HHsearch alignment for GI: 254780332 and conserved domain: TIGR00956

>TIGR00956 3a01205 Pleiotropic Drug Resistance (PDR) Family protein; InterPro: IPR005285 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 family includes transporters, whose physiological function is not yet established. These proteins are thought to confer resistance to the chemicals cycloheximide and sulphomethuron methyl, BFA, azole antifungal agents, other antifungal agents: amorolfine and terbinafine. Some of them could serve as an efflux pump of various antibiotics..
Probab=96.22  E-value=0.0059  Score=41.98  Aligned_cols=151  Identities=20%  Similarity=0.229  Sum_probs=85.3

Q ss_pred             HHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEE-CCC-----CHHHHHHHHH
Q ss_conf             7765564167726776213100276999999999985101112333332124797589995-852-----1799987899
Q gi|254780332|r  209 LDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYS-LEM-----SSEQLATRII  282 (504)
Q Consensus       209 LD~~~gGl~~G~l~Viaarpg~GKTalalniA~~~A~~~~~~~~~~~~~~~~~g~~Vl~fS-lEM-----s~~el~~R~i  282 (504)
T Consensus       843 L~~V~GwvkPG~lTALMG~SGAGKTTLLn~La~R--------------------~t~GvIT~G~~lVNG~~lD~sF~R~i  902 (1466)
T TIGR00956       843 LNNVDGWVKPGTLTALMGASGAGKTTLLNVLAER--------------------VTTGVITDGDRLVNGRPLDSSFQRSI  902 (1466)
T ss_pred             CCCCCEEEECCEEEECCCCCCCCHHHHHHHHHCC--------------------CCCCEEECCEEEECCCCCCCCCCCCC
T ss_conf             1575327877857651578876357888644330--------------------43217705715508845575557441


Q ss_pred             HHHHH----HC----------CCCCCCC-CCCHHHHHHHHHHHHHHHHCCEEEE-----CCC-CCCHHHHH--HHHHHHC
Q ss_conf             99874----10----------1100012-1376889989999999862780782-----589-98899999--9886402
Q gi|254780332|r  283 SEQTE----VP----------SSKIRRG-ELTRPDYEKIVACSQVMQKLPLYID-----QTG-GISMSQLA--TRARRLK  339 (504)
Q Consensus       283 s~~s~----I~----------~~~i~~g-~l~~~e~~~i~~a~~~l~~~~l~I~-----d~~-~~ti~~I~--~~~r~~~  339 (504)
T Consensus       903 GYvQQQD~Hl~~~TVREaL~FSA~LRqP~~vs~~EK~~YVe~vI~lLEMe~YaDAvVG~pG~tGLNVEQRKRLTIGVELv  982 (1466)
T TIGR00956       903 GYVQQQDLHLETSTVREALRFSAYLRQPKSVSKSEKMEYVEEVIKLLEMESYADAVVGVPGETGLNVEQRKRLTIGVELV  982 (1466)
T ss_pred             CCEEECCEECCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCHHHCCEEEECCCCCCCCHHHHHHHHHHHHHH
T ss_conf             32454221224202889999999845985678653246888887664101022113515677888732321010334322


Q ss_pred             CCCCCC-EEEECCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEE
Q ss_conf             244474-677671353256644321137889999999999998827919997
Q gi|254780332|r  340 RQRGLD-LLIVDYIQLMTTSKKIEENRVLEITGITMALKALAKELNIPIIAL  390 (504)
Q Consensus       340 ~~~gi~-~vvIDYLqli~~~~~~~~~r~~~i~~is~~lK~lA~e~~ipvi~l  390 (504)
T Consensus       983 A--kPkLL~FLD-----EPTS-GLDS--QtAWsi~~l~RKLad-~GQaILCT 1023 (1466)
T TIGR00956       983 A--KPKLLLFLD-----EPTS-GLDS--QTAWSICKLLRKLAD-HGQAILCT 1023 (1466)
T ss_pred             H--CCCHHEECC-----CCCC-CHHH--HHHHHHHHHHHHHHH-CCCEEEEC
T ss_conf             1--632000215-----8897-0558--999999999998875-59838860