HHsearch alignment for GI: 254780386 and conserved domain: TIGR01843
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family; InterPro: IPR010129 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). Type I secretion is an ABC transporter that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C terminus of the transported protein. This entry represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This entry selects a group of sequences closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.; GO: 0015031 protein transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=97.32 E-value=6.9e-05 Score=50.94 Aligned_cols=348 Identities=13% Similarity=0.132 Sum_probs=154.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHEEEE---EEEEEEEEEEEE-----CCCEEEEECCCCCEEEEEECCCCCEEECCC
Q ss_conf 568616899999999999999987640671---258999799995-----387389846888689999857898933697
Q gi|254780386|r 11 RNHPASLKRMTLLSIIGIIGLITWSILLPI---EISVSSSGEILN-----EDNVVEIKSPFSGIIKKFQVENGSQILQGT 82 (440)
Q Consensus 11 ~~~p~~~~~~~~~~~~~~~~~~~w~~~~~~---~~~v~~~G~i~~-----~~~~~~I~s~~~G~V~~i~VkeGd~VkkGq 82 (440)
T Consensus 1 ~~~~r~~~~~~~~~v~~~~~WA~~~~ld~va~A~G~V~~~g~~k~vQhlegGi~~~I~V~EG~-----~V~~Gq~L~~Ld 75 (434)
T TIGR01843 1 SRFARLITWLIALLVVIFLLWAAFAPLDSVATAQGKVVPSGNVKVVQHLEGGIVREILVREGD-----RVKAGQVLVELD 75 (434)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEECCCEEEEECCCCCEEEEEEECCCC-----EECCCCCCEEEC
T ss_conf 932798899999999999998887610258998669997074779966865344135522586-----420377013541
Q ss_pred EE-EEECHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89-99964899888999874343323321001233-3322211455542235-688887765546788654333655420
Q gi|254780386|r 83 PL-LTFEDIETTDLIDLKKVSIKNLRCHIDTEKSA-LDFLNNKYDVLEKAFE-SREEQLLDFLGKYHSTCSKVFNYGISS 159 (440)
Q Consensus 83 ~L-~~ld~~~~~~~l~~~~~~l~~l~~~l~~~~~~-l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (440)
T Consensus 76 ~t~~~A~~~~~~~~~~~l~~~~~R~~Ae~~~~~~~~~~~~~~~~~~~~~p~~r~~~~~~~~~~~~~f~~~~~~l~~~~~~ 155 (434)
T TIGR01843 76 ATSVEADAAELESQVLALEAEVARLRAEINSEEASVIEFPDILLSAIDDPFERRAVAELVKGQQSLFESRKSALRAQLES 155 (434)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 35789999999999999999999999998323257544675776201141203712899999999999999988899999
Q ss_pred CCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCC
Q ss_conf 01122211221002232101122322222210233332221012222221110000111002466653101223322222
Q gi|254780386|r 160 VYRSLKMKLTRMRSIYLNRLDLENKSSLLRALLSSHQKDLTMMKNLFEKNAVSQNDLNQQERIVYKSTLELRENIHEQKN 239 (440)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~el~~~~~l~~~~~~~~~~l~~~~~~~~~~~~el~~~~~~~~~ 239 (440)
T Consensus 156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~L~~~g~~~~~~~L~~e~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (434)
T TIGR01843 156 ILAQIKQLEAELEGLQAQLQALRQQLELISEELEALRKLKEKGLVSRLELLELERERAELQGELARLEAELEVLKAQIDE 235 (434)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999998789999999999998630663343216789999999999999999879999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------CCCCCCCCCCCCCEEEEECCEEECCCC
Q ss_conf 22222210001223332112332221222222221222332212---------222212345554116873121201222
Q gi|254780386|r 240 MLRHINELYDEANLEFANYLKEISRDLEQNQRTFADEMSKLTIL---------EKTREQKTILSPIAGTIVYNQSFSSSN 310 (440)
Q Consensus 240 ~~~~l~~~~~~~~~~~~~~~~e~~~~l~e~~~~l~~~~~~l~~l---------~~~l~~~~I~AP~~G~V~~l~~~~~G~ 310 (440)
T Consensus 236 ~~~~~~~~~~~~~~e~~~~l~~A~~~l~~~~~~l~~a~~~~~~~~irsPvdG~v~~l~~~T----~GgVv------~pG~ 305 (434)
T TIGR01843 236 LQLKLQQLEQTFREEVLEELTEAQARLAELREELSKARDRLQRLIIRSPVDGTVQSLKVHT----VGGVV------QPGE 305 (434)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEECCCCEEEEEEEEEE----ECCEE------CCCC
T ss_conf 9999988999999999999999999999999999999987532114425451999999984----05443------2786
Q ss_pred ----CCCCCCCCC---CCCCCC-----CCEEEEEE---ECHHHHHHCCCCCCEEEEEEECCCCC-----CCEEEEEEEEE
Q ss_conf ----124445542---103355-----65047753---26223110158983179998128875-----44399999997
Q gi|254780386|r 311 ----YAQQSQPLM---KIVPHS-----KLTYIRAK---VTPKQIQHVKKGYTATVRFPHYADIR-----EKKFKAIIEKI 370 (440)
Q Consensus 311 ----~v~~G~~l~---~Ivp~~-----~~l~v~~~---v~~~di~~i~~Gq~v~i~~~a~~~~~-----~~~~~G~V~~I 370 (440)
T Consensus 306 ~lm~IVP~~~~l~iEa~~~~~Dig~v~~Gq~a~ik~~AF~~~ryG~~~-G~V~~iS~D~~~DE~~~~~~~~yY~~ri-~~ 383 (434)
T TIGR01843 306 TLMEIVPEDDPLEIEAKLSNKDIGFVHVGQPAEIKFSAFPYTRYGLLN-GKVKSISPDTVEDERQGRQQGLYYRVRI-SI 383 (434)
T ss_pred CEEEEECCCCCEEEEEEECCCCCCEEECCCEEEEEEECCCCCCCCCEE-EEEEEECCCCHHHHHCCCCCCCEEEEEE-EE
T ss_conf 178983399965899997354653455587169999636860335189-9999862751144424787676667999-97
Q ss_pred ECCCC
Q ss_conf 13344
Q gi|254780386|r 371 DPIIS 375 (440)
Q Consensus 371 s~~~~ 375 (440)
T Consensus 384 ~~~~~ 388 (434)
T TIGR01843 384 DENTL 388 (434)
T ss_pred CCCEE
T ss_conf 32001