HHsearch alignment for GI: 254780724 and conserved domain: TIGR01187

>TIGR01187 potA polyamine ABC transporter, ATP-binding protein; InterPro: IPR005893 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 comprises the spermidine/putrescine ABC transporter, ATP binding subunit in bacteria and its equivalents in archaea. This transport system belongs to the larger ATP-Binding Cassette (ABC) transporter superfamily. Polyamines like spermidine and putrescine play a vital role in cell proliferation, differentiation, and ion homeostasis. The concentration of polyamines within the cell are regulated by biosynthesis, degradation and transport (uptake and efflux included).; GO: 0015417 polyamine-transporting ATPase activity, 0015846 polyamine transport, 0016020 membrane.
Probab=96.46  E-value=0.0043  Score=40.23  Aligned_cols=169  Identities=20%  Similarity=0.293  Sum_probs=81.8

Q ss_pred             ECCCCCCHHHHHHHHHHHCCCCCCEEEE--EC----CHHHC-----------CCC----CC-------------------
Q ss_conf             8188888889999998303876767999--64----21312-----------567----87-------------------
Q gi|254780724|r  256 SGGTGSGKTTLLNCLTRYIDKDERIVTC--ED----TAELQ-----------LQQ----PH-------------------  295 (483)
Q Consensus       256 sG~TGSGKTT~L~al~~~i~~~~rivtI--ED----~~El~-----------l~~----~~-------------------  295 (483)
T Consensus         2 LGpSGcGKTTlLrlLAGf~~pd~G~i~ldg~d~~~vPp~~R~in~vFQsYALFPHMTv~~NvAfgLk~~k~~~~ei~~RV   81 (331)
T TIGR01187         2 LGPSGCGKTTLLRLLAGFEQPDSGSIMLDGEDVTEVPPHLRSINMVFQSYALFPHMTVEENVAFGLKMRKVPRAEIKPRV   81 (331)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEECCCCCCCCCHHHHCCCCCCCCCCCHHHHHHHH
T ss_conf             78888747999999834587775507756710121572206146057354356212277645444351788856688999


Q ss_pred             -----EEEEEEE--CCCCCCCCCCHHHHHHHHHHHCCCCEEEECCCCCH---HHH---HH-HHHHHCCCCEEEHHH-CCC
Q ss_conf             -----5677874--16666530001899998752059988996575879---999---99-999873970102000-478
Q gi|254780724|r  296 -----VVRLETR--PPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGP---EVL---DL-LQAMNTGHDGSMGTI-HAN  360 (483)
Q Consensus       296 -----~v~~~~~--~~~~e~~~~~t~~~ll~~aLR~~PD~IiVGEiRg~---Ea~---~~-l~A~~TGH~G~ltTl-Ha~  360 (483)
T Consensus        82 ~e~L~~V~L~~~a~rkp~qLSGGQ~QRvAlARa~v~kPk~LLlDEpLsALD~kLR~~MQ~ELk~~~~~-LG-iT~v~VTH  159 (331)
T TIGR01187        82 KEALRLVQLEEFAKRKPHQLSGGQQQRVALARALVFKPKILLLDEPLSALDKKLRDQMQLELKTLQEQ-LG-ITFVFVTH  159 (331)
T ss_pred             HHHHHHCCCCHHHCCCCCCCCCCHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHH-CC-CEEEEEEC
T ss_conf             99974213001104673104685289999999986089567711772264389899889999999872-68-28999701


Q ss_pred             CHHHHHH---HHHHHHHH--CCCCCCHHHHH---------HHHHHH-CCEEEEEEECCC-----C--CEEEEEEEEEEEE
Q ss_conf             8888999---99975530--46799989999---------999742-358899987699-----9--8789999999841
Q gi|254780724|r  361 NARESFG---RMEAMIAM--GGFTLPSQMVR---------EIITSS-LDVIVQTQRLRD-----G--SRRITNICEIVGM  418 (483)
Q Consensus       361 s~~~ai~---RL~~m~~~--~~~~~~~~~~~---------~~ia~a-vd~iV~~~r~~d-----G--~Rrv~~I~Ev~g~  418 (483)
T Consensus       160 DQ~EA~TMsDRI~~l~~Gki~Q~~-~PeeiY~~P~~~FvA~FiGe~nvf~~~~~e~~~~~~v~~~P~~~r~~~~~~~~~v  238 (331)
T TIGR01187       160 DQEEALTMSDRIAILRKGKIAQIG-TPEEIYEEPSNLFVARFIGEINVFEATVIERKEEQLVLAGPVEGRECKIYEDLPV  238 (331)
T ss_pred             CHHHHHHHHCEEEEECCCEEEEEC-CCHHHHHCCCCCCCEEECCCEEEEEEEEEEECCCCEEECCCCCCEEEEEEECCCC
T ss_conf             848987540202421387588836-8468751777531000106145556788862578668428743147765321666


Q ss_pred             ECC---EEEEEE
Q ss_conf             498---899867
Q gi|254780724|r  419 EGN---VIITQD  427 (483)
Q Consensus       419 e~~---~~~~~~  427 (483)
T Consensus       239 ~~~~~~~v~LRP  250 (331)
T TIGR01187       239 EAKQPLHVVLRP  250 (331)
T ss_pred             CCCCCEEEEECC
T ss_conf             777516899838