SII-SWORD/CoKE huggingface dataset:
TRAP transporter solute receptor, DctP family (TRAP_DctP)
Type: Family

Substrate-binding proteins (SBPs) are extracytoplasmic proteins involved in substrate recognition for several different bacterial transporters. This entry includes a subset of the DctP family of the substrate-binding proteins. They are part of the DctP-TRAP (tripartite ATP-independent periplasmic) transporter. Proteins in this family include DctP from R. capsulatus, SiaP from Haemophilus influenzae and DctB from Bacillus subtilis .

The tripartite ATP-independent periplasmic (TRAP) transporters are substrate-binding protein (SBP)-dependent secondary transporters found in prokaryotes. They consist of a substrate-binding protein (SBP) of the DctP or TAXI families and two integral membrane proteins that form the DctQ and DctM protein families .
Type III secretion system substrate exporter FlhB-like (T3SS_FlhB-rel)
Type: Family

This group describes a short protein (80-93 residues) homologous to the C terminus of the flagellar biosynthetic protein FlhB. It is found so far only in species that also have FlhB. In a phylogenetic tree based on alignment of both this family and the homologous region of FlhB and its homologues, the members of this family form a monophyletic set.
2-keto-3-deoxygluconate permease (2keto-3dGluconate_permease)
Type: Family

This family includes the characterised 2-Keto-3-Deoxygluconate transporters from Bacillus subtilis and Erwinia chrysanthemi. There are homologues of this protein found in both Gram-positive and Gram-negative bacteria.

In E. chrysanthemi, a phytopathogenic bacterium, degraded pectin products from plant cell walls are transported by 2-keto-3-deoxygluconate permease into the bacterial cell to provide a carbon and energy source . 2-keto-3-deoxygluconate permease can mediate the uptake of glucuronate with a low affinity .
Branched-chain amino acid transport system II carrier protein (Brnchd-chn_aa_trnsp_Livcs)
Type: Family

Characterised members of the branched chain Amino Acid:Cation Symporter (LIVCS) family transport all three of the branched chain aliphatic amino acids (leucine (L), isoleucine (I) and valine (V)) . They function by a Na+ or H+ symport mechanism and display 12 putative transmembrane helical spanners.
Tricarboxylate/iron carrier (Mtc)
Type: Family

The MTC family consists of a limited number of homologues, all from eukaryotes. One member of the family has been functionally characterised as a tricarboxylate carrier from rat liver mitochondria. The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. It presumably functions by a proton symport mechanism. The rest of the characterised proteins appear to be sideroflexins involved in iron transport.
Lysosomal-associated transmembrane protein 4/5 (LAPTM4/5)
Type: Family

The lysosome associated protein transmembrane (LAPTM) family is comprised of three members: LAPTM5, LAPTM4a and LAPTM4b; they are lysosome-associated transmembrane proteins, found in mammals, insects and nematodes.
Transition metal uptake transporter nickel/cobalt (Ni/Co_transpt)
Type: Family

This family is found in both Gram-negative and Gram-positive bacteria. The functionally characterised members of the family catalyse uptake of either Ni2+ or Co2+ in a proton motive force-dependent process . Topological analyses with the HoxN Ni2+ transporter of Ralstonia eutropha suggest that it possesses 8 TMSs with its N- and C-termini in the cytoplasm .
Malonate transporter MadL subunit (Maln_transptMadL)
Type: Family

The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra . It consists of two integral membrane proteins, MadL and MadM. The transporter is believed to catalyse the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity .
Malonate/sodium symporter MadM subunit (Mal/Na_symporter_MadM)
Type: Family

The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra. It consists of two integral membrane proteins, MadL and MadM .The transporter is believed to catalyze the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity.
Preprotein translocase SecG subunit (SecG)
Type: Family

Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.

The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion . Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA.
Silicon transporter (Silicon_transpt)
Type: Family

Marine diatoms such as Cylindrotheca fusiformis encode at least six silicon transport protein homologues which exhibit similar size and topology. One characterised member of the family (Sit1) functions in the energy-dependent uptake of either silicic acid [Si(OH)4] or silicate [Si(OH)3O-] by a Na
+
symport mechanism . The system is found in marine diatoms, which make their "glass houses" out of silicon.
Hydroxy amino acid transporter (Hydroxy_aa_transpt)
Type: Family

The Hydroxy/Aromatic Amino Acid Permease (HAAAP) family includes well characterised aromatic amino acid:H+ symport permeases and hydroxy amino acid permeases. This group is specific for hydroxy amino acid transporters and includes the serine permease, SdaC and threonine/serine permease, TdcC, of Escherichia coli .
Transporter protein SLAC1/Mae1/ Ssu1/TehA (SLAC1/Mae1/Ssu1/TehA)
Type: Family

Each of these transporters has ten α helical transmembrane segments . The structure of a bacterial homologue of SLAC1 shows it to have a trimeric arrangement. The pore is composed of five helices with a conserved Phe residue involved in gating. One homologue, Mae1 from the yeast Schizosaccharomyces pombe, functions as a malate uptake transporter; another, Ssu1from Saccharomyces cerevisiae and other fungi including Aspergillus fumigatus, is characterised as a sulfite efflux pump; and TehA from Escherichia coli is identified as a tellurite resistance protein by virtue of its association in the tehA/tehB operon. In plants, homologues are found in the stomatal guard cells functioning as an anion-transporting pore . Many homologues are incorrectly annotated as tellurite resistance or dicarboxylate transporter (TDT) proteins.
Triose phosphate/phosphoenolpyruvate translocator (Tpt_PEP_transl)
Type: Family

Functionally characterised members of the 6-8 TMS Triose-phosphate Transporter (TPT) family are derived from the inner envelope membranes of chloroplasts and non-green plastids of plants. Under normal physiological conditions, chloroplast TPTs mediate a strict antiport of substrates, frequently exchanging an organic three carbon compound phosphate ester for inorganic phosphate (Pi) .

Normally, a triose-phosphate, 3-phosphoglycerate, or another phosphorylated C3 compound made in the chloroplast during photosynthesis, exits the organelle into the cytoplasm of the plant cell in exchange for Pi. However, experiments with reconstituted translocator in artificial membranes indicate that transport can also occur by a channel-like uniport mechanism with up to 10-fold higher transport rates. Channel opening may be induced by a membrane potential of large magnitude and/or by high substrate concentrations. Non-green plastid and chloroplast carriers, such as those from maize endosperm and root membranes, mediate transport of C3 compounds phosphorylated at carbon atom 2, particularly phosphoenolpyruvate, in exchange for Pi. These are the phosphoenolpyruvate:Pi antiporters (PPT). Glucose-6-P has also been shown to be a substrate of some plastid translocators (GPT). The three types of proteins (TPT, PPT and GPT) are divergent in sequence as well as substrate specificity, but their substrate specificities overlap.

TPT paralogues are also present in Saccharomyces cerevisiae, which are functionally uncharacterised.
p-Aminobenzoyl-glutamate transport protein AbgT (AbgT)
Type: Family

AbgT catalyzes the concentration-dependent uptake of p-aminobenzoyl-glutamate (PABA-GLU) into cells. This allows accumulation of PABA-GLU to a concentration enabling AbgAB to catalyze cleavage into p-aminobenzoate and glutamate .
Zinc/iron permease, fungal/plant (Zn/Fe_permease_fun/pln)
Type: Family

Members of the zinc (Zn2+)-Iron (Fe2+) permease (ZIP) family consist of proteins with eight putative transmembrane spanners. They are derived from animals, plants and yeast. They comprise a diverse family, with several paralogues in any one organism (e.g., at least five in Caenorhabditis elegans, at least five in Arabidopsis thaliana and two in Saccharomyces cerevisiae (Baker's yeast). The two S. cerevisiae proteins, Zrt1 and Zrt2, both probably transport Zn2+ with high specificity, but Zrt1 transports Zn2+ with ten-fold higher affinity than Zrt2. Some members of the ZIP family have been shown to transport Zn2+ while others transport Fe2+, and at least one transports a range of metal ions. The energy source for transport has not been characterised, but these systems probably function as secondary carriers.
Phosphotransferase system, enzyme II sorbitol-specific factor (PTS_IID_sorb)
Type: Family

Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.

It is the only PTS family in which members possess a IID protein.

It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue.

Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.

The Gut family consists only of glucitol-specific transporters, but these occur both in Gram-negative and Gram-positive bacteria. Escherichia coli consists of IIA protein, a IIC protein and a IIBC protein.
Phosphotransferase system, mannose/fructose/sorbose family, IIC subunit (PTS_IIC_man)
Type: Family

Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Mannose (Man) family is unique in several respects among PTS permease families .

It is the only PTS family in which members possess a IID protein.

It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue.

Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.

The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine.
Phosphotransferase system, mannose-type IIA component (PTS_EIIA_man-typ)
Type: Domain

The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.

The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).

According to structural and sequence analyses, the PTS EIIA domain can be divided in different groups. The mannose class of EIIA consists of a single five-stranded mixed β sheet, flanked by helices on both sides . The phosphorylation site (His) is located at the end of the third β strand, in a shallow crevice lined with hydrophobic residues.

This entry represents the mannose-type EIIA domain. This type of domain can also be found in the multidomain protein dihydroxyacetone kinase DhaM from some bacteria .
Phosphotransferease, sorbitol phosphotransferase enzyme II (PTS_sorb_EIIBC)
Type: Family

Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Man family is unique in several respects among PTS permease families.

It is the only PTS family in which members possess a IID protein.

It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue.

Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.

The Gut family consists only of glucitol-specific permeases, but these occur both in Gram-negative and Gram-positive bacteria. Escherichia coli consists of IIA protein, a IIC protein and a IIBC protein.

This family is specific for the IIBC component.
Phosphotransferase system, sugar-specific permease component (PTS_sugar-sp_permease)
Type: Family

The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), a major carbohydrate active-transport system, catalyses the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane.

This family includes the IIC component of the ascorbate-specific PTS system, UlaA, and the IIC component of the galactitol-specific PTS system.
Phosphotransferase system, mannose/fructose/sorbose family IID component (PTS_IID_man)
Type: Family

The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.

The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).

Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Mannose (Man) family is unique in several respects among PTS permease families.

It is the only PTS family in which members possess a IID protein.

It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue.

Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.

The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine.
Cation/H+ exchanger, CPA1 family, bacteria (Cation/H_exchanger_CPA1_bac)
Type: Family

Sodium proton exchangers (NHEs) constitute a large family of integral membrane protein transporters that are responsible for the counter-transport of protons and sodium ions across lipid bilayers . These proteins are found in organisms across all domains of life. In archaea, bacteria, yeast and plants, these exchangers provide increased salt tolerance by removing sodium in exchanger for extracellular protons. In mammals they participate in the regulation of cell pH, volume, and intracellular sodium concentration, as well as for the reabsorption of NaCl across renal, intestinal, and other epithelia . Human NHE is also involved in heart disease, cell growth and in cell differentiation . The removal of intracellular protons in exchange for extracellular sodium effectively eliminates excess acid from actively metabolising cells. In mammalian cells, NHE activity is found in both the plasma membrane and inner mitochondrial membrane. To date, nine mammalian isoforms have been identified (designated NHE1-NHE9) . These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N terminus and a large cytoplasmic region at the C terminus. The transmembrane regions M3-M12 share identity with other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions. The cytoplasmic region has little similarity throughout the family. There is some evidence that the exchangers may exist in the cell membrane as homodimers, but little is currently known about the mechanism of their antiport .

This entry represents bacterial Na+/H+ exchanger proteins such as YjcE from Escherichia coli .
Arsenical-resistance protein Acr3 (Arsenical-R_Acr3)
Type: Family

Members of the ACR3 family of arsenite (As(III)) permeases confer resistance to arsenic by extrusion from cells . They exist in prokaryotes and eukaryotes (lower plants and fungi) . The ACR3 permeases have ten-transmembrane span topology . Corynebacterium glutamicum has three Acr3 proteins, CgAcr3-1, CgAcr3-2, and CgAcr3-3. CgAcr3-1 is thought to be an antiporter that catalyses arsenite-proton exchange .

The Shewanella oneidensis Acr3 is not able to transport As(III) and confers resistance only to arsenate (As(V)) , whereas the Acr3 orthologue from Synechocystis mediates tolerance to As(III), As(V) and antimonite (Sb(III)) .

In budding yeast, overexpression of the Acr3 gene confers an arsenite- but not an arsenate-resistance phenotype . Saccharomyces cerevisiae Acr3 is a plasma membrane metalloid/H+ antiporter that transports arsenite and antimonite .
Membrane transport protein MmpL family (MmpL_fam)
Type: Family

This entry represents the MmpL family of membrane transport proteins, which may be involved in lipid transport . Mycobacterium tuberculosis MMPL10 is required for the biosynthesis of polyacyltrehalose (PAT) and the transport of diacyltrehalose (DAT) and possibly PAT to the cell surface , while MMPL4 is a part of an export system required for biosynthesis and secretion of siderophores .
Aspartate ammonia-lyase (ApsA)
Type: Family

A number of enzymes, belonging to the lyase class, for which fumarate is a substrate have been shown to share a short conserved sequence around a methionine which is probably involved in the catalytic activity of this type of enzymes.

Aspartate ammonia-lyase catalyses the conversion of aspartate to fumarate.
Na+/H+ exchanger (NaH_exchanger)
Type: Family

Sodium proton exchangers (NHEs) constitute a large family of integral membrane protein transporters that are responsible for the counter-transport of protons and sodium ions across lipid bilayers . These proteins are found in organisms across all domains of life. In archaea, bacteria, yeast and plants, these exchangers provide increased salt tolerance by removing sodium in exchanger for extracellular protons. In mammals they participate in the regulation of cell pH, volume, and intracellular sodium concentration, as well as for the reabsorption of NaCl across renal, intestinal, and other epithelia . Human NHE is also involved in heart disease, cell growth and in cell differentiation . The removal of intracellular protons in exchange for extracellular sodium effectively eliminates excess acid from actively metabolising cells. In mammalian cells, NHE activity is found in both the plasma membrane and inner mitochondrial membrane. To date, nine mammalian isoforms have been identified (designated NHE1-NHE9) . These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N terminus and a large cytoplasmic region at the C terminus. The transmembrane regions M3-M12 share identity with other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions. The cytoplasmic region has little similarity throughout the family. There is some evidence that the exchangers may exist in the cell membrane as homodimers, but little is currently known about the mechanism of their antiport .
Bile acid:sodium symporter (Bilac:Na_transpt)
Type: Family

Functionally characterised members of the bile Acid:Na+ Symporter (BASS) family catalyse Na+:bile acid symport. These systems have been identified in intestinal, liver and kidney tissues of animals. These symporters exhibit broad specificity, taking up a variety of non bile organic compounds as well as taurocholate and other bile salts. Functionally uncharacterised homologues are found in plants and bacteria.
Benzoate transporter (Benzoate_Transporter)
Type: Family

Several proteins in this entry have been identified as benzoate transporters . They exhibit about 30% identity to each other and show limited sequence similarity to members of the aromatic acid:H+symporter (AAHS) family of the major facilitator superfamily (MFS). Interestingly, they have different protein structures comparing to the MFS members. For instance, Corynebacterium glutamicum BenE (NCgl2326) is predicted to have 11 transmembrane α-helices, instead of 12 transmembrane α-helices found in the MFS members. BenE is also lacking some conserved domains/amino acids usually found in the MFS members . Therefore, BenE is thought to be a novel type of benzoate transporter. This family is classified as TC number 2.A.46 under the transporter classification (TC) system .
Na+/H+ antiporter, fungi (Na+/H+_antiporter_fungi)
Type: Family

This entry represents a group of fungal Na+/H+ antiporters, including Nha1 from budding yeasts and Sod2 (SPAC977.10) from fission yeasts. Nha1 is involved in sodium and potassium efflux through the plasma membrane. It plays a role in the homeostatic regulation of the plasma membrane potential . Sod2 is a Na+/H+ exchanger that is responsible for salt tolerance . The structure of Sod2 has been revealed .
Calcium/proton exchanger (CaH_exchang)
Type: Family

Proteins of the Ca2+:Cation Antiporter (CaCA) family are found ubiquitously, having been identified in animals, plants, yeast, archaea and widely divergent bacteria. All of the characterised animal proteins catalyze Ca2+:Na+ exchange although some also transport K+. The NCX1 plasma membrane protein exchanges 3 Na+ for 1 Ca2+. The Escherichia coli ChaA protein catalyses Ca2+:H+ antiport but may also catalyze Na+:H+ antiport. All remaining well-characterised members of the family catalyze Ca2+:H+ exchange.