HHsearch alignment for GI: 254780806 and conserved domain: TIGR01166

>TIGR01166 cbiO cobalt ABC transporter, ATP-binding protein; InterPro: IPR005876 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 the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. This superfamily includes two groups, one which catalyses the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drives both the process of uptake and efflux.; GO: 0006824 cobalt ion transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=95.94  E-value=0.046  Score=31.52  Aligned_cols=158  Identities=19%  Similarity=0.214  Sum_probs=87.8

Q ss_pred             CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH-HCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCC
Q ss_conf             98768749999808898888999999999999-87995999987877680112124633345411676302577121024
Q gi|254780806|r    1 MEEKKSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILI   79 (265)
Q Consensus         1 ~~~~~~kvI~v~s~KGGvGKTT~a~nlA~~la-~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~   79 (265)
T Consensus        13 ~~~~~G~~~aLl-G~NGaGKsTLl~~LnG~LrP~~G--~v~~dG~~l~Ysrkg----L~~~R~~V~~VfQdPD--DQlF~   83 (190)
T TIGR01166        13 FAVERGEVLALL-GANGAGKSTLLLHLNGLLRPQSG--KVLLDGEPLDYSRKG----LLEVRQRVGLVFQDPD--DQLFA   83 (190)
T ss_pred             EEECCCCEEEEE-CCCCCCHHHHHHHHCCCCCCCCC--EEEECCEECCCCCHH----HHHHCCEEEEEEECHH--HHCCC
T ss_conf             022057168987-28998578998874367779755--587678540357244----6752503003762634--42026


Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHH-----HHHCCCCCC
Q ss_conf             444442000148874577500012322221023332247651027820331013332222101123-----310011111
Q gi|254780806|r   80 QTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAA-----ADSILVPLQ  154 (265)
Q Consensus        80 ~~~~~~l~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~~~~~~~al~a-----ad~viip~~  154 (265)
T Consensus        84 a~V~~DVaFGPlNLGL~e~Ev~--------~RV~eAL~~vg~~~~~~rp~h~L-S~GekkRvAIAGAvAM~Pd~l~L-DE  153 (190)
T TIGR01166        84 ADVDQDVAFGPLNLGLSEAEVE--------RRVREALTAVGISGLEERPTHLL-SGGEKKRVAIAGAVAMRPDVLLL-DE  153 (190)
T ss_pred             CCCCCCCCCCCCCCCCCHHHHH--------HHHHHHHHHCCHHHHHHCCHHHC-CCCCHHHHHHHHHHHHCCCEEEE-EC
T ss_conf             7622100335456733715767--------87899998606322441224115-58613577777588616634664-27


Q ss_pred             CC-CHHHHHHHHHHHHHHHHHHHH
Q ss_conf             23-113788875335777655432
Q gi|254780806|r  155 CE-FFALEGLSQLLETVEEVRRTV  177 (265)
Q Consensus       155 p~-~~s~~~~~~~~~~i~~~~~~~  177 (265)
T Consensus       154 PTAGLDp~G~~q~~~~l~~L~~~G  177 (190)
T TIGR01166       154 PTAGLDPAGAEQLLAILRRLRAEG  177 (190)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             888978747999999988787239