SII-SWORD/CoKE huggingface dataset:
Pfam PF21381: Mucolipin, extracytosolic domain (domain)
Mucolipins 1-3 are ion channel proteins that belong to the transient receptor potential (TRP) superfamily of cation channels and are the major Ca2+-permeable channels on late endosomes and lysosomes (LEL). This entry represents the extracytosolic domain (ECD) which consists of two beta sheets and two extracytosolic helices that tetramerize into a ring that caps the extracytosolic side of the channel.
Pfam PF18712: Family of unknown function (DUF5644) (domain)
This is a domain of unknown function found at the C-terminal region of Helicobacterial proteins of unknown function.
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 PF08406: CbbQ/NirQ/NorQ C-terminal (family)
This domain is found at the C-terminus of proteins of the CbbQ/NirQ/NorQ family of proteins which play a role in the post-translational activation of Rubisco.  It is also found in the Thauera aromatica TutH protein which is similar to the CbbQ/NirQ/NorQ family, as well as in putative chaperones. The ATPase family associated with various cellular activities (AAA) [pfam:PF07728] is found in the same bacterial and archaeal proteins as the domain described here.
Pfam PF03331: UDP-3-O-acyl N-acetylglycosamine deacetylase (family)
The enzymes in this family catalyse the second step in the biosynthetic pathway for lipid A.
Wikipedia: In molecular biology, UDP-3-O-N-acetylglucosamine deacetylase, EC 3.5.1.-, is a bacterial enzyme involved in lipid A biosynthesis.
Pfam PF10426: Recombination-activating protein 1 zinc-finger domain (domain)
This is a C2-H2 zinc-finger domain closely resembling the classical TFIIIA-type zinc-finger, CX3FX5LX2-3H, despite having a valine and a tyrosine at the core instead of a phenylalanine and a leucine, hence CX3VX1LX2YX2H.  The structure, nevertheless, contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with the zinc-RING-finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1). The function of the whole is to bind double-stranded DNA.
Pfam PF09104: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 (domain)
Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding.
Wikipedia: BRCA2 and BRCA2 are human genes and their protein products, respectively. The official symbol and the official name are maintained by the HUGO Gene Nomenclature Committee. One alternative symbol, FANCD1, recognizes its association with the FANC protein complex. Orthologs, styled Brca2 and Brca2, are common in other vertebrate species. BRCA2 is a human tumor suppressor gene, found in all humans; its protein, also called by the synonym breast cancer type 2 susceptibility protein, is responsible for repairing DNA.
Pfam PF22960: E3 ubiquitin-protein ligase UBR1-like, winged-helix domain (domain)
This entry represents the winged-helix domain of human E3 ubiquitin-protein ligase UBR1, which recognises and binds to proteins bearing specific N-terminal residues that are destabilising according to the N-end rule, leading to their ubiquitination and subsequent degradation.
Pfam PF20455: Family of unknown function (DUF6708) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 200 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 PF09102: Exotoxin A, targeting (domain)
Members of this family are found in Pseudomonas aeruginosa exotoxin A, and are responsible for transmembrane targeting of the toxin, as well as transmembrane translocation of the catalytic domain into the cytoplasmic compartment. A furin cleavage site is present within the domain: cleavage generates a 37 kDa carboxy-terminal fragment, which includes the enzymatic domain, which is then is translocated into the cytoplasm. The domain adopts a helical structure, with six alpha-helices forming a bundle.
Pfam PF07047: Optic atrophy 3 protein (OPA3) (family)
This family consists of several optic atrophy 3 (OPA3) proteins. OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity.
Pfam PF18162: Arc C-lobe (domain)
This is the C-terminal domain of Arc protein present in found in Rattus norvegicus. The Arc protein modulates the trafficking of AMPA-type glutamate receptors. This domains tertiary structure is similar to the capsid domain of HIV gag protein. The domain is thought to have evolved from the capsid domain of Ty3/Gypsy retrotransposon.
Pfam PF15846: Domain of unknown function (DUF4720) (family)
This family of proteins is found in vertebrates. Proteins in this family are typically between 101 and 117 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 PF08181: DegQ (SacQ) family (family)
This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis. DegQ is 46 amino acids long and activates the synthesis of degradative enzymes.  The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation.
Pfam PF12967: Domain of Unknown Function with PDB structure (DUF3855) (family)
Family based on orphan protein (TM0875) from Thermotoga maritima that has been structurally determined as PDB:1022. The TM0875 gene of Thermotoga maritima encodes a hypothetical protein NP_228683 of unknown function. Analysis of TM0875 genomic context reveals the presence of MMT1 (a predicted Co/Zn/Cd cation transporter) and an inactive homolog of metal-dependent proteases. 1O22 shows weak structural similarity with the phosphoribosylformylglycinamidine synthase 1t4a (Dali Z-scr=4.6), the yggU protein (PDB structure:1n91; with DALI Z-scr=3), and with the thioesterase superfamily member (PDB structure 2cy9 - found using FATCAT), even though they have very low sequence identity.
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 PF13869: Nucleotide hydrolase (domain)
Nudix hydrolases are found in all classes of organism and hydrolyse a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, di-nucleoside and diphospho-inositol polyphosphates, nucleotide sugars and RNA caps, with varying degrees of substrate specificity.
Pfam PF03739: Lipopolysaccharide export system permease LptF/LptG (family)
Members of this family are predicted integral membrane proteins of about 350 amino acids long and containing about 6 trans-membrane regions. Characterised members include LptF and LptG, two homologous tandem-encoded permeases of an export ATP transporter for lipopolysaccharide (LPS) assembly in most Gram-negative bacteria.
Pfam PF06139: BphX-like (family)
Family of bacterial proteins located in the phenyl dioxygenase (bph) operon. The function of this family is unknown.
Pfam PF05893: Acyl-CoA reductase (LuxC) (family)
This family consists of several bacterial Acyl-CoA reductase (LuxC) proteins. The channelling of fatty acids into the fatty aldehyde substrate for the bacterial bioluminescence reaction is catalysed by a fatty acid reductase multienzyme complex, which channels fatty acids through the thioesterase (LuxD), synthetase (LuxE) and reductase (LuxC) components.
Pfam PF18571: von Willebrand factor type A C-terminal domain (family)
This is the C-terminal domain of von Willebrand factor type A [pfam:PF13768].
Wikipedia: The von Willebrand factor type A (vWA) domain is a protein domain named after its occurrence in von Willebrand factor (vWF), a large multimeric glycoprotein found in blood plasma. Mutant forms of vWF are involved in the aetiology of bleeding disorders. This type A domain is the prototype for a protein superfamily.
Pfam PF00067: Cytochrome P450 (domain)
Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures.
Wikipedia: Cytochromes P450 are a superfamily of enzymes containing heme as a cofactor that mostly, but not exclusively, function as monooxygenases. However, they are not omnipresent; for example, they have not been found in Escherichia coli. In mammals, these enzymes oxidize steroids, fatty acids, xenobiotics, and participate in many biosyntheses. By hydroxylation, CYP450 enzymes convert xenobiotics into hydrophilic derivatives, which are more readily excreted.
Pfam PF14310: Fibronectin type III-like domain (family)
This domain has a fibronectin type III-like structure. It is often found in association with [pfam:PF00933] and [pfam:PF01915]. Its function is unknown.
Pfam PF22339: YgxA-like substrate binding domain (domain)
This entry represents the substrate binding domain of YgxA from Bacillus subtilis and similar sequences.
Pfam PF24342: P-granule-associated protein DEPS-1, second OB-fold domain (domain)
This domain is found in the P-granule-associated protein DEPS-1 from C.elegans and related proteins. DEPS-1 is a component of the P-granules and is required for their formation and integrity in adult germ cells. This protein is also involved in RNA-mediated silencing (RNAi) of germline-expressed genes. DEPS-1 is predicted to contain six OB-fold-like beta-barrel domains. This entry represents the second of these domains.
Pfam PF10711: Hypothetical protein (DUF2513) (family)
This family is found in bacteria. The function is not known.
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 PF04971: Bacteriophage P21 holin S (family)
Phage_holin_2_1 is a family of small hydrophobic holin proteins with one or more transmembrane domains. Members of this family fall into the holin superfamily II, and Phage 21 S holin is the prototype for this superfamily.  It has two transmembrane segments with both the N- and C-termini on the cytoplasmic side of the inner membrane in E. coli. Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the build up of a holin oligomer which causes the lysis.
Pfam PF24179: Neuropathy Target Esterase family P-loop like domain (domain)
This domain is fond in a variety of Neuropathy Target Esterase family proteins. This domain appears to be structurally realted to P-loop ATPases, but it appears to not contain the typical APT-binding motifs.  The NTE family comprises intracellular phospholipases B that catalyze the double deacylation of phosphatidylcholine (PC) to glycerophosphocholine (GroPCho). These enzymes play a crucial role in membrane lipid homeostasis and are responsible for the rapid turnover of PC in response to various stimuli such as inositol, elevated temperatures, or choline presence. Additionally, some members of the family, like the neuropathy target esterase (NTE), are involved in the signaling mechanisms between neurons and glia, regulating glia wrapping during brain development and ensuring cell survival. The family also includes lysophospholipases that preferentially deacylate unsaturated lysophosphatidylcholine, generating glycerophosphocholine and other lysophospholipids.
Pfam PF02969: TATA box binding protein associated factor (TAF) (domain)
TAF proteins adopt a histone-like fold.
Wikipedia: The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II.
Pfam PF06144: DNA polymerase III, delta subunit (domain)
DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction. The delta subunit is also known as HolA. This entry represents the ATPase domain
Wikipedia: In molecular biology, the δ (delta) subunit of DNA polymerase III is encoded by the holA gene in E. coli and other bacteria. Along with the γ, δ', χ, and ψ subunits that make up the core polymerase, and the β accessory proteins, the δ subunit is responsible for the high speed and processivity of polIII.
Pfam PF14914: LRRC37A/B like protein 1 C-terminal domain (family)
This family represents the C-terminal domain of the putative Leucine Rich Repeat Containing protein 37A or protein 37B (LRRC37A/B) found in eukaryotes. The Leucine Rich Repeats (LRR) lies in the central region. The gene that encodes this protein is found in the chromosomal position 17q11.2, and its microdeletion results in the disease, neurofibromatosis type-1 (NF1). The function of the protein, LRRC37B is unknown, however experimental data shows expression in the aorta, heart, skeletal muscle, liver and brain during gestation.
Pfam PF03665: Uncharacterised protein family (UPF0172) (family)
In Chlamydomonas reinhardtii the protein TLA1 (truncated light-harvesting chlorophyll antenna size) apparently regulates genes that define the chlorophyll-a antenna size in the photosynthetic apparatus. This family was formerly known as UPF0172.
Pfam PF16711: Actin-binding domain of plant-specific actin-binding protein (domain)
SCAB-ABD is the actin-binding domain of plant-specific actin-binding proteins or SCABs. SCAB proteins bind, bundle and stabilise actin filaments and regulate stomatal movement. The Ig-PH fusion domain is at the C-terminus.  The ABD is structurally independent from the first coiled-coil, CC1, domain which is also involved in binding; the CC1 is likely to function as a dimerisation module,
Pfam PF01723: Chorion protein (family)
This family consists of the chorion superfamily proteins classes A, B, CA, CB and high-cysteine HCB from silk,  gypsy and polyphemus moths. The chorion proteins make up the moths egg shell a complex extracellular structure.
Pfam PF22455: PQQ synthase PqqF, C-terminal lobe domain 3 (domain)
This entry represents domain 3 from the C-terminal lobe of PQQ synthase PqqF, a protein required for coenzyme pyrroloquinoline quinone (PQQ) biosynthesis. It consists of four structurally similar domains organised in N-terminal (domain 1 represented in Pfam: PF00675 and domain 2 in [pfam:PF22454]) and C-terminal (domain 3 and domain 4) lobes.
Pfam PF04774: Hyaluronan / mRNA binding family (family)
This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1.  HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo.  It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function.
Pfam PF00439: Bromodomain (domain)
Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Wikipedia: A bromodomain is an approximately 110 amino acid protein domain that recognizes acetylated lysine residues, such as those on the N-terminal tails of histones. Bromodomains, as the "readers" of lysine acetylation, are responsible in transducing the signal carried by acetylated lysine residues and translating it into various normal or abnormal phenotypes. Their affinity is higher for regions where multiple acetylation sites exist in proximity. This recognition is often a prerequisite for protein-histone association and chromatin remodeling. The domain itself adopts an all-α protein fold, a bundle of four alpha helices each separated by loop regions of variable lengths that form a hydrophobic pocket that recognizes the acetyl lysine.
Pfam PF09516: CfrBI restriction endonuclease (family)
This family includes the CfrBI (recognises and cleaves C^CWWGG) restriction endonuclease.
Pfam PF03704: Bacterial transcriptional activator domain (repeat)
Found in the DNRI/REDD/AFSR family of regulators. This region of AFSR ([swissprot:P25941]) along with the C terminal region is capable of independently directing actinorhodin production. This family contains TPR repeats.
Pfam PF00707: Translation initiation factor IF-3, C-terminal domain (domain)
Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit . The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 .
Wikipedia: In molecular biology, translation initiation factor IF-3 is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consists of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit. The chloroplast homolog enhances the poly(A,U,G)-dependent binding of the initiator tRNA to its ribosomal 30s subunits. IF1–IF3 may also perform ribosome recycling.
Pfam PF16597: Thyroglobulin_1 repeat associated disordered domain (disordered)
This domain of conserved disorder lies almost invariably between the two repeated Thyroglobulin_1 domains, [pfam:PF00086].
Pfam PF07203: Protein of unknown function (DUF1412) (family)
This family consists of several Caenorhabditis elegans proteins of around 70-75 residues in length. 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 PF23687: YkiD-like (family)
This protein family includes Protein YkiD from Escherichia coli, a 27-residues long sequence predicted to adopt an alpha -helical configuration.
Pfam PF00193: Extracellular link domain (domain)
The link domain  is a hyaluronan(HA)-binding region found in proteins of vertebrates that are involved in the assembly of extracellular matrix, cell adhesion, and migration. The structure has been shown  to consist of two Î± helices and two antiparallel Î² sheets arranged around a large hydrophobic core similar to that of C-type lectin. This domain contains four conserved cysteines involved in two disulphide bonds. The link domain has also been termed HABM  (HA binding module) and PTR  (proteoglycan tandem repeat). Proteins with such a domain include the proteoglycans aggrecan, brevican, neurocan and versican, which are expressed in the CNS; the cartilage link protein (LP), a proteoglycan that together with HA and aggrecan forms multimolecular aggregates; Tumour necrosis factor-inducible protein TSG-6, which may be involved in cell-cell and cell-matrix interactions during inflammation and tumourgenesis; and CD44 antigen, the main cell surface receptor for HA.
Wikipedia: A Link domain or Link module, also known as Xlink domain, is a protein domain that binds to hyaluronic acid. It is important in blood cell migration and apoptosis. The link domain is found in some extracellular proteins in vertebrates such as the hyalectans. It appears to be involved in extracellular matrix assembly and stability, cell adhesion, and migration.
Pfam PF14514: Tetracyclin repressor-like, C-terminal domain (domain)
This family comprises proteins that belong to the TetR family of transcriptional regulators. This family features the C-terminal region of these sequences, which does not include the N-terminal helix-turn-helix.
Pfam PF00596: Class II Aldolase and Adducin N-terminal domain (domain)
This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.