQLAAQLNLRSWQFVKLVEWPVLRRQILPVAALIFMLCFASFAVVLSLGGGPQATTLELAIYQALLYDYDLAKAALLA 240 (519)
T ss_pred HHHHHHHHHCCCCCEEEEEEECHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 57799997167753056663051233211258999999998889998735898406899999999987316846899999
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHH
Q ss_conf 55788999998530134332211112222356410001454699999999999974123221000110013467643835
Q gi|255764501|r 248 LVQIFCCLSLVLFNQKFNVSFSSGYSSRFLWKNEDDSRWSRWWDFFLISCAIWFFILPLLAIIIEGMNAKLLLRLLQQSG 327 (535)
Q Consensus 248 ~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~i~pl~~ii~~~~~~~~~~~~~~~~~ 327 (535)
T Consensus 241 lLQ~V~CL~L~~L~~RlS~~~~~G~~~~~~W~~P~~~~~~~I~~~~~~~~~~llLl~P~L~~~~~~~~s~~L~~V~~~~~ 320 (519)
T TIGR01253 241 LLQFVFCLILVLLSSRLSKAIANGLSLLNIWFDPDDKLAVKIFDILLLLLALLLLLSPLLAVLVDALSSRNLLEVLANSV 320 (519)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999998878764057752011455887522789999999999999986479999997531234688873247
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 47999999999999765665211112210002211565126799999997465532376676643012346775665534
Q gi|255764501|r 328 LWSSFFNSIYIAINAGVLCMIFTIMLLWTKRELRLRRLKFFNHIFELSELLILAVPSIVLAVGFFLLLKNTVNLTSSSYS 407 (535)
Q Consensus 328 ~~~a~~~Sl~~s~~~~~i~~~l~l~~a~~~~~~~~~~~~~~~~~~~~~~~lp~~iP~iv~~~~~~~~~~~~~~~~~~~~~ 407 (535)
T Consensus 321 LW~AL~~SL~IA~~~~~L~~~l~~~LL~~SR~L~~~~~~~~~Q~~~~~GM~ILA~P~~VLA~GlFLLL~~~~~~~~~~~~ 400 (519)
T TIGR01253 321 LWRALGYSLRIALLAALLALVLAIALLLLSRRLRALQKQKISQVLINAGMLILAIPILVLATGLFLLLNDRIFLNIDLDI 400 (519)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCH
T ss_conf 89999889999999999999999999987588999987889889998428999977999999899986134677754201
Q ss_pred CCCEEEEEEECHHHHHHHHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCC
Q ss_conf 43102465212156999999897289778999997397876999999999546899999999999985110116786489
Q gi|255764501|r 408 LIIVTNALMAVPYAVKILENPMYDLAERYNALCISLQIKGINRLYLIEFKALKRLMAQTFSFSCLLSIGDFGIIALFGND 487 (535)
Q Consensus 408 ~iila~~~~~lP~~~~~l~~~l~~i~~~l~eaA~~lGa~~~~~f~~I~lPll~p~i~~~~~l~f~~s~~e~~~~~ll~~~ 487 (535)
T Consensus 401 IV~F~NAL~A~Py~L~~L~~P~~~~~~~Y~~LC~SLGI~GW~Rl~~~E~~~L~~PL~~AlAl~~~LS~GDF~~~ALFGN~ 480 (519)
T TIGR01253 401 IVVFTNALSAIPYVLKVLEAPFRDITARYENLCNSLGIVGWSRLKLVELKALKAPLAYALALALVLSLGDFTVVALFGND 480 (519)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCC
T ss_conf 01345477763599998405157889999875532173300477888799987799999999999852115620010375
Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 83028989998861798136999999999999999999
Q gi|255764501|r 488 NFCTLPCYLYQQLGSYRQSDAVVTALLLLSLCLGLFSL 525 (535)
Q Consensus 488 ~~~Tl~~~i~~~~~~~~~~~a~a~a~il~~i~~~~~~l 525 (535)
T Consensus 481 ~F~~LP~~LYQQ~G~YR~QD~AVTA~ILLLLC~~LF~~ 518 (519)
T TIGR01253 481 DFRSLPFLLYQQLGSYRSQDAAVTALILLLLCFLLFAV 518 (519)
T ss_pred CCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 32113789998723533613899999999999999850