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