HHsearch alignment for GI: 254780606 and conserved domain: TIGR02211

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein; InterPro: IPR011924 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 entry represents LolD, a member of the ABC transporter family. LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on the residue immediately following the modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. Excluded from this entry are homologs from the archaeal genus Methanosarcina .; GO: 0005524 ATP binding, 0006810 transport, 0016020 membrane.
Probab=93.65  E-value=0.048  Score=33.01  Aligned_cols=168  Identities=18%  Similarity=0.243  Sum_probs=87.5

Q ss_pred             HCCCCCCEEEEEEECCCCCEEECCHHHCCCEEEEECCCCCHHHHHHHHHHHHHHHCCHHHEEEEEECCCCC---------
Q ss_conf             11467836898420578873211201148469970787534479999999999856801107999723421---------
Q gi|254780606|r  385 FSHSKANLALCLGKTISGESVIADLANMPHILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVDPKML---------  455 (744)
Q Consensus       385 ~~~~~~~l~~~~g~~~~g~~~~~dl~~~PH~lvaG~TgsGKS~~l~~~i~sl~~~~~p~~~~~~liD~k~~---------  455 (744)
T Consensus        11 Y~~G~~~~~vL~g-------~sl~i~~GE~~~IvG~SGSGKSTLLH-lLGGL-D~PT~G~v~f~G~~l~~lS~~~~~~LR   81 (221)
T TIGR02211        11 YQEGKLQTRVLKG-------VSLSIGKGEIVAIVGSSGSGKSTLLH-LLGGL-DNPTSGEVLFNGQSLSKLSSNERAKLR   81 (221)
T ss_pred             EEECCEEEEEECC-------CCCEEECCCEEEEECCCCCCHHHHHH-HHHCC-CCCCCCEEEECCCCHHHCCHHHHHHHH
T ss_conf             5408623665227-------45123066337987367871689999-87306-899631589706323440446788751


Q ss_pred             --EECCCCCCCCEEEEEEECHHHHHHHH----HHHHHHHHHHHHHHHHCCCCCHHHH---------HHHHHHHHCCCCCC
Q ss_conf             --00012577520000444417876899----9999866769999998077867999---------99886420267766
Q gi|254780606|r  456 --ELSVYDGIPHLLTPVVTNPKKAVMAL----KWAVREMEERYRKMSHLSVRNIKSY---------NERISTMYGEKPQG  520 (744)
Q Consensus       456 --~~~~~~~~ph~~~~v~~~~~~~~~~l----~~~~~em~~r~~~~~~~~~~~i~~~---------n~~~~~~~~~~~~~  520 (744)
T Consensus        82 N~~LGFiYQFHHLL~-dFtaLENVaMP~LIg~~s~~ea~~~A~~mL~~VgL~~R~~h~PSELSGGERQRvAIARALvN--  158 (221)
T TIGR02211        82 NKKLGFIYQFHHLLP-DFTALENVAMPLLIGKKSKKEAKERAYEMLEKVGLEHRINHRPSELSGGERQRVAIARALVN--  158 (221)
T ss_pred             HHHCCCEEEHHHCCC-CCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHC--
T ss_conf             222584443202030-00026887777753589988999999999886073344555777345633799999998618--


Q ss_pred             CCCCCCCCCEEEEEHHHHHH-HHHHCCHHHHHHHHHHHHHHHCCEEEEEEEECCCC
Q ss_conf             65432338679998445687-67531035899999999964201358999851654
Q gi|254780606|r  521 CGDDMRPMPYIVIIVDEMAD-LMMVAGKEIEGAIQRLAQMARAAGIHLIMATQRPS  575 (744)
Q Consensus       521 ~~~~~~~~p~ivvviDE~a~-l~~~~~~~~e~~~~~la~~~ra~GihlilatQrp~  575 (744)
T Consensus       159 -------~P~lv-lADEPTGNLD~---~~a~~iF~L~~eLN~~~~TsflvVTHD~~  203 (221)
T TIGR02211       159 -------QPSLV-LADEPTGNLDN---NNAKSIFELMLELNRELNTSFLVVTHDLE  203 (221)
T ss_pred             -------CCCEE-ECCCCCCHHHH---HHHHHHHHHHHHHHHHCCCEEEEEECCHH
T ss_conf             -------97658-61298853237---77999999999988653916999834757