HHsearch alignment for GI: 254780606 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=93.61  E-value=0.17  Score=29.30  Aligned_cols=169  Identities=20%  Similarity=0.332  Sum_probs=92.3

Q ss_pred             EECCCCCHHHHHHHHHHHHHHHCCHHHEEEEEEC-------CC----CCEECCCCCCCCEEEEEEECHHHHHHHHHHHHH
Q ss_conf             7078753447999999999985680110799972-------34----210001257752000044441787689999998
Q gi|254780606|r  418 AGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVD-------PK----MLELSVYDGIPHLLTPVVTNPKKAVMALKWAVR  486 (744)
Q Consensus       418 aG~TgsGKS~~l~~~i~sl~~~~~p~~~~~~liD-------~k----~~~~~~~~~~ph~~~~v~~~~~~~~~~l~~~~~  486 (744)
T Consensus         2 LGpSGcGKTTlLr-lLAGf~---~pd~G~i~ldg~d~~~vPp~~R~in~vFQsYALFPHMT--v~~NvAfgLk~~k~~~~   75 (331)
T TIGR01187         2 LGPSGCGKTTLLR-LLAGFE---QPDSGSIMLDGEDVTEVPPHLRSINMVFQSYALFPHMT--VEENVAFGLKMRKVPRA   75 (331)
T ss_pred             CCCCCCCHHHHHH-HHHCCC---CCCCCEEEECCCCCCCCCCCCCCCCCEEECCCCCCCCC--HHHHCCCCCCCCCCCHH
T ss_conf             7888874799999-983458---77755077567101215722061460573543562122--77645444351788856


Q ss_pred             HHHHHH------HHHHHCCCCCHHH----HHHHHHHHHCCCCCCCCCCCCCCCEEEEEHHH-HHHHHHHCCHHHHHHHH-
Q ss_conf             667699------9999807786799----99988642026776665432338679998445-68767531035899999-
Q gi|254780606|r  487 EMEERY------RKMSHLSVRNIKS----YNERISTMYGEKPQGCGDDMRPMPYIVIIVDE-MADLMMVAGKEIEGAIQ-  554 (744)
Q Consensus       487 em~~r~------~~~~~~~~~~i~~----~n~~~~~~~~~~~~~~~~~~~~~p~ivvviDE-~a~l~~~~~~~~e~~~~-  554 (744)
T Consensus        76 ei~~RV~e~L~~V~L~~~a~rkp~qLSGGQ~QRvAlARa~v~---------kPk~LL-lDEpLsALD----~kLR~~MQ~  141 (331)
T TIGR01187        76 EIKPRVKEALRLVQLEEFAKRKPHQLSGGQQQRVALARALVF---------KPKILL-LDEPLSALD----KKLRDQMQL  141 (331)
T ss_pred             HHHHHHHHHHHHCCCCHHHCCCCCCCCCCHHHHHHHHHHHHC---------CCCEEE-ECCCHHHHH----HHHHHHHHH
T ss_conf             688999999742130011046731046852899999999860---------895677-117722643----898998899


Q ss_pred             HHHHHHHCCEEEEEEEECCCCCCCCHHHHHHCCCCEEEE----ECCCHHHCCHHCCCCCHHHH
Q ss_conf             999964201358999851654444146788505630572----03681110032676316885
Q gi|254780606|r  555 RLAQMARAAGIHLIMATQRPSVDVITGTIKANFPIRISF----QVTSKIDSRTILGEHGAEQL  613 (744)
Q Consensus       555 ~la~~~ra~GihlilatQrp~~~vi~~~ik~n~~~ri~~----~v~~~~dsr~il~~~gae~l  613 (744)
T Consensus       142 ELk~~~~~LGiT~v~VTHDQ~-EA~TM------sDRI~~l~~Gki~Q~~~PeeiY~~P~~~Fv  197 (331)
T TIGR01187       142 ELKTLQEQLGITFVFVTHDQE-EALTM------SDRIAILRKGKIAQIGTPEEIYEEPSNLFV  197 (331)
T ss_pred             HHHHHHHHCCCEEEEEECCHH-HHHHH------HCEEEEECCCEEEEECCCHHHHHCCCCCCC
T ss_conf             999998726828999701848-98754------020242138758883684687517775310