HHsearch alignment for GI: 254780725 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=98.17  E-value=0.00023  Score=46.06  Aligned_cols=220  Identities=16%  Similarity=0.177  Sum_probs=131.1

Q ss_pred             EECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             81687189999999765626431899989999976310233222345675379997469887756899999999996269
Q gi|254780725|r  112 IGDTNDVSLYRALISNHVSEYLIEPLSVADIINSISAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFA  191 (427)
Q Consensus       112 ig~~~d~~l~r~l~r~Gv~dyl~~P~~~~~l~~ai~~~~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~LA~~~~  191 (427)
T Consensus        37 ~~~~~~~~~~~e~~~~~l~~~~~~~~~~~~~~~~~~~~----~~~~~~kp~Vil~VG-VNG~GKTTTIaKLA~~l~~-~G  110 (284)
T TIGR00064        37 GKKVKDEEKLKEILKEALKEILKEILDKDTLLDLEQIE----ELPEEKKPNVILFVG-VNGVGKTTTIAKLANKLKK-QG  110 (284)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH----HCCCCCCCEEEEEEE-EECCCHHHHHHHHHHHHHH-CC
T ss_conf             35577078999999999999874112321133443344----301478977999984-4088601028899999987-49


Q ss_pred             CCEEEEECCCCCCCCHHHCCCCCCCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEECCCC-CCCHHCCCHHHHHHHHHH
Q ss_conf             9499997879898603343899878988863184561243376532024898068724876-120320799999998999
Q gi|254780725|r  192 METLLADLDLPYGTANINFDKDPINSISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAM-LSRTYDFDEKMIVPVLDI  270 (427)
Q Consensus       192 ~~VlLvDlDl~~g~~~~~l~~~~~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~a~~~-~~~~~~~~~~~l~~ll~~  270 (427)
T Consensus       111 k~V~laAgDTF-RAAA--------------~EQ--------L~~Wa~--R~gv~vi~~~~gn~DP----AaV~fDAi~~A  161 (284)
T TIGR00064       111 KSVLLAAGDTF-RAAA--------------IEQ--------LEVWAK--RLGVDVIKQKEGNADP----AAVIFDAIQAA  161 (284)
T ss_pred             CEEEEECCCHH-HHHH--------------HHH--------HHHHHH--HHCCEEEECCCCCCCC----HHHHHHHHHHH
T ss_conf             90899827524-7999--------------999--------999898--8387554078898871----78999989999


Q ss_pred             HHHCCCEEEECCCCCCCH---HH------HHHH------HHCCCCCCCCCCCHH--HHHHHHHHHHHHHHCCCCCCCCEE
Q ss_conf             851288899738888898---99------9998------620125435787768--899999999999981987675389
Q gi|254780725|r  271 LEQIFPLVILDVPHVWNS---WT------QEVL------TLSDKVVITTSLDLA--GLRNSKNLIDVLKKLRPADKPPYL  333 (427)
Q Consensus       271 l~~~yd~VIiD~p~~~~~---~~------~~~L------~~AD~vviV~~p~~~--slr~a~~ll~~l~~~~~~~~~~~i  333 (427)
T Consensus       162 k~~niDvvliDTAGRLqnk~NLm~EL~KI~RV~~k~~~~~aP~e~lLVlDAt~Gqna~~QA~~F~eav-------~ltGi  234 (284)
T TIGR00064       162 KARNIDVVLIDTAGRLQNKVNLMDELKKIKRVIKKVDPVDAPDEVLLVLDATTGQNALEQAKVFNEAV-------GLTGI  234 (284)
T ss_pred             HHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHC-------CCCEE
T ss_conf             87499789973475454662039999999998732102578755754220222030899999986540-------68858


Q ss_pred             EEECCCCCCCCHHHHHHHHHHHCCCEEEE---------ECCCHHHHHHHH
Q ss_conf             99565898752005999999848953799---------068799999988
Q gi|254780725|r  334 VLNQVKTPKKPEISISDFCAPLGITPSAI---------IPFDGAVFGMSA  374 (427)
Q Consensus       334 VlNr~~~~~~~~i~~~~~~~~lg~~~~~~---------IP~D~~~~~~A~  374 (427)
T Consensus       235 iLTKLDg~AKGG~~-l~i~~~l~~Pv~~~G~GE~~dDL~~Fd~~~fv~~L  283 (284)
T TIGR00064       235 ILTKLDGTAKGGII-LAIAYELKLPVKFIGVGEKIDDLAPFDADWFVEAL  283 (284)
T ss_pred             EEECCCCCCHHHHH-HHHHHHHCCCEEEEECCCCHHHHCCCCHHHHHHHC
T ss_conf             99634688037899-98899857976998548873320147978998750