HHsearch alignment for GI: 254780426 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=98.08  E-value=3e-05  Score=54.28  Aligned_cols=120  Identities=17%  Similarity=0.192  Sum_probs=98.1

Q ss_pred             EEHHEEECC-CEEEEEEECCCHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEHHHHHHHHHHCCCCCCCCCCCCCCCHHH
Q ss_conf             764131200-1299986301036778979865981799841886642241029999987662235643223334576788
Q gi|254780426|r   88 RIDDIMISR-VSINAVEDKATVYEAMLMFEKYGRSWMPVYKNSLDNPRGMVHMRDVISYISHMYAKTNNINLNIQLSESN  166 (320)
Q Consensus        88 ~v~diMtPr-~~i~~i~~~~~~~e~~~~i~~~~~sR~PV~~~~~d~iiGiv~~kDll~~~~~~~~~~~~~~~~~~~~l~~  166 (320)
T Consensus       243 ~~~~i~~~~~~~~i~~t~~~gp~~Al~Lm~~~~~~s~yvv~~~~-~l~G~v~~~~~~~a~~~~------------~~~~~  309 (372)
T TIGR01186       243 DAERIAKRMNTVPITKTADKGPRSALKLMRDERVDSLYVVDRQN-KLVGVVDVESIKQARKKA------------QSLQD  309 (372)
T ss_pred             CHHHHHHHCCCCCEEECCCCCHHHHHHHHHHCCCCEEEEEECCC-EEEEEEEHHHHHHHHHHH------------HHHHH
T ss_conf             88999965277326865898878999999865971799997285-488778588999888787------------78999


Q ss_pred             HC-CCCEEECCCCCHHHHHHHHHCCCCCCEEEEECCCCCEEEEEHHHHHHHHHHH
Q ss_conf             51-5657971788512323432013565116540776620466758899998742
Q gi|254780426|r  167 LI-KNILFVPSSMLVSDLLTNIQESRIRMALVIDEHGGTDGLVSYEDIVSVLMRD  220 (320)
Q Consensus       167 ~~-r~~~~Vpe~~~l~~lL~~m~~~~~~~aiVvDE~G~~~GiVTleDIle~ivGe  220 (320)
T Consensus       310 ~l~~~~~tV~~~t~L~e~~~~v~~~~~~YvpVVDE~~~~~GIv~r~~L~~~l~d~  364 (372)
T TIGR01186       310 VLIDDILTVDEGTLLRELLRKVLKAGIKYVPVVDEDQRLVGIVTRASLVDALYDS  364 (372)
T ss_pred             HHHHCCCCCCCCCCHHHHHHHHHHCCCCEEEEECCCCCEEEEEEHHHHHHHHHCC
T ss_conf             8620011105876048999998507995666661456458676477899987166