HHsearch alignment for GI: 254780341 and conserved domain: TIGR02139

>TIGR02139 permease_CysT sulfate ABC transporter, permease protein CysT; InterPro: IPR011865 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 CysT, one of two homologous, tandem permeases in the sulphate ABC transporter system; the other is CysW (IPR011866 from INTERPRO). The sulphate transporter has been described in Escherichia coli as transporting sulphate, thiosulphate, selenate, and selenite. Sulphate transporters may also transport molybdate ion if a specific molybdate transporter is not present.; GO: 0015116 sulfate transmembrane transporter activity, 0008272 sulfate transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=99.62  E-value=3.7e-16  Score=115.78  Aligned_cols=179  Identities=22%  Similarity=0.319  Sum_probs=132.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCHH-HHHCCCHHHHHHHHCCCCCHHHHHHHHC-------------C----CCHH
Q ss_conf             99999999997887666776421012112-3202350345442012021011000000-------------2----1017
Q gi|254780341|r   95 ETLSLVLVSTFISMFIGVPLGVLAAWYPR-FYSIIRLFLDSMQTIPTFVYLIPALVLF-------------G----LGMV  156 (281)
Q Consensus        95 ~Tl~~~~~~~~ia~~igiplGi~~~~~~~-~~~~~~p~l~~~~~iP~~v~l~p~i~~f-------------G----~g~~  156 (281)
T Consensus        54 ~sf~~Al~Aa~~N~vFG~l~AWVLVRY~FPGKri~DAlVDLPFALPTAVAGIaL~TlY~~NGWiG~~l~~lGIKvAfTpl  133 (265)
T TIGR02139        54 LSFGTALIAALINAVFGTLLAWVLVRYRFPGKRIVDALVDLPFALPTAVAGIALATLYAPNGWIGSFLEPLGIKVAFTPL  133 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCEEEEECC
T ss_conf             99999999999999999999889861247505777666233542034799999999962889401258554987887201


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----
Q ss_conf             8899999988789999958874129989999999607882010122368862679999999999999999999999----
Q gi|254780341|r  157 PGIVATIVFSIPTSVRLTRLGIISTPPILKEAACAFGATPFQVFRKVELPFAIPQIVASLTQTIMLSLSMVVVTAL----  232 (281)
Q Consensus       157 ~~i~a~~i~~~~pi~~~t~~gl~~v~~~~~eaa~~~Gas~~q~l~~V~lP~a~P~i~~Gi~~~~~~~l~~vvia~~----  232 (281)
T Consensus       134 Gi~~Al~FvsLPFVVRTVQPVL~e~~~E~EEAA~~LGAS~w~tF~~vilP~L~PALLTG~A----LaFAR-a~GEYGSVi  208 (265)
T TIGR02139       134 GIVVALVFVSLPFVVRTVQPVLEEIEKELEEAAASLGASRWQTFWKVILPALLPALLTGFA----LAFAR-AVGEYGSVI  208 (265)
T ss_pred             CEEEEEEEECCCCEEEEECCCCCCCCHHHHHHHHHHCCCCHHEEEEEECCCCCCHHHHHHH----HHHHH-HHHHHHCEE
T ss_conf             0143423325882573114300058864899976516882000222331444006999789----98875-432333000


Q ss_pred             -HCCC------CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH---HHHHHHHHHH
Q ss_conf             -7058------80499999997407898999999999999999---9999987421
Q gi|254780341|r  233 -VGSN------GLGVPVLRALNTVDIGRGFESGLCIVILAIIL---DRLFSIPDPR  278 (281)
Q Consensus       233 -ig~~------GLG~~i~~a~~~~~~~~~~~~~l~Iv~lai~l---Dri~~~~~~r  278 (281)
T Consensus       209 FIAGN~P~~tEI~PLLI~~kLEqYDY~gATaIA~vmL~~SF~~Ll~IN~lQ~~~~r  264 (265)
T TIGR02139       209 FIAGNLPMKTEIAPLLIFIKLEQYDYAGATAIAVVMLLISFVLLLFINLLQWRALR  264 (265)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             22268880678899999777544123789999999999999999999999997506