>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=91.76  E-value=0.87  Score=23.48  Aligned_cols=247  Identities=17%  Similarity=0.235  Sum_probs=149.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHC-CCCEEEE-ECCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             79999999950146999999999987301210344410-3720352-0100035453-5567004688778899999999
Q gi|254780171|r  128 ICRVYVEVFRNIPPLVVIFFLYKSVLSVLPIPDHSIVL-PFGMFLN-NRGLSFPTLT-MDTNAKIFVFSFVLGIVLSLFA  204 (398)
Q Consensus       128 la~~YVE~~RN~PLLlql~fwy~~v~~~lP~~~~~~~~-~~~~fls-nRGL~iP~p~-~~~g~~~~l~~lilaiila~~l  204 (398)
T Consensus        51 lA~~R~~LGLd~PLyvqY~~wl~~----------~~hLDFGiSYi~i~rpV~De~~~~LPaTl~LA~~aL~i~vlvSvPL  120 (315)
T TIGR02789        51 LADVRHELGLDQPLYVQYVNWLWK----------ALHLDFGISYISIDRPVLDEVARSLPATLELAGLALVIVVLVSVPL  120 (315)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHHH----------HHHHCCCCEEEECCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             998867517888077878999999----------9873146405666895088897435388999999999999998408


Q ss_pred             HHHHHHHHHH----HCCCCCCEEEEEEECCHHHHHHHHHHHHHHHHH-HHHCCCCCCCCCCC--CCHHHHHHHHHHHHHH
Q ss_conf             9999998643----112233204554210103558999765444332-21001311126821--4878999999999997
Q gi|254780171|r  205 TRLSRHFHEK----TGKALPLLYISTFLIFGLPTLVLIALKYQLHFD-KPVLGQFNFIGGST--VSPEFMSLYIALSCYT  277 (398)
Q Consensus       205 ~~~a~~~~~~----tg~~~~~~~~~~~~~~~~p~l~~~~~~~~~~~~-~p~l~~f~~~gG~~--l~p~f~a~~iaL~l~t  277 (398)
T Consensus       121 G~LAA~~r~~~~D~~~R~~~FlG~siPnFWL---A~LLv~~fsvyL~lLP~~G----~gtW~HlvLP-----~~tlal~~  188 (315)
T TIGR02789       121 GILAARYRDRLPDHAVRFISFLGVSIPNFWL---AFLLVFLFSVYLDLLPVEG----AGTWQHLVLP-----AVTLALMS  188 (315)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHCCCCCC----CCCCCHHHHH-----HHHHHHHH
T ss_conf             8999887368640789999999643056899---9999999999861337677----8733113388-----89999999


Q ss_pred             HHHHHHHHHHHHHHC-CHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH-HHHH
Q ss_conf             787999999999834-6367899989689989988898768999997410478999999754999999-999999-9999
Q gi|254780171|r  278 AAFIAEIVRSGLIAV-PRGQMEAAIALGLTHRKATRLVLLPQAMRSIIPPLTSQYLNLLKNSSLAVAV-GFADLV-SVGG  354 (398)
Q Consensus       278 aAyiaEivR~gI~sV-pkGQ~EAA~aLGls~~q~~r~VIlPQAlR~~iP~l~nq~i~l~K~SSLa~~I-g~~dl~-~~~~  354 (398)
T Consensus       189 ~a~y~RLLRaS~Ld~~qe~yv~yAR~RGi~~~~v~~~H~Lrna~~p~iTA~GM~~g~Ll~GT~viE~iFswPG~GRy~i~  268 (315)
T TIGR02789       189 VAIYARLLRASMLDNLQERYVTYARVRGIKERNVIRRHILRNAILPMITALGMHIGELLGGTLVIENIFSWPGVGRYAIS  268 (315)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEHECCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCEEEEEECCCCCHHHHHHH
T ss_conf             99999999999998628870730110264657768863241110256776001388784071145410126661045743


Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHC
Q ss_conf             998313775899999999999999-999999999967874304
Q gi|254780171|r  355 TIINQTGQAIEIILIWMFIYLSLS-IMIALFMNRLNAKIALKE  396 (398)
Q Consensus       355 ~~~~~t~~~~e~~~i~~~~Yl~is-l~iS~~~n~~~rr~~l~e  396 (398)
T Consensus       269 AifNRDyPviQcy~Ll~~~lfv~cNLivD~~~a~lDPR~rR~E  311 (315)
T TIGR02789       269 AIFNRDYPVIQCYTLLMALLFVLCNLIVDLLQALLDPRIRRKE  311 (315)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             3562376389999999999999999999999985187611104