HHsearch alignment for GI: 254780711 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=100.00  E-value=0  Score=659.84  Aligned_cols=268  Identities=37%  Similarity=0.561  Sum_probs=244.4

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC------CCCCCCCCCC
Q ss_conf             9999999999998524696999999999999983031112699899999999999998718774------2100025884
Q gi|254780711|r   27 ISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQPGQMVIKIVHDELVEVLGKES------IELDLNAPSP  100 (461)
Q Consensus        27 i~~~l~ei~~aLLeaDV~~~vv~~~~~~Ik~k~~~~~~~~~~~~~~~i~kiv~~eL~~lLg~~~------~~l~~~~~~p  100 (461)
T Consensus         3 de~~~EELE~~Ll~~Dv~~~~v~~i~~~l~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~kp   82 (284)
T TIGR00064         3 DEDFFEELEEILLESDVGLEVVEKIIEELKKELVGKKVKDEEKLKEILKEALKEILKEILDKDTLLDLEQIEELPEEKKP   82 (284)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCC
T ss_conf             03689989999998505189999999998875403557707899999999999987411232113344334430147897


Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCC-CHHHHHHHHHHHHH
Q ss_conf             18996234433346889999999986148950782054221004779999851034742223321-03689999999999
Q gi|254780711|r  101 LVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPE-QSPEKIAIRATQSA  179 (461)
Q Consensus       101 ~vIllvGl~GsGKTTT~aKLA~~~~~~~~~kV~lv~~Dt~R~aA~eQL~~~a~~~~v~~~~~~~~-~dp~~i~~~a~~~a  179 (461)
T Consensus        83 ~Vil~VGVNG~GKTTTIaKLA~~l~~-~Gk~V~laAgDTFRAAA~EQL~~Wa~R~gv~vi~~~~gn~DPAaV~fDAi~~A  161 (284)
T TIGR00064        83 NVILFVGVNGVGKTTTIAKLANKLKK-QGKSVLLAAGDTFRAAAIEQLEVWAKRLGVDVIKQKEGNADPAAVIFDAIQAA  161 (284)
T ss_pred             EEEEEEEEECCCHHHHHHHHHHHHHH-CCCEEEEECCCHHHHHHHHHHHHHHHHHCCEEEECCCCCCCCHHHHHHHHHHH
T ss_conf             79999844088601028899999987-49908998275247999999999898838755407889887178999989999


Q ss_pred             HHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCC-------CCCCCCCCCHHCCHHHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             7415886998334422211246899999985138-------511000310111225688889887635844077641157
Q gi|254780711|r  180 RDGGYDAVILDTAGRNHINDSLMQEISEIKSLTN-------PHEILLVADALTGQDAVHLARNFDKIVDLTGIILTRMDG  252 (461)
Q Consensus       180 ~~~~~D~iiiDTaGR~~~d~~lm~El~~i~~~~~-------p~e~~lV~da~~Gq~a~~~a~~F~~~~~i~giIlTKlD~  252 (461)
T Consensus       162 k~~niDvvliDTAGRLqnk~NLm~EL~KI~RV~~k~~~~~aP~e~lLVlDAt~Gqna~~QA~~F~eav~ltGiiLTKLDg  241 (284)
T TIGR00064       162 KARNIDVVLIDTAGRLQNKVNLMDELKKIKRVIKKVDPVDAPDEVLLVLDATTGQNALEQAKVFNEAVGLTGIILTKLDG  241 (284)
T ss_pred             HHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             87499789973475454662039999999998732102578755754220222030899999986540688589963468


Q ss_pred             CCCCCHHHHHHHHHCCCHHHEECCCCCCCCCCCCHHHHHHHHH
Q ss_conf             6633036777888478730261586723210013688998773
Q gi|254780711|r  253 DGRGGAALSMRTVTGKPIKAIGTGEKINDLENFFPDRIANRIL  295 (461)
Q Consensus       253 ~akgG~als~~~~~~~PI~fig~GE~~~dle~F~p~~~~~riL  295 (461)
T Consensus       242 ~AKGG~~l~i~~~l~~Pv~~~G~GE~~dDL~~Fd~~~fv~~L~  284 (284)
T TIGR00064       242 TAKGGIILAIAYELKLPVKFIGVGEKIDDLAPFDADWFVEALF  284 (284)
T ss_pred             CCHHHHHHHHHHHHCCCEEEEECCCCHHHHCCCCHHHHHHHCC
T ss_conf             8037899988998579769985488733201479789987509