HHsearch alignment for GI: 254780705 and conserved domain: TIGR01581

>TIGR01581 Mo_ABC_porter NifC-like ABC-type porter; InterPro: IPR006469 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 entry represents a clade of ABC porter genes with relatively weak homology compared to its neighbour clades, the molybdate (IPR006229 from INTERPRO) and sulphate (IPR005667 from INTERPRO) porters. Neighbour-Joining, PAM-distance phylogenetic trees support the separation of these clades in this way. Included in this group are the NifC genes of Clostridium pasteurianum and Pasteurella multocida, which are involved in the biosynthesis and/or control of nitrogenase. It would be reasonable to presume that NifC acts as a molybdate porter since the most common form of nitrogenase is a molybdoenzyme. Several other sequences falling within this group are annotated as molybdate porters and one, from Halobacterium, is annotated as a sulphate porter. There is presently no experimental evidence to support annotations with this degree of specificity.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane.
Probab=99.96  E-value=1.1e-27  Score=195.28  Aligned_cols=194  Identities=23%  Similarity=0.286  Sum_probs=158.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC------
Q ss_conf             26678999999999999999999999999986437302456789899887653369999999999998626663------
Q gi|254780705|r  203 IGVAVVGSLYMMLIVIGLSFPLGIASAIYLEEFSHKGFFSSFVQANINNLASVPSIVYGILGSAVLINFFKMPR------  276 (425)
Q Consensus       203 i~~ai~gTl~~~~ia~~ia~pigv~~aiyl~e~a~~~~~~~~i~~~i~~la~vPSIv~Gl~gl~~~~~~~~~~~------  276 (425)
T Consensus        19 ~~~al~lSl~Ts~~sl~l~~~~g~P~A~~lar~~-n~pl~~~l~~ll~LP~VlPPlV~G~aLLl~FG~~g~lG~~l~~aG   97 (226)
T TIGR01581        19 LIKALRLSLLTSLASLLLAVVLGIPTAYVLARVR-NFPLKKLLDTLLDLPLVLPPLVAGIALLLLFGRLGLLGPYLEAAG   97 (226)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHCC
T ss_conf             9999999999999999999999988999998875-068547789998665424665888999999720212689998644


Q ss_pred             ----CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ----0046897533454366899999999851106789899870772127777883975332589999999999876779
Q gi|254780705|r  277 ----STALVGGLILALMTLPSIIIATGVALRTVPSSIRSAALGLGASKVQTVFHHVLPLAMPAILTGSTVSLARALGETA  352 (425)
Q Consensus       277 ----~~~l~g~~~l~~m~lP~i~~~~~~al~~vp~~~~eaa~~LGas~~~~~~~v~lp~a~pgi~~g~il~~~ra~GEta  352 (425)
T Consensus        98 i~~~Fs~~gvvlAQ~FVa~p~~vr~~r~~f~~v~~~ye~va~~lG~g~~~t~~~v~lPl~~~~ll~G~vLafaRalGEFG  177 (226)
T TIGR01581        98 IQVIFSTLGVVLAQTFVASPYLVRVARSTFESVDPDYEDVARSLGAGPLETFRKVTLPLARPGLLAGLVLAFARALGEFG  177 (226)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             16788889999999999999999999976730383489999880787226788875775336888879999999756567


Q ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             999985432101366561344557999999860366500699999999999999999
Q gi|254780705|r  353 PLLFVGMVAFVTDYPVGVTDIATAFPVQIYLWAADAERPFVERTFGAILLLLIFLAV  409 (425)
Q Consensus       353 ~ll~~~~~~~~~~~p~~~~~p~~tlp~~Iy~~~~~~~~~~~~~~~aa~lvLl~~~~~  409 (425)
T Consensus       178 ATL~~AG~~---------~g~TrTlPl~iY~~~~~d~---~~~aV~~a~~Ll~ia~~  222 (226)
T TIGR01581       178 ATLMFAGSL---------QGKTRTLPLAIYLNIESDD---IEAAVALAVLLLVIAFL  222 (226)
T ss_pred             HHHHHHCCC---------CCCCEEHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHH
T ss_conf             899984367---------7753012788864574177---32799999999999999