Protein sequences of M.truncatula and their annotations were derived from the Medicago Genome Sequence Consortium (MGSC) project. Transport protein sequences of Arabidopsis thaliana and their annotations came from the TAIR database, version 9. Pfam annotations came from the Pfam database, version 24.0. 3D structure annotations are provided by the protein data bank (PDB).In addition, we obtain the supplementary transporters information from the Medicago genome portal at the Noble Foundation.

We use both computational prediction and manual curation to predict the members in each gene family. We used BLAST and HMMER searches in computational prediction to identify putative M.truncatula transporters.

The transporter function annotation include Mtid, transporter type, transporter family, substrate/function, TC annotation and arath contrast.It Overall describes the function of transporter protein.

The transporter function annotation include Mtid, transporter type, transporter family, substrate/function, TC annotation and arath contrast.It Overall describes the function of transporter protein.

We submit the protein sequences to the service at http://www.cbs.dtu.dk/services/TMHMM/, and then TMHMM outputs some statistics and a list of the location of the predicted transmembrane helices and the predicted location of the intervening loop regions. This information can be shown graphically.

The ‘structure’ section has been added to MTDB describing experimentally determined 3D structures of membrane transporters. We used the transport protein sequences of M.truncatula to conduct a BLAST search with sequences, provided by the protein data bank (PDB).

We provided a way to explore expression of putative M.truncatula transporter genes under stress treatments. In order to explore expression of M.truncatula transporter genes, we retrieved and categorized microarray expression data from MtED . MtED collect roots at 0 hour,6 hour,24 hour,48 hour after salt stress for further microarray experiment,each time point with 3 biological replicates.

The chromosome map was created by GenomePixelizer. Each transporter type was represented as one color-specific blocks. A color description image was provided, and can offer links to the information browse page. The genes on the up side of the chromosome line mean they on the plus chain, accordingly other side means minus chain.

Channel-type facilitators. Proteins in this category have transmembrane channels which consist largely of α-helical or β-strand-type spanners. Transport systems of this type catalyze facilitated diffusion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. They do not exhibit stereospecificity but may be specific for a particular molecular species or class of molecules.

Transmembrane channel proteins of this class are ubiquitously found in the membranes of all types of organisms from bacteria to higher eukaryotes. These transporters usually catalyze the movement of solutes by an energyindependent process by passage through a transmembrane aqueous pore without evidence for a carrier-mediated mechanism. These channel proteins consist largely of a-helical spanners, although b-strands may be present and may even contribute to the channel. Outer membrane porin-type channel proteins are excluded from this class and are instead included in class 1.B.

These proteins form transmembrane pores that usually allow the energy-independent passage of solutes across a membrane. The transmembrane portions of these proteins consist exclusively of b-strands that usually form b-barrels. Porin-type proteins are found in the outer membranes of gram-negative bacteria, mitochondria, plastids, and possibly acid-fast gram-positive bacteria.

These proteins and peptides are synthesized by one cell and secreted for insertion into the membrane of another cell, where they form transmembrane pores. They may exert their toxic effects by allowing the free flow of electrolytes and other small molecules across the membrane, or they may allow entry into the target cell cytoplasm of a toxin protein that ultimately kills or controls the cell. Both protein (large) and ribosomally synthesized peptide (small) toxins are included in this category.

Many substances (neurotransmitters, protein, complex carbohydrates, small molecules such as ATP) in eukaryotes are sequestered in vesicles which then fuse with the plasma membrane releasing to the extracellular medium the intra-vesicular contents. The vesicles can then either reform or remain associated with the plasma membrane. In the latter case, the lipids flow from the vesicle into the plasma membrane. Recently, fusion has been shown to initiate by formation of a pore complex of various pore sizes.

Three distinct classes of viral membrane fusion proteins have been identified based on structural criteria. In addition, there are at least four distinct mechanisms by which viral fusion proteins can be triggered to undergo fusion-inducing conformational changes. Viral fusion proteins also contain different types of fusion peptides and vary in their reliance on accessory proteins. These differing features combine to yield a rich diversity of fusion proteins.

Secondary carrier-type facilitators. Transport systems are included in this category if they utilize a carrier-mediated process to catalyze uniport (a single species is transported by facilitated diffusion in a process not coupled to the utilization of a primary source of energy), antiport (two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy) and/or symport (two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy). These systems are usually stereospecific. Solute:solute countertransport is a characteristic feature of secondary carriers. These transporters can associate with lipid rafts in both eukaryotes and prokaryotes

Porters (uniporters, symporters, antiporters). Transport systems are included in this subclass if they utilize a carrier-mediated process to catalyze uniport (a single species is transported either by facilitated diffusion or in a membrane potential-dependent process if the solute is charged), antiport (two or more species are transported in opposite directions in a tightly coupled process, not coupled to a direct form of energy other than chemiosmotic energy) and/or symport (two or more species are transported together in the same direction in a tightly coupled process, not coupled to a direct form of energy other than chemiosmotic energy) of secondary carriers.

Normally, outer membrane porins (1.B) of Gram-negative bacteria catalyze passive transport of solutes across the membrane, but coupled to eeenergizers,, they may accumulate their substrates in the periplasm against large concentration gradients. These energizers use the ppproton motive force (pmf) across the cytoplasmic membrane, probably by allowing the electrophoretic transport of protons, and conveying conformational change to the outer membrane receptor/porins. Homologous energizers drive bacterial flagellar motility. The mechanism is poorly understood, but these energizers undoubtedly couple proton (H+) or sodium (Na+) fluxes through themselves to the energized process.

These transporters use a primary source of energy to drive active transport of a solute against a concentration gradient. A secondary ion gradient is not considered a primary energy source because it is created by the expenditure of a primary energy source. Primary energy sources known to be coupled to transport are chemical, electrical and solar.

Transport systems are included in this subclass if they hydrolyze the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate, to drive the active uptake and/or extrusion of a solute or solutes. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated.

Transport systems that drive solute (e.g., ion) uptake or extrusion by decarboxylation of a cytoplasmic substrate are included in this subclass. These transporters are currently thought to be restricted to prokaryotes.

Transport systems that drive transport of a solute (e.g., an ion) energized by the exothermic flow of electrons from a reduced substrate to an oxidized substrate are included in this subclass.

Transport systems that utilize light energy to drive transport of a solute (e.g., an ion) are included in this subclass.

Group translocation involves a combined chemical and vectorial reaction where the transported substrate is modified during the transport process. This can be in a tightly coupled process where transport can not occur at an appreciable rate without substrate modification, or in a more loosely coupled process where transport can occur without derivatization, but the normal process involves coupling. Such processes can involve sugar phosphorylation using phosphoenolpyruvate (PEP) mediated by the phosphotransferase system (PTS; 4.A), nucleoside phosphorylation using ATP as the phosphoryl donor (PnuC; 4.B), or carboxylic acid thioesterification using Coenzyme A as the derivatizing agent (FAT; 4.C).

PEP-dependent, phosphoryl transfer-driven group translocators of the bacterial phosphoenolpyruvate:sugar phosphotransferase system are the best characterized group translocators included in TC category 4. The product of the reaction, derived from extracellular sugar, is a cytoplasmic sugar-phosphate. The enzymatic constituents, catalyzing sugar phosphorylation, are superimposed on the transport process in a tightly coupled process. The PTS is also involved in regulation and chemotaxis.

The third type of group translocators are the putative acyl-CoA ligase-coupled transporters.(4.C.1, 2 and 3) They use the energy of ATP to thioesterify fatty acids and other acids such as carnitine in a process believed to be coupled to transport. A role in group translocation is not fully accepted, and many acyl-CoA ligases clearly do not function directly in transport.

Transmembrane electron flow systems influence the energetics of a cell or organelle, influencing the magnitude of the membrane potential. Systems that catalyze electron flow across a biological membrane, from donors localized to one side of the membrane to acceptors localized on the other side, are grouped into TC category 5. These systems contribute to or subtract from the membrane potential, depending on the direction of electron flow. They are therefore important to cellular energetics.

Two electrons (an electron pair) are transferred across the membrane simultaneously from an electron donor on one side of the membrane to an electron acceptor on the other side.

Single electrons are transferred across the membrane from an electron donor on one side of the membrane to an electron acceptor on the other side.

Auxiliary transport proteins. Proteins that function with or are complexed to known transport proteins are included in this category. An example would be the membrane fusion proteins that facilitate transport across the two membranes of the Gram-negative bacterial cell envelope in a single step driven by the energy source (ATP or the pmf) utilized by a cytoplasmic membrane transporter. Energy coupling and regulatory proteins that do not actually participate in transport represent other possible examples. In some cases auxiliary proteins are considered to be part of the transport system with which they function, and in such cases no distinct entry in category 8 is provided.

Auxiliary transport proteins. Proteins that in some way facilitate transport across one or more biological membranes but do not themselves participate directly in transport are included in this class. These proteins always function in conjunction with one or more established transport systems. They may provide a function connected with energy coupling to transport, play a structural role in complex formation, serve a biogenic or stability function or function in regulation.

Many toxins and activators target transporters, particularly ion channels. For example, venomous creatures deploy a wide arsenal of biologically active compounds to capture prey, acting on a vast array of targets. Prey immobilization is achieved by either inhibiting or activating the electrical activity. Venom components belong to a number of compound classes, including small molecular weight compounds, electrolytes, polyamines, neurotransmitters, amino acids, small peptides and high MW proteins. A single type of spider venom contains up to 500 peptides.

Transporters of unknown classification. Transport protein families of unknown classification are grouped under TC category 9.

Transport protein families of unknown classification are grouped in this subclass and will be classified elsewhere when the transport mode and/or energy coupling mechanism are characterized. These families include at least one member for which a transport function has been established, but either the mode of transport or the energy coupling mechanism is not known.

Putative transport protein families are grouped in this subclass and will either be classified elsewhere when the transport function of a member becomes established, or will be eliminated from the TC classification system if the proposed transport function is disproven. These families include a member or members for which a transport function has been suggested, but evidence for such a function is not yet compelling.

Transporters of particular physiological significance will be included in this category even though a family assignment cannot be made. When their sequences are identified, they will be assigned to an established family. This is the only protein subclass which includes individual proteins rather than protein families.