HHsearch alignment for GI: 254780889 and conserved domain: TIGR01186
>TIGR01186 proV glycine betaine/L-proline transport ATP binding subunit; InterPro: IPR005892 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 comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits this transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L. lactis functionally complements an Escherichia coli proU mutant. The complementing locus is similar to a opuA locus in Bacillus subtlis. This clarifies the differences in nomenclature.; GO: 0005524 ATP binding, 0015171 amino acid transmembrane transporter activity, 0006865 amino acid transport, 0016020 membrane.
Probab=95.94 E-value=0.014 Score=37.97 Aligned_cols=140 Identities=21% Similarity=0.328 Sum_probs=84.6
Q ss_pred EEEECCCCHHHHHHHHHHHCCCCEEEECCCCEEEEEEEEHHHHC----------CCC------CCCCC---CCCCCCCCC
Q ss_conf 89946543034565667605041678668860278872354500----------143------44672---440026786
Q gi|254780889|r 103 VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVR----------FAS------NAQQA---VGELMTRNL 163 (493)
Q Consensus 103 Vti~pd~TI~ea~~lm~~~~is~iPVVD~~~gkLiGIVT~rDir----------~~~------~~~~~---V~eiMt~~l 163 (493)
T Consensus 185 vFitHD--lDEA~rigDR-----Ivilk~--GeiVQvGTPdeIL~NPaneyVe~F~~~~dl~qv~~P~~~~i~~~~~~~~ 255 (372)
T TIGR01186 185 VFITHD--LDEALRIGDR-----IVILKA--GEIVQVGTPDEILRNPANEYVEEFIGKVDLSQVLSPDAERIAKRMNTVP 255 (372)
T ss_pred EEEECC--HHHHHHHHHH-----HHHEEC--CCEEEECCCHHHHCCCCHHHHHHHHCCCEEEEECCCCHHHHHHHCCCCC
T ss_conf 999417--6788767513-----201106--8678842846874288067999873751157523888899996527732
Q ss_pred CCCCCCCCHHHHHHHHHHCCCCEEEEECCCCCEEEEEEECCCHHCCCCCCCCCCCCCC--EEEEEEEECCCHHHHHHHHH
Q ss_conf 3257303589999999865533064574799786889802100010174223265687--65556651370156789998
Q gi|254780889|r 164 ITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNATKDSKGR--LRVAAAVSVAKDIADRVGPL 241 (493)
Q Consensus 164 itv~~~~~l~eA~~iM~~~ki~~LPVVDe~g~LvGIIT~~DIlk~~~~p~A~~D~~gr--L~VgAAIg~~~d~~eRa~~L 241 (493)
T Consensus 256 i~~t~~~gp~~Al~Lm~~~~~~s~yvv~~~~~l~G~v~~~~~~~a~~~~~~~~~~l~~~~~tV~--~~t~--L~e~~~~v 331 (372)
T TIGR01186 256 ITKTADKGPRSALKLMRDERVDSLYVVDRQNKLVGVVDVESIKQARKKAQSLQDVLIDDILTVD--EGTL--LRELLRKV 331 (372)
T ss_pred EEECCCCCHHHHHHHHHHCCCCEEEEEECCCEEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCC--HHHHHHHH
T ss_conf 6865898878999999865971799997285488778588999888787789998620011105--8760--48999998
Q ss_pred HHCCCC-EEEEECCC
Q ss_conf 731366-69982484
Q gi|254780889|r 242 FDVNVD-LVVVDTAH 255 (493)
Q Consensus 242 veaGvD-viviD~ah 255 (493)
T Consensus 332 ~~~~~~YvpVVDE~~ 346 (372)
T TIGR01186 332 LKAGIKYVPVVDEDQ 346 (372)
T ss_pred HHCCCCEEEEECCCC
T ss_conf 507995666661456