HHsearch alignment for GI: 254780705 and conserved domain: TIGR02140
>TIGR02140 permease_CysW sulfate ABC transporter, permease protein CysW; InterPro: IPR011866 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 CysW, one of two homologous, tandem permeases in the sulphate ABC transporter system; the other is CysT (IPR011865 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=99.90 E-value=5.7e-24 Score=171.48 Aligned_cols=203 Identities=27% Similarity=0.245 Sum_probs=150.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HH----HCCC
Q ss_conf 667899999999999999999999999998643730245678989988765336999999999999----86----2666
Q gi|254780705|r 204 GVAVVGSLYMMLIVIGLSFPLGIASAIYLEEFSHKGFFSSFVQANINNLASVPSIVYGILGSAVLI----NF----FKMP 275 (425)
Q Consensus 204 ~~ai~gTl~~~~ia~~ia~pigv~~aiyl~e~a~~~~~~~~i~~~i~~la~vPSIv~Gl~gl~~~~----~~----~~~~ 275 (425)
T Consensus 46 ~sA~~LTlLv~~I~VPlN~~FGv~~Aw~~~rf~FpG--k~lL~t~iDlPFSVSPVvAGL~~~LLyGrqGW~~PliedGvr 123 (275)
T TIGR02140 46 LSAIKLTLLVALIVVPLNTVFGVAAAWVLTRFQFPG--KRLLLTIIDLPFSVSPVVAGLIFVLLYGRQGWSQPLIEDGVR 123 (275)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC--HHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCHHHCCCC
T ss_conf 999989886676533078899999999987431674--576777776044322489999999984310013622343420
Q ss_pred CCHH---------------HHHH-HHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 3004---------------6897-53345436689999999985110678989987077212777788397533258999
Q gi|254780705|r 276 RSTA---------------LVGG-LILALMTLPSIIIATGVALRTVPSSIRSAALGLGASKVQTVFHHVLPLAMPAILTG 339 (425)
Q Consensus 276 ~~~~---------------l~g~-~~l~~m~lP~i~~~~~~al~~vp~~~~eaa~~LGas~~~~~~~v~lp~a~pgi~~g 339 (425)
T Consensus 124 fsG~lG~~l~~~d~~IiF~~PGivLAT~FVT~PFVAREliPvl~~qG~~~EeAAltLGAs~WqtFwrVTLPnIkWgLlYG 203 (275)
T TIGR02140 124 FSGWLGPWLEDRDIKIIFSLPGIVLATIFVTLPFVARELIPVLEEQGTEQEEAALTLGASWWQTFWRVTLPNIKWGLLYG 203 (275)
T ss_pred EECCCHHHHHHCCCEEEECCHHHHHHHHHHCCCEEEEECCHHHHHCCCHHHHHHHHHCCCCEEEEEEEECCCCHHHHHHH
T ss_conf 00420278886288588714134102343258801220011363159468999987277622333566168715789854
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999998767799999854321013665613445579999998603665006999999999999999999999999999
Q gi|254780705|r 340 STVSLARALGETAPLLFVGMVAFVTDYPVGVTDIATAFPVQIYLWAADAERPFVERTFGAILLLLIFLAVINTAMLWLRN 419 (425)
Q Consensus 340 ~il~~~ra~GEta~ll~~~~~~~~~~~p~~~~~p~~tlp~~Iy~~~~~~~~~~~~~~~aa~lvLl~~~~~~n~~a~~lr~ 419 (425)
T Consensus 204 ~~LcnARamGEFGAVsVVSG---------~IrG~TnTLPL~Ve~lY~---~Y~~~AAFA~AslLal~Al~TL~lK~~LE~ 271 (275)
T TIGR02140 204 VILCNARAMGEFGAVSVVSG---------HIRGKTNTLPLHVELLYN---EYQSEAAFAAASLLALLALVTLVLKAILER 271 (275)
T ss_pred HHHHCCHHHCCCCCEEEEEC---------CCCCCCCCCHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 67751302002112568852---------689998763243232324---013478899999999999999999999986
Q ss_pred H
Q ss_conf 7
Q gi|254780705|r 420 R 420 (425)
Q Consensus 420 r 420 (425)
T Consensus 272 r 272 (275)
T TIGR02140 272 R 272 (275)
T ss_pred H
T ss_conf 4