HHsearch alignment for GI: 254780561 and conserved domain: TIGR01256

>TIGR01256 modA molybdate ABC transporter, periplasmic molybdate-binding protein; InterPro: IPR005950 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 describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represents a hydrophylioc periplasmic-binding protein in Gram-negative organisms and its counterpart in Gram-positive organisms is a lipoprotein. The other components of the system include ModB, an integral membrane protein and ModC, the ATP-binding subunit. Almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.; GO: 0015412 molybdate transmembrane-transporting ATPase activity, 0015689 molybdate ion transport, 0030288 outer membrane-bounded periplasmic space.
Probab=99.58  E-value=1.2e-13  Score=97.68  Aligned_cols=211  Identities=16%  Similarity=0.157  Sum_probs=147.1

Q ss_pred             HHHHHHHHHHHHHHC-CEEEEEECCCHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHHHHCCCCCCCCHHHCCCCCCCC
Q ss_conf             233889999998848-8799997288689997887531266410110133378999887521261367700021000124
Q gi|254780561|r   45 GAGPKIKQAFERKCN-CELKLIGLSDGVALLNKLRMEGENSAADIVLGFDNNLIDLARKTGLFAKSNIDASQLKLPIKWD  123 (338)
Q Consensus        45 ~~~~~i~~~Fek~~g-ikV~~~~~~~~~~~~~~~~a~~~~~~~Dv~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  123 (338)
T Consensus         6 ~Al~~i~~~F~k~~g~~~Vv~-sFgsSg~L~~QI~---~GAP~D~F~SA~~~~~~~L~~~g~~v~~~~~~----------   71 (225)
T TIGR01256         6 DALKEIAKQFEKRTGKNKVVF-SFGSSGTLYTQIE---NGAPADVFISADEKRPKKLVDKGLVVKGSEFV----------   71 (225)
T ss_pred             HHHHHHHHHHHCCCCCCEEEE-EECCCHHHHHHHH---CCCCEEEEECCCCCCCHHHHHCCCEECCCCEE----------
T ss_conf             899999988620089956999-8768178999997---17978876614634540466378730254458----------


Q ss_pred             CCCCCCEEEEEEHHHHCCCCCCCCCCCHHHHCCCCCC-----CEEEEEECCCCCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             3211532431000110011124587645652120006-----82898504765303678999987177313789877762
Q gi|254780561|r  124 DDIFVPYDYGYLAFIYDKRQITQPPKNFDELINSTKP-----WKIIYQDPRTSTLGLGLLLWIQKIYGDNSAQVWKKIAT  198 (338)
Q Consensus       124 ~~~~~~~~~~~~~~~y~~~~~~~~p~s~~~l~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  198 (338)
T Consensus        72 ------~~~n--~LVL~~~~~~~~~~~~~~l~~p~~~~~l~~~~vaigdP~~~P~G~~A~E~L~~lgl~------~~l~~  137 (225)
T TIGR01256        72 ------YAGN--KLVLISPKNSRVVDSLDILKKPGWVIVLKDKTVAIGDPKHAPYGAAAKEVLQKLGLW------EKLKK  137 (225)
T ss_pred             ------EEEE--EEEEEECCCCCCCCCHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCC------HHHHC
T ss_conf             ------9862--189985355420130221138974899863702346824443579999999707976------25644


Q ss_pred             CCCEEEC-CCHHHHHHHHCCCCCEEEEECCHHHHHHHHHC-CCCEEEEECCCCEEEEEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8846830-84789888622586569995044999998507-997378831698088886424337899989999999996
Q gi|254780561|r  199 KTATVTK-GWTESYGFFLKGESDFVLSYSTSPGFYLLNYG-QDDYVAALFSEGHYLQIEVAAQLVRSKQPQLAQEFMQFM  276 (338)
Q Consensus       199 ~~~~~~~-~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~eG~~~~~~~~~i~k~a~n~~~A~~Fi~fl  276 (338)
T Consensus       138 kLV~-g~P~vrQA~~~V~~~nA~~GiVa~Sdv~----~~~K~~~~v~~~p~~ly~Pi~yp~~i~~~g~n~~~a~~f~dyL  212 (225)
T TIGR01256       138 KLVY-GEPDVRQALQFVETGNAPIGIVALSDVI----PSGKKVGSVAVIPEDLYKPIKYPAVIVKGGKNNAAAKAFIDYL  212 (225)
T ss_pred             CEEE-CCCCHHHHHHHHHHCCCCEEEEEHHEEE----ECCCCCCEEEEECHHHCCCEEEEEEEEECCCCHHHHHHHHHHH
T ss_conf             8652-4888999988877258866687311022----0003662799963312796021178871687608999999870


Q ss_pred             CCHHHHHHHHHC
Q ss_conf             399999998850
Q gi|254780561|r  277 ISPSFQRILPTT  288 (338)
Q Consensus       277 ls~e~Q~~~a~~  288 (338)
T Consensus       213 ~sp~A~~il~~Y  224 (225)
T TIGR01256       213 KSPEAKEILRKY  224 (225)
T ss_pred             CCHHHHHHHHCC
T ss_conf             796476786305