>TIGR02789 nickel_nikB nickel ABC transporter, permease subunit NikB; InterPro: IPR014156 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 consists of the NikB family of nickel ABC transporter permeases. Operons that contain this protein also contain a homologous permease subunit NikC. Nickel is used in cells as part of urease or certain hydrogenases or superoxide dismutases..

Probab=97.47  E-value=0.005  Score=37.08  Aligned_cols=219  Identities=20%  Similarity=0.265  Sum_probs=149.7

Q ss_pred             CCCCCCCCCC------CCCHHHHHHHHHHHHHH----HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCH--HHHH
Q ss_conf             3357411111------10024787799999999----9998756775444127868899978988887614722--8999
Q gi|254780172|r  162 GGLGLSIVET------SLWGGLLVTLVISFFGI----IISMPLGILLALGRNSNIPVLRYACITFIELFRGVPL--VTVL  229 (386)
Q Consensus       162 gg~gl~~V~t------~~~gGl~~Tl~l~~~~~----~~~~~lG~llal~r~s~~~~l~~~~~~~ie~~Rg~Pl--i~~l  229 (386)
T Consensus        78 LDFGiSYi~i~rpV~De~~~~LPaTl~LA~~aL~i~vlvSvPLG~LAA~~r~~---~~D~~~R~~~FlG~siPnFWLA~L  154 (315)
T TIGR02789        78 LDFGISYISIDRPVLDEVARSLPATLELAGLALVIVVLVSVPLGILAARYRDR---LPDHAVRFISFLGVSIPNFWLAFL  154 (315)
T ss_pred             HCCCCEEEECCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             31464056668950888974353889999999999999984088999887368---640789999999643056899999


Q ss_pred             --HHHHHHHHHHCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             --9999976641558877-387999999999998999899999999845-866789999962168999999996998998
Q gi|254780172|r  230 --FMASIMLPLFLPDTWD-VDKLLRALLGVSAFASAYIAEVLRGGLQSI-SKGQFEAANSLGLSYLQKMRLIIMPQVIKR  305 (386)
Q Consensus       230 --f~~~~~lp~~lp~g~~-~~~~~~a~i~l~l~~aAy~aEi~Rggl~sv-p~GQ~EAA~alGls~~q~~~~IilPQAlr~  305 (386)
T Consensus       155 Lv~~fsvyL~lLP~~G~gtW~HlvLP~~tlal~~~a~y~RLLRaS~Ld~~qe~yv~yAR~RGi~~~~v~~~H~Lrna~~p  234 (315)
T TIGR02789       155 LVFLFSVYLDLLPVEGAGTWQHLVLPAVTLALMSVAIYARLLRASMLDNLQERYVTYARVRGIKERNVIRRHILRNAILP  234 (315)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEHECCCCHHHHHHHHHHCCCCHHH
T ss_conf             99999998613376778733113388899999999999999999999862887073011026465776886324111025


Q ss_pred             HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHCC--
Q ss_conf             6200479999999612899999999999999997410100355136999999999999999999-9999999998433--
Q gi|254780172|r  306 VIPGIVNTFIGLFKDSSLISIINMFDLLGIVRVNFSESTWISSVTPTTGLIFIGFVFWIFCFSI-SLYSVFIEKTLHK--  382 (386)
Q Consensus       306 ~iP~l~n~~i~l~KdTsL~~~Ig~~el~~~~~~~~~~~~~~~~~~~~e~y~~~a~iY~ii~~~l-s~~~~~lE~rl~~--  382 (386)
T Consensus       235 ~iTA~GM~~g~Ll~GT~viE~i--FswPG~GRy~i~-AifNRDyPviQcy~Ll~~~lfv~cNLivD~~~a~lDPR~rR~E  311 (315)
T TIGR02789       235 MITALGMHIGELLGGTLVIENI--FSWPGVGRYAIS-AIFNRDYPVIQCYTLLMALLFVLCNLIVDLLQALLDPRIRRKE  311 (315)
T ss_pred             HHHHHHHHHHHHHHCCEEEEEE--CCCCCHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             6776001388784071145410--126661045743-3562376389999999999999999999999985187611104


Q ss_pred             CCCC
Q ss_conf             7899
Q gi|254780172|r  383 GSKK  386 (386)
Q Consensus       383 ~~rR  386 (386)
T Consensus       312 G~~a  315 (315)
T TIGR02789       312 GVHA  315 (315)
T ss_pred             CCCC
T ss_conf             6889