SII-SWORD/CoKE huggingface dataset:
Pfam PF00034: Cytochrome c (domain)
The Pfam entry does not include all Prosite members.  The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, [pfam:PF06181], has now been merged into this family.
Wikipedia: Cytochromes c  cytochromes, or heme-containing proteins, that have heme C covalently attached to the peptide backbone via one or two thioether bonds. These bonds are in most cases part of a specific Cys-X-X-Cys-His (CXXCH) binding motif, where X denotes a miscellaneous amino acid. Two thioether bonds of cysteine residues bind to the vinyl sidechains of heme, and the histidine residue coordinates one axial binding site of the heme iron. Less common binding motifs can include a single thioether linkage, a lysine or a methionine instead of the axial histidine or a CXnCH binding motif with n&gt;2. The second axial site of the iron can be coordinated by amino acids of the protein, substrate molecules or water. Cytochromes c possess a wide range of properties and function as electron transfer proteins or catalyse chemical reactions involving redox processes. A prominent member of this family is mitochondrial cytochrome c.
Pfam PF03435: Saccharopine dehydrogenase NADP binding domain (family)
This family contains the NADP binding domain of saccharopine dehydrogenase. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase.
Wikipedia: In molecular biology, the protein domain Saccharopine dehydrogenase (SDH), also named Saccharopine reductase, is an enzyme involved in the metabolism of the amino acid lysine, via an intermediate substance called saccharopine. The Saccharopine dehydrogenase enzyme can be classified under EC 1.5.1.7, EC 1.5.1.8, EC 1.5.1.9, and EC 1.5.1.10. It has an important function in lysine metabolism and catalyses a reaction in the alpha-Aminoadipic acid pathway. This pathway is unique to fungal organisms therefore, this molecule could be useful in the search for new antibiotics. This protein family also includes saccharopine dehydrogenase and homospermidine synthase. It is found in prokaryotes, eukaryotes and archaea.
Pfam PF18568: TRIM C-terminal subgroup One Signature domain (domain)
This domain is found in the C-terminal region of the TRIM subgroup C-1 proteins such as E3 ubiquitin-protein ligase Midline-1 protein which is required for the proper development during embryogenesis. Mutations of MID1 are associated with X-linked Opitz G syndrome, characterized by midline anomalies. This domain is also found in MURF1-3 proteins that do not contain the FNIII and B30.2 domains. MUF1-3 proteins are also associated with microtubules. Deletion of the COS domain does not affect MID1 dimerization but disrupts the localization to the microtubules.
Pfam PF22770: POP1 C-terminal domain (domain)
This entry represents the C-terminal domain of human Ribonuclease P/MRP protein subunit POP1 and similar eukaryotic sequences. POP1 is a component of Ribonuclease P that cleaves the 5' leader from precursor tRNAs. The C-terminal domain of POP1 interacts with H1 RNA and has a stabilizing role. This domain adopts a beta-barrel structure that is structurally very similar to the C-terminal beta-barrel domains of eIF2 gamma, EF-Tu and tRNA thiouridylase MnmA.
Pfam PF24475: DEAH11-like, RNA-binding domain (domain)
This presumed RNA binding domain (RBD) is found in ATP-dependent RNA helicase DEAH11 from Arabidopsis thaliana and similar sequences from plants. Its specific function is unknown.
Pfam PF21692: Talin, R4 domain (domain)
Talin is a cytoskeletal protein that plays a critical role in the formation of cell adhesions and regulation of integrin signalling. It activates integrins, couples them to F-actin, and recruits vinculin to focal adhesions. It is a long protein comprising an N-terminal globular head and a long C-terminal rod which has 13 helical bundles (R1-R13) organized into a compact cluster of four-helix bundles (R2-R4) within a linear chain of five-helix bundles. Nine of the helical bundles contain vinculin-binding sites (VBS), one of them is R4, represented in this entry.
Pfam PF07062: Clc-like (family)
This family contains a number of Clc-like proteins that are approximately 250 residues long.
Pfam PF16396: Domain of unknown function (DUF5005) (repeat)
This small family of proteins is functionally uncharacterised. This family is found in bacteroides. Proteins in this family are typically around 440 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF00529: Cation efflux system protein CusB domain 1 (family)
The cation efflux system protein CusB from E. coli can be divided into four different domains, the first three domains of the protein are mostly beta-strands and the fourth forms an all alpha-helical domain. This entry represents the first beta-domain (domain 1) of CusB and it is formed by the N and C-terminal ends of the polypeptide (residues 89-102 and 324-385). CusB is part of the copper-transporting efflux system CusCFBA. This domain can also be found in other membrane-fusion proteins, such as HlyD, MdtN, MdtE and AaeA. HlyD is a component of the prototypical alpha-haemolysin (HlyA) bacterial type I secretion system, along with the other components HlyB and TolC. HlyD is anchored in the cytoplasmic membrane by a single transmembrane domain and has a large periplasmic domain within the carboxy-terminal 100 amino acids, HlyB and HlyD form a stable complex that binds the recombinant protein bearing a C-terminal HlyA signal sequence and ATP in the cytoplasm. HlyD, HlyB and TolC combine to form the three-component ABC transporter complex that forms a trans-membrane channel or pore through which HlyA can be transferred directly to the extracellular medium. Cutinase has been shown to be transported effectively through this pore.
Pfam PF10153: rRNA-processing protein Efg1 (family)
Efg1 is involved in rRNA processing.
Pfam PF07075: Exo-beta-N-acetylmuramidase NamZ, N-terminal (domain)
NamZ is an exo-beta-N-acetylmuramidase which catalyzes an exo-lytic cleavage of beta-1,4-acetylmuramic acid from from the non-reducing ends of peptidoglycan chains and it is a founding member of a new family of glycosidases (GH171). NamZ consists of a N-terminal catalytic domain with a Rossmann-like fold (represented in this entry) and a C-terminal auxiliary alpha/beta domain.
Pfam PF17703: Family of unknown function (DUF5549) (family)
This is a family of unknown function found in mammals.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23451: PaaD zinc beta ribbon domain (domain)
This domain is found in a number of bacterial and archaeal proteins including PaaD from Escherichia coli that is thought to be a component of 1,2-phenylacetyl-CoA epoxidase multicomponent enzyme system which catalyzes the reduction of phenylacetyl-CoA to form 1,2-epoxyphenylacetyl-CoA. This domain is predicted to adopt a zinc beta ribbon fold and contains two invariant CxxC sequence motifs. In addition, toward the C terminus it has a semi-conserved [EQ]PF[DEQ] sequence motif.
Pfam PF10165: Guanine nucleotide exchange factor synembryn (family)
Ric8 is involved in the EGL-30 neurotransmitter signalling pathway. It is a guanine nucleotide exchange factor that regulates neurotransmitter secretion.
Pfam PF10730: Protein of unknown function (DUF2521) (family)
Family of unknown function specific to Bacillus.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02875: Mur ligase, glutamate ligase domain (domain)
This entry contains a number of related ligase enzymes which have EC numbers 6.3.2.* which includes: MurC ([swissprot:P17952]), MurD ([swissprot:P14900]), MurE ([swissprot:P22188]),  MurF ([swissprot:P11880]), Mpl ([swissprot:P37773]) and FolC ([swissprot:P08192]). MurC, MurD, MurE and MurF catalyse consecutive steps in the synthesis of peptidoglycan.  Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide.  The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesised by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This entry also includes folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin).
Pfam PF19646: Family of unknown function (DUF6149) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are typically between 191 and 204 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF19383: Family of unknown function (DUF5958) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001920) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24615: Nuclear anchorage protein 1, spectrin repeat (domain)
This entry represents spectrin-like repeats found in Nuclear anchorage protein 1 from Caenorhabditis elegans, which plays a central role in nuclear and mitochondrial anchoring.
Pfam PF03817: Malonate transporter MadL subunit (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 .
Pfam PF12904: Putative collagen-binding domain of a collagenase (domain)
This domain is likely to be the collagen-binding domain of a family of bacterial collagenase enzymes. It is the C-terminal part of the PDB:3kzs structure determined from [swissprot:Q8A905] (information derived from TOPSAN).
Pfam PF25083: GIPC1-3 GH1 domain (domain)
This entry includes GIPC proteins (GAIP C-terminus-interacting protein) GIPC1-3, PDZ domain-containing proteins that may act as scaffold proteins linking heterotrimeric G-proteins to seven-transmembrane-type WNT receptor or to receptor tyrosine kinases. They might play key roles in carcinogenesis and embryogenesis through modulation of growth factor signaling and cell adhesion. GIPCs are proteins with a GIPC homology 1 (GH1) domain, a central PDZ domain and a GH2 domain ([pfam:PF25082]). This entry represents the GH1 domain.
Pfam PF11594: Mediator complex subunit 28 (family)
Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours.
Wikipedia: Mediator of RNA polymerase II transcription subunit 28 is an enzyme that in humans is encoded by the MED28 gene. It forms part of the Mediator complex.
Pfam PF06702: Golgi casein kinase, C-terminal, Fam20 (family)
Fam20C represents the C-terminus of eukaryotic secreted Golgi casein kinase proteins. Fam20C is the Golgi casein kinase that phosphorylates secretory pathway proteins within Ser-x-Glu/pSer motifs. Mutations in Fam20C cause Raine syndrome, an autosomal recessive osteosclerotic bone dysplasia.
Pfam PF12396: Protein of unknown function (DUF3659) (family)
This domain family is found in bacteria and eukaryotes, and is approximately 70 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF21114: Discoidin domain-containing receptor 1/2, DS-like domain (domain)
Discoidin domain-containing receptor 1/2 (DDR1/2) are receptor tyrosine kinases (RTKs) whose activating ligands are various collagens and consist of extracellular domains comprising the N-terminal discoidin domain (DS, [pfam:PF00754]) followed by a DS-like domain and the cytoplasmic kinase domain ([pfam:PF07714]). Impairment in signaling by DDR1 and DDR2 is associated with the progression of various human diseases, including fibrosis, atherosclerosis and cancer, therefore, inhibition of signaling using monoclonal antibodies (mAbs) may be an useful therapy. This entry represents the DS-like domain, which mediates binding to triple-helical collagen together with the DS domain and contains the epitopes of all mAbs.
Pfam PF24112: Amanitin toxin (family)
Members of this family are ribosomally produced precursors of toxins produced by several mushrooms. These precursors undergo extensive post-translational modification to become amatoxins (e.g. alpha-amanitin). They are members of the MSDIN fungal toxin family. Amanitin is a major toxin belonging to the bicyclic octapeptides amatoxins that acts by binding non-competitively to RNA polymerase II and greatly slowing the elongation of transcripts from target promoters. Amanitin complex with dual function macrocyclase-peptidase enzyme was structurally characterised.
Pfam PF05679: Chondroitin N-acetylgalactosaminyltransferase (family)
This family represents Chondroitin N-acetylgalactosaminyltransferase. Proteins have a type II transmembrane topology. The enzyme is involved in the biosynthetic initiation and elongation of chondroitin sulphate and is the key enzyme responsible for the selective chain assembly of chondroitin/dermatan sulphate on the linkage region tetrasaccharide common to various proteoglycans containing chondroitin/dermatan sulphate or heparin/heparan sulphate chains .
Pfam PF19368: AraR C-terminal winged HTH domain (domain)
This entry represents the C-terminal DNA-binding domain of AraR proteins which are involved in regulating Arabinose utilisation. This domain has a winged helix-turn-helix structure.
Pfam PF07142: Repeat of unknown function (DUF1388) (repeat)
This family consists of several repeats of around 29 residues in length. Members of this family are found in the variable surface lipoproteins in Mycoplasma bovis and in mammalian neurofilament triplet H (NefH or NF-H) proteins. This repeat contains several Lys-Ser-Pro (KSP) motifs and in NefH these are thought to function as the main target for neurofilament directed protein kinases in vivo.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF06931: Mastadenovirus E4 ORF3 protein (family)
This family consists of several Mastadenovirus E4 ORF3 proteins. Early proteins E4 ORF3 and E4 ORF6 have complementary functions during viral infection. Both proteins facilitate efficient viral DNA replication, late protein expression, and prevention of concatenation of viral genomes. A unique function of E4 ORF3 is the reorganisation of nuclear structures known as PML oncogenic domains (PODs). The function of these domains is unclear, but PODs have been implicated in a number of important cellular processes, including transcriptional regulation, apoptosis, transformation, and response to interferon.
Pfam PF02387: IncFII RepA protein family (family)
This protein is plasmid encoded and found to be essential for plasmid replication.
Pfam PF16468: Domain of unknown function (DUF5049) (family)
This family consists of some uncharacterized proteins around 60 residues in length and is mainly found in various Lactobacillus and Selenomonas species. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11964: SpoIIAA-like (family)
These proteins adopt an alpha/beta SpoIIAA-like fold, similar to that found in STAT ([pfam:PF01740]). They adopt open and closed conformations arising from different arrangements of their alpha-2 and alpha-3 helices. They may be membrane associated and may function as carriers of non-polar compounds.
Pfam PF03333: Adhesin biosynthesis transcription regulatory protein (family)
This family includes PapB, DaaA, FanA, FanB, and AfaA.
Pfam PF09850: Type VI secretion system protein DotU (family)
DotU is a family of Gram-negative bacterial proteins that form part of the membrane-joining complex of the type VI secretion system. DotU binds tightly to IcmF and together they are tethered to the inner membrane at one end and the peptidoglycan layer at the other; they interact with Lip1 which then tethers the peptidoglycan layer to the outer membrane.
Pfam PF24433: Family of unknown function (DUF7556) (family)
This entry represents a small family of uncharacterised proteins found in archaea. These proteins are predicted to be largely disordered. They contain a semi-conserved VIADxx[DE]xAW sequence motif.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF16499: Alpha galactosidase A (family)
O-Glycosyl hydrolases (3.2.1.) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Glycoside hydrolase family 27 GH27 comprises enzymes with several known activities; alpha-galactosidase (3.2.1.22); alpha-N-acetylgalactosaminidase (3.2.1.49); isomalto-dextranase (3.2.1.94).

Alpha-galactosidase (melibiase) catalyses the hydrolysis of melibiose into galactose and glucose . In man, deficiency in the enzyme results in Fabry's disease (X-linked sphingolipidosis). Alpha-N-acetylgalactosaminidase catalyses the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D-galactosaminides . Two conserved Asp residues may be involved in the catalytic mechanism in these enzymes. Deficiency in this enzyme results in Schindler and Kanzaki diseases.
Wikipedia: In molecular biology, glycoside hydrolase family 27 is a family of glycoside hydrolases.
Pfam PF15048: Organic solute transporter subunit beta protein (family)
Organic solute transporter subunit beta (OSTbeta, also known as SLC51B) is an essential component of the Ost-alpha/Ost-beta complex, a heterodimer that acts as the intestinal basolateral transporter responsible for bile acid export from enterocytes into portal blood .

OSTbeta is a single-TM domain polypeptide that forms a transporter complex with Ost-alpha protein, which is a 7-transmembrane (TM) domain containing protein. This heterodimerisation is required for the delivery of the complex to the plasma membrane. The OSTalpha-OSTbeta complex serves as a multispecific transporter that may participate in cellular uptake of bile acids, some endogenous and exogenous steroids, and eicosanoids. It functions via a facilitated diffusion mechanism. Interestingly, this transporter also transports dehydroepiandrosterone sulfate (DHEAS) and pregnenolone sulfate (PREGS), which are major excitatory neurosteroids. This suggests a possible function for OSTalpha-OSTbeta complex in the brain .
Wikipedia: Organic solute transporter beta, also known as OST-beta, is a protein which in humans is encoded by the OSTB gene.
Pfam PF13359: DDE superfamily endonuclease (domain)
This family of proteins are related to [pfam:PF00665] and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.