HHsearch alignment for GI: 254780724 and conserved domain: TIGR01193

>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter; InterPro: IPR005897 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 contains ABC-type bacteriocin transporter. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc. Peptide bacteriocins are exported across the cytoplasmic membrane by a dedicated ATP-binding cassette (ABC) transporter. These ABC-transporters have an N-terminal peptidase domain that belong to MEROPS peptidase family C39 (clan CA); a central multi-pass transmembrane region and a C-terminal ABC transporter domain. These transporters have dual function: (i) they remove the N-terminal leader peptide from its bacteriocin precursor by cleavage at a Gly-Gly bond and (ii) transport the mature bacteriocin across the cytoplasmic membrane. This represents a novel strategy for secretion of bacterial proteins . Many bacteria are known to regulate diverse physiological processes through this system, such as bioluminescence, regulation of sporulation, virulence factor expression, antibiotics production, competence for genetic transformation, and activation of biofilm formation .; GO: 0008234 cysteine-type peptidase activity, 0019534 toxin transporter activity, 0006810 transport, 0016020 membrane.
Probab=95.87  E-value=0.011  Score=37.49  Aligned_cols=189  Identities=15%  Similarity=0.245  Sum_probs=91.0

Q ss_pred             HHHHHHHHC-CHHHHHHC-CHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCEEEEE
Q ss_conf             999998851-97876408-9899999999999999974187789678999999999988565633588588332179985
Q gi|254780724|r   65 IFTTLIEMI-DITQLSQY-DSQSARDEIATLMNEIVSVKKITMSLDEQLDLFEDLCNDILGYGPLQPLIARDDIADIMVN  142 (483)
Q Consensus        65 i~~~l~~~~-d~~~~~~~-~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~l~~~i~~e~~glGpL~~ll~D~~VsdI~in  142 (483)
T Consensus       333 LnSsIIEd~nGIETIKsL~sE~~~y~KId~~F~~yL~K~f~y~k~~~~Q~AiK~~~~LiL~------------Vv-ILW~  399 (710)
T TIGR01193       333 LNSSIIEDLNGIETIKSLTSEAERYKKIDSEFEDYLNKSFKYQKADQVQQAIKAVLKLILN------------VV-ILWV  399 (710)
T ss_pred             HHHHHHHCCCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HH-HHHH
T ss_conf             4447662587510010052366777666788888888887778889998999999878876------------66-5344


Q ss_pred             CCCCEEEEE--CCEEEECC---CCCCCHHHHHHHHH---HH--HHHHCCCCCCCCCEEEEEECCCCEEEEECCCCCCCCC
Q ss_conf             699189982--78389717---62079899999999---99--9980981243387787982376203453155357881
Q gi|254780724|r  143 GSNKVFIEV--NGKTVETG---INFRDNEQLLSVCQ---RI--VNQVGRRVDESSPICDARLLDGSRVNVIIPPLALDGP  212 (483)
Q Consensus       143 g~~~I~ve~--~G~~~~~~---~~f~~~~~l~~~i~---rl--a~~~g~~i~~~~P~~d~~lpdg~Ri~~~~~p~s~~G~  212 (483)
T Consensus       400 Ga~lVm~~k~tlGqLiTfNALl~YFl~P--LeNIINLQpKLQ~ArVANnRLNEVY-LV~SEF~~~~~~t~~~---~lng-  472 (710)
T TIGR01193       400 GAILVMRGKLTLGQLITFNALLSYFLTP--LENIINLQPKLQAARVANNRLNEVY-LVDSEFEKKKKITELE---NLNG-  472 (710)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHCH--HHHHHHCCCHHHHHHHHHHHCCEEE-ECCHHHCCCCCCCHHH---CCCC-
T ss_conf             2233432464147899999999875163--4545622513556876441145344-0120100564002201---5776-


Q ss_pred             EEEEEECCCCCCCHHHHHHCCCCCHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             68884057654667888650699889999989862258848998188888889999998303876767999
Q gi|254780724|r  213 TLTIRKFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDKDERIVTC  283 (483)
Q Consensus       213 ~i~IRk~~~~~~~l~~l~~~g~~~~~~~~~l~~~v~~~~nilVsG~TGSGKTT~L~al~~~i~~~~rivtI  283 (483)
T Consensus       473 di~~~~~-----s----y~YG~g~~~L~d-i~L~I~~n~k~tiVGmSGSGKsTLaKLLV~FfePQ~~sG~I  533 (710)
T TIGR01193       473 DIVVNDV-----S----YSYGYGSNVLSD-ISLTIKKNEKITIVGMSGSGKSTLAKLLVGFFEPQAESGEI  533 (710)
T ss_pred             CEEEEEE-----E----EECCCCCCCCCC-CEEEEECCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCEE
T ss_conf             5467434-----6----644788732026-42365078548997367974899998752035899887736