HHsearch alignment for GI: 254780766 and conserved domain: TIGR01257

>TIGR01257 rim_protein rim ABC transporter; InterPro: IPR005951 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). Rim protein (ABCR), is an ATP binding cassette (ABC)1 transporter found in vertebrate retinal photoreceptor cells. It is localized along the rim region of photoreceptor rod outer segment disc membranes and more recently has been found in human foveal and peripheral cone outer segments. Several studies have implicated ABCR in the retinoid cycle, possibly functioning as a retinal extruder or retinal-phosphatidylethanolamine flippase to facilitate the removal of all-trans-retinal from disc membranes following the photobleaching of rhodopsin . ABCR contains eight glycosylation sites. Four sites reside in a 600-amino acid exocytoplasmic domain of the N-terminal half between the first transmembrane segment H1 and the first multi-spanning membrane domain, and four sites are in a 275-amino acid domain of the C half between transmembrane segment H7 and the second multi-spanning membrane domain. This leads to a model in which each half has a transmembrane segment followed by a large exocytoplasmic domain, a multi-spanning membrane domain, and a nucleotide binding domain. ; GO: 0005524 ATP binding, 0042626 ATPase activity coupled to transmembrane movement of substances, 0006810 transport, 0005887 integral to plasma membrane.
Probab=96.39  E-value=0.0022  Score=41.27  Aligned_cols=80  Identities=25%  Similarity=0.362  Sum_probs=64.0

Q ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHCCCHHHHHHHHHHHHHC--CCCEEEEECCHHHHHHHHCCE
Q ss_conf             312205899999999999999999870899789980122015989999999997417--980999806967854321260
Q gi|254780766|r  285 AHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI--GSQIFMTGTDKSVFDSLNETA  362 (375)
Q Consensus       285 ~~~S~Gqqk~~~l~l~La~~~~~~~~~~~~pilLiDdi~s~LD~~~~~~ll~~l~~~--~~Qv~iTt~~~~~~~~~~~~~  362 (375)
T Consensus      1060 ~dlsGG~qrklsvaiaf---------vGd~kvv~ldePtsGvdPysrrsiWdlllkyrsGrtiimsthhmdead~lGdr- 1129 (2272)
T TIGR01257      1060 QDLSGGMQRKLSVAIAF---------VGDAKVVVLDEPTSGVDPYSRRSIWDLLLKYRSGRTIIMSTHHMDEADLLGDR- 1129 (2272)
T ss_pred             HHHHCCHHHEEEEEEEE---------ECCEEEEEEECCCCCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCHHHHCCCE-
T ss_conf             43202111100234556---------52604899607878878521467999887622786689740332223440130-


Q ss_pred             EEEEECCCEEEEC
Q ss_conf             0799728968959
Q gi|254780766|r  363 KFMRISNHQALCI  375 (375)
Q Consensus       363 ~~~~i~~g~~~~~  375 (375)
T Consensus      1130 -iaii~qGrlyCs 1141 (2272)
T TIGR01257      1130 -IAIISQGRLYCS 1141 (2272)
T ss_pred             -EEEEECCEEEEC
T ss_conf             -223245603324