HHsearch alignment for GI: 254780705 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=98.81  E-value=2.2e-06  Score=59.50  Aligned_cols=268  Identities=16%  Similarity=0.122  Sum_probs=178.3

Q ss_pred             CCCCHHHHHHHHHHHCCHHHHHHHHHHHHCHHHCCCE-EEEEEEECCCCHHHHCCCCCCCCHHCCCCHHHHHH-------
Q ss_conf             6666034898998730016899999974063215974-78999704530233034556530000599999999-------
Q gi|254780705|r  100 SDSNHALLRQASQMLSTTARYHLRKTLMTDPSLIGKT-VEVSLLASANIDSALKGYLYSPANVHRMSDYQWKW-------  171 (425)
Q Consensus       100 ~~~~r~~kr~l~~liS~~a~~~Lrd~v~~np~liG~t-~~~~llAsddvD~~~KG~i~r~e~~rrisd~ql~~-------  171 (425)
T Consensus       231 yD~~~AAllAlLQ~V~CL~L~~L~~RlS~~~-~~G~~~~~~W~~P~~~-------------~~~~I~~~~~~~~~~llLl  296 (519)
T TIGR01253       231 YDLAKAALLALLQFVFCLILVLLSSRLSKAI-ANGLSLLNIWFDPDDK-------------LAVKIFDILLLLLALLLLL  296 (519)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCHHCCCCCCCCC-------------HHHHHHHHHHHHHHHHHHH
T ss_conf             6846899999999999999999988787640-5775201145588752-------------2789999999999999986


Q ss_pred             -------HHHHHHHHHHHHCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCHHHH
Q ss_conf             -------99998745664112202321344321101202667899999999999999999999999998643--730245
Q gi|254780705|r  172 -------FQKLDSDGALFLDFNYGFFINGASSRPEVAGIGVAVVGSLYMMLIVIGLSFPLGIASAIYLEEFS--HKGFFS  242 (425)
Q Consensus       172 -------~d~L~~~g~i~~~fn~~f~t~~~s~~~e~~Gi~~ai~gTl~~~~ia~~ia~pigv~~aiyl~e~a--~~~~~~  242 (425)
T Consensus       297 ~P~L~~~~~~~~s~~L~~V~--------------~~~~LW~AL~~SL~IA~~~~~L~~~l~~~LL~~SR~L~~~~~~~~~  362 (519)
T TIGR01253       297 SPLLAVLVDALSSRNLLEVL--------------ANSVLWRALGYSLRIALLAALLALVLAIALLLLSRRLRALQKQKIS  362 (519)
T ss_pred             HHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             47999999753123468887--------------3247899998899999999999999999999875889999878898


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCHH
Q ss_conf             6789899887653369999999999998-626663004689753345436689999999985110678989987077212
Q gi|254780705|r  243 SFVQANINNLASVPSIVYGILGSAVLIN-FFKMPRSTALVGGLILALMTLPSIIIATGVALRTVPSSIRSAALGLGASKV  321 (425)
Q Consensus       243 ~~i~~~i~~la~vPSIv~Gl~gl~~~~~-~~~~~~~~~l~g~~~l~~m~lP~i~~~~~~al~~vp~~~~eaa~~LGas~~  321 (425)
T Consensus       363 Q~~~~~GM~ILA~P~~VLA~-GlFLLL~~~~~~~~~~~~IV~F~NAL~A~Py~L~~L~~P~~~~~~~Y~~LC~SLGI~GW  441 (519)
T TIGR01253       363 QVLINAGMLILAIPILVLAT-GLFLLLNDRIFLNIDLDIIVVFTNALSAIPYVLKVLEAPFRDITARYENLCNSLGIVGW  441 (519)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-HHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCH
T ss_conf             89998428999977999999-89998613467775420101345477763599998405157889999875532173300


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             77778839753325899999999998767799999854321013665613445579999998603665006999999999
Q gi|254780705|r  322 QTVFHHVLPLAMPAILTGSTVSLARALGETAPLLFVGMVAFVTDYPVGVTDIATAFPVQIYLWAADAERPFVERTFGAIL  401 (425)
Q Consensus       322 ~~~~~v~lp~a~pgi~~g~il~~~ra~GEta~ll~~~~~~~~~~~p~~~~~p~~tlp~~Iy~~~~~~~~~~~~~~~aa~l  401 (425)
T Consensus       442 ~Rl~~~E~~~L~~PL~~AlAl~~~LS~GDF~~~ALFGN------------~~F~~LP~~LYQQ~G~YR~QD---~AVTA~  506 (519)
T TIGR01253       442 SRLKLVELKALKAPLAYALALALVLSLGDFTVVALFGN------------DDFRSLPFLLYQQLGSYRSQD---AAVTAL  506 (519)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECC------------CCCCHHHHHHHHHHCCCCCHH---HHHHHH
T ss_conf             47788879998779999999999985211562001037------------532113789998723533613---899999


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999999
Q gi|254780705|r  402 LLLIFLAVIN  411 (425)
Q Consensus       402 vLl