HHsearch alignment for GI: 254780901 and conserved domain: TIGR00064

>TIGR00064 ftsY signal recognition particle-docking protein FtsY; InterPro: IPR004390 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 includes the cell division ABC transporter and the periplasmic substrate-binding protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In Escherichia coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.; GO: 0005525 GTP binding.
Probab=92.78  E-value=0.94  Score=25.84  Aligned_cols=139  Identities=21%  Similarity=0.324  Sum_probs=92.8

Q ss_conf             89889999998819999999999967889-78988661966777189955614879999999999977997--9999407
Q Consensus        25 ~~~~~~~~l~~~~~~~~~~a~iL~~Rgi~-~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ek--I~I~gDy  101 (600)
T Consensus        19 v~~~~v~~i~~------~l~~~~~~~~~~~~~~~~e~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~kp~Vil~VG--   89 (284)
T ss_conf             51899999999------98875403557707899999999999987-4112321133443344301478977999984--

Q ss_conf             8861---5289999999997699479980787433668897898874202----68689996488-7----623455555
Q Consensus       102 D~DG---itstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~----g~~LiItvD~G-i----~~~e~i~~a  169 (600)
T Consensus        90 -VNG~GKTTTIaKLA~~l~~~Gk~V~laAgDTFR------AAA~EQL~~Wa~R~gv~-vi~~~~gn~DPAaV~fDAi~~A  161 (284)
T ss_conf             -408860102889999998749908998275247------99999999989883875-5407889887178999989999

Q ss_pred             HHCCCCEEEEC
Q ss_conf             41798279961
Q gi|254780901|r  170 TNQGIDVIVID  180 (600)
Q Consensus       170 ~~~GidvIVtD  180 (600)
T Consensus       162 k~~niDvvliD  172 (284)
T TIGR00064       162 KARNIDVVLID  172 (284)
T ss_pred             HHCCCCEEEEE
T ss_conf             87499789973