HHsearch alignment for GI: 254781113 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=99.84  E-value=2.1e-20  Score=130.81  Aligned_cols=200  Identities=17%  Similarity=0.197  Sum_probs=148.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHH
Q ss_conf             899999999999999999999999999999999999999999706763799999999999855532222---22111223
Q gi|254781113|r    5 WFNLIIDSFPQLLYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQ---LFVIFYGL   81 (226)
Q Consensus         5 w~~~~~~~~~~~l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~---l~~~~f~~   81 (226)
T Consensus        39 FW~~~~~---P~vlaay~~sf~~Al~Aa~~N~vFG~l~AWVLVRY~FP-GKri~DAlVDLPFALPTAVAGIaL~TlY~~N  114 (265)
T TIGR02139        39 FWQIITE---PRVLAAYKLSFGTALIAALINAVFGTLLAWVLVRYRFP-GKRIVDALVDLPFALPTAVAGIALATLYAPN  114 (265)
T ss_pred             HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHHHCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             9999853---89999999999999999999999999998898612475-0577766623354203479999999996288


Q ss_pred             HHHHCCCCC--------CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             332101443--------333331001100000157899988752833689986517463565778752235764456778
Q gi|254781113|r   82 PHIGIVFDS--------FVAIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLS  153 (226)
Q Consensus        82 ~~~g~~~~~--------~~~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~  153 (226)
T Consensus       115 GWiG~~l~~lGIKvAfTplGi~~Al~FvsLPFVVRTVQPVL~e~~~E~EEAA~~LGAS~w~tF~~vilP~L~PALLTG--  192 (265)
T TIGR02139       115 GWIGSFLEPLGIKVAFTPLGIVVALVFVSLPFVVRTVQPVLEEIEKELEEAAASLGASRWQTFWKVILPALLPALLTG--  192 (265)
T ss_pred             CCCHHHHHHCCCEEEEECCCEEEEEEEECCCCEEEEECCCCCCCCHHHHHHHHHHCCCCHHEEEEEECCCCCCHHHHH--
T ss_conf             940125855498788720101434233258825731143000588648999765168820002223314440069997--


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             788987526799999769999999999983----------------2357799999999999999999999999999986
Q gi|254781113|r  154 SEFISILKSTSVASTITIPEIFQTAQRIVS----------------TTYQPLIIYCELAFVYLILTSFCYIIQIKIESSV  217 (226)
Q Consensus       154 ~~~i~lik~tsl~s~ig~~el~~~a~~i~~----------------~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr~  217 (226)
T Consensus       193 ---------~ALaFARa~GEYGSViFIAGN~P~~tEI~PLLI~~kLEqYD-Y~gATaIA~vmL~~SF~~Ll~IN~lQ~~~  262 (265)
T TIGR02139       193 ---------FALAFARAVGEYGSVIFIAGNLPMKTEIAPLLIFIKLEQYD-YAGATAIAVVMLLISFVLLLFINLLQWRA  262 (265)
T ss_pred             ---------HHHHHHHHHHHHHCEEEECCCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             ---------89988754323330002226888067889999977754412-37899999999999999999999999975


Q ss_pred             HHC
Q ss_conf             213
Q gi|254781113|r  218 TQH  220 (226)
Q Consensus       218 ~~~  220 (226)
T Consensus       263 ~r~  265 (265)
T TIGR02139       263 LRY  265 (265)
T ss_pred             CCC
T ss_conf             069