SII-SWORD/CoKE huggingface dataset:
Pfam PF04238: Protein of unknown function (DUF420) (family)
Predicted membrane protein with four transmembrane helices.
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 PF03374: Phage antirepressor protein KilAC domain (family)
This domain was called the KilAC domain by Iyer and colleagues.
Pfam PF03043: Herpesvirus UL87 family (family)
Members of this family are functionally uncharacterised. This family groups together EBV BcRF1 [swissprot:P25215], HSV-6 U58 [swissprot:P24437], HVS-1 24 [swissprot:Q01007] and HCMV UL87 [swissprot:P16730]. The proteins range from 575 to 950 amino acids in length.
Pfam PF21121: Nucleoporin Nup49 C-terminal helical region (family)
This entry represents a C-terminal helical region from the Nup49 protein. Nup49 is one of three proteins that form the channel nucleoporin heterotrimer (CNT).
Pfam PF03971: Monomeric isocitrate dehydrogenase (family)
NADP(+)-dependent isocitrate dehydrogenase (ICD) is an important enzyme of the intermediary metabolism, as it controls the carbon flux within the citric acid cycle and supplies the cell with 2-oxoglutarate [ec:1.1.1.42] and NADPH for biosynthetic purposes.
Wikipedia: Isocitrate dehydrogenase (IDH) (EC 1.1.1.42) and (EC 1.1.1.41) is an enzyme that catalyzes the oxidative decarboxylation of isocitrate, producing alpha-ketoglutarate (α-ketoglutarate) and CO2. This is a two-step process, which involves oxidation of isocitrate (a secondary alcohol) to oxalosuccinate (a ketone), followed by the decarboxylation of the carboxyl group beta to the ketone, forming alpha-ketoglutarate. In humans, IDH exists in three isoforms: IDH3 catalyzes the third step of the citric acid cycle while converting NAD+ to NADH in the mitochondria. The isoforms IDH1 and IDH2 catalyze the same reaction outside the context of the citric acid cycle and use NADP+ as a cofactor instead of NAD+. They localize to the cytosol as well as the mitochondrion and peroxisome.
Pfam PF18326: RFX5 N-terminal domain (domain)
This is the N-terminal domain of regulatory factor X (RFX)-5 protein of the RFX complex present in Homo sapiens. The RFX complex is made up of RFX5, RFXAP and RFXB. The complex is involved in the regulation of the expression of the major histocompatibility complex class II (MHCII) gene products. These gene products are essential for the initiation and regulation of the mammalian immune response. The N-terminal domain of RFX5 is responsible for homodimerization of RFX5 which promotes folding of the C-terminal domain of RFXAP. The folding of RFXAP results in the formation of a potential binding site for RFXB to bind to the MHCII promoter.
Pfam PF20634: Interferon gamma receptor 1, transmembrane region (domain)
This entry represents the cytoplasmic juxtamembrane region of Interferon gamma receptor 1 (IFNGR1) from animals, that includes the transmembrane domain and three lysine ubiquitin acceptor sites (K277, K279 and K285) to guide the proteasome degradation of the receptor, a process that seems to be necessary for efficient IFN-gamma signalling.
Pfam PF00444: Ribosomal protein L36 (domain)
Ribosomal protein bL36 (also known as L36) is the smallest protein from the large subunit of the prokaryotic ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities can be grouped into: bacterial L36; algal and plant chloroplast L36; Cyanelle L36; fungal and animal L36. L36 is a small basic and cysteine-rich protein of around 40 amino-acid residues probably involved in late assembly of the 50S particle, in vitro translation and cell growth. This protein shows a zinc-binding CxxC motif. Its paralogue encoded by ykgO (as named in Escherichia coli), lacks the zinc-binding site and replaces RpmJ when zinc availability is low .
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF14054: Domain of unknown function (DUF4249) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 279 and 365 amino acids in length and contain an lipoprotein attachment site at their N-terminus.
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 PF04492: Bacteriophage replication protein O (family)
Replication protein O is necessary for the initiation of bacteriophage DNA replication.  Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction (annotation of Swiss: P14815).
Pfam PF17858: Platypus intermediate defensin-like peptide (domain)
This entry represents a defensin like peptide identified in the platypus genome.  Structurally it resembles the beta defensins. The peptide was found to display potent antimicrobial activity against Staphylococcus aureus and Pseudomonas aeruginosa.
Pfam PF15603: Immunity protein 74 (family)
A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Tox-ARC family. This domain is also found in heterogeneous poly-immunity loci.
Pfam PF06287: Protein of unknown function (DUF1039) (family)
This family consists of several hypothetical bacterial proteins from Escherichia coli and Citrobacter rodentium. 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 PF05772: NinB protein (family)
The ninR region of phage lambda contains two recombination genes, orf (ninB) and rap (ninG), that have roles when the RecF and RecBCD recombination pathways of E. coli, respectively, operate on phage lambda. NinB binds to single-stranded DNA.
Pfam PF21307: Glycoside hydrolase family 95, C-terminal domain (domain)
This domain is found in Alpha-fucosidase from Bifidobacterium bifidum (AfcA) and in other members of the glycoside hydrolase family 95 from bacteria and plants. AfcA hydrolyses the glycosidic linkage of Fuc1-2Gal via an inverting mechanism. This entry represents the C-terminal beta domain present within the catalytic region of this protein. The domain forms a two- layered jelly roll fold. Its specific function remains unknown.
Pfam PF13041: PPR repeat family (repeat)
This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.
Pfam PF02567: Phenazine biosynthesis-like protein (family)
PhzC/PhzF is involved in dimerisation of two 2,3-dihydro-3-oxo-anthranilic acid molecules to create PCA by P. fluorescens. This family also contains [swissprot:P28176], though there is no significant sequence similarity to [pfam:PF00303] members. This family appears to be distantly related to [pfam:PF01678], including containing a weak internal duplication. However members of this family do not contain the conserved cysteines that are hypothesised to be active site residues (Bateman A pers obs).
Pfam PF16726: Inositol polyphosphate 5-phosphatase clathrin binding domain (domain)
This domain is a clathrin binding domain found at the N-terminus of inositol polyphosphate 5-phosphatase OCRL. It has a PH domain-like fold.
Pfam PF07433: Protein of unknown function (DUF1513) (repeat)
This entry represents bacterial proteins that are predicted to be the outer membrane component of an efeUOB-like ferrous iron, uptake system.
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 PF18590: Immune Mapped Protein 2 (IMP2) N-terminal domain (domain)
Immune Mapped Protein 2 (IMP2) N-terminal domain which is conserved across both IMP1 and IMP2 families. It is suggested that the globular domain likely contributes to a shared function, hence it is termed 'IMP1-like domain'.
Pfam PF06888: Putative Phosphatase (family)
This family contains a number of putative eukaryotic acid phosphatases. Some family members represent the products of the PSI14 phosphatase family in Lycopersicon esculentum (Tomato).
Pfam PF13838: Clathrin-H-link (repeat)
This short domain is found on clathrins, and often appears on proteins directly downstream from the Clathrin-link domain [pfam:PF09268].
Pfam PF15585: Immunity protein 7 (family)
A predicted immunity protein with an alpha+beta fold and a conserved GxaG motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a Tox-REase-3 domain.
Pfam PF09985: C-terminal binding-module, SLH-like, of glucodextranase (domain)
Glucodextran_C is the C-terminal domain of glucodextranase-like proteins found in various prokaryotic membrane-anchored proteins. It shows homology to the carbohydrate-binding unit of some glycosidases.
Pfam PF15443: Domain of unknown function (DUF4630) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 124 and 286 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 PF00873: AcrB/AcrD/AcrF family (family)
Members of this family are integral membrane proteins. Some are involved in drug resistance. AcrB cooperates with a membrane fusion protein, AcrA, and an outer  membrane channel TolC. The structure shows the AcrB forms a  homotrimer.
Wikipedia: The Escherichia coli Acriflavine resistance encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents.
Pfam PF12310: Transcription factor protein N terminal (family)
This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with [pfam:PF00178]. There is a conserved PAVIVE sequence motif. Elf-1 is an immune cell specific transcription factor. It is found in T cells, B cells, megakaryocytes,and mast cells and is involved in the control of transcription for various immune proteins. These include IL-2, GM-CSF, IL-5, IL-2 receptor alpha chain, and CD4 in T cells, IgH, blk, and lyn in B cells, TdT in T and B cells, IL-3 in megakaryocytes, and SCL and Fc-epsilon-RI alpha chain in mast cells.
Pfam PF15273: NHS-like protein (disordered)
This family of proteins includes Nance-Horan syndrome protein (NHS).
Wikipedia: Nance-Horan syndrome protein is a protein that in humans is encoded by the NHS gene.
Pfam PF04183: IucA / IucC family (family)
IucA and IucC catalyse discrete steps in biosynthesis of the siderophore aerobactin from N epsilon-acetyl-N epsilon-hydroxylysine and citrate. This family represents the N-terminal region.  The C-terminal region appears to be related to iron transporter proteins.
Pfam PF23099: Small subunit processome component 20 homolog, C-terminal (domain)
This domain is found at the C-terminal end of human Small subunit processome component 20 homolog (UTP20), which is involved in the 18S rRNA processing. UTP20 is a huge alpha -solenoid that functions as a scaffold. This domain is often found C-terminal to [pfam:PF20416].
Pfam PF07074: Translocon-associated protein, gamma subunit (TRAP-gamma) (family)
This family consists of several eukaryotic translocon-associated protein, gamma subunit (TRAP-gamma) sequences. The translocation site (translocon), at which nascent polypeptides pass through the endoplasmic reticulum membrane, contains a component previously called 'signal sequence receptor' that is now renamed as 'translocon-associated protein' (TRAP). The TRAP complex is comprised of four membrane proteins alpha, beta, gamma and delta which are present in a stoichiometric relation, and are genuine neighbours in intact microsomes.  The gamma subunit is predicted to span the membrane four times.
Pfam PF21987: YajR YAM domain (domain)
This entry represents the C-terminal domain of YajR, an Escherichia coli transporter that belongs to the major facilitator superfamily. This domain has been termed YAM domain, whose precise regulatory role is not yet known. It may sense environmental changes, such as pH and halogen ion variation.
Pfam PF19143: OMP85 superfamily (domain)
This entry represents the membrane spanning beta barrel domain of various Omp85 superfamily related proteins that have often have POTRA and Patatin domains. This family contains mainly flavobacterial proteins.
Pfam PF08722: TnsA-like endonuclease N terminal (domain)
The Tn7 transposase is composed of proteins TnsA and TnsB.  DNA breakage at the 5' end of the transposon is carried out by TnsA, and breakage and joining at the 3' end is carried out by TnsB. The N terminal domain of TnsA is catalytic. This domain is also found in Bacteriophage T4 gp4-like head completion protein whose nuclease activity is required for packaging. This domain contains the catalytic triad of one basic and two acidic residues that form a restriction endonuclease-like active site and conserved between TnsA with gp4 proteins.
Pfam PF18041: MapZ extracellular domain 1 (domain)
This is the extracellular domain 1 (MapZextra1) found in Streptococcus pneumoniae cell division site positioning protein MapZ. MapZ ensures accurate placement of the bacterial division site. The domain is a rigid four alpha-helices with two flexible linkers. The N-terminal end of MapZextra1 is connected to the trans-membrane segment of MapZ whilst the C-terminal is linked to MapZextra2 via a serine rich linker (SRL).The highly conserved residues are not accessible at the surface but are directly involved in many inter-helices interactions allowing for rigidity.
Pfam PF05536: Neurochondrin (repeat)
This family contains several eukaryotic neurochondrin proteins. Neurochondrin induces hydroxyapatite resorptive activity in bone marrow cells resistant to bafilomycin A1, an inhibitor of macrophage- and osteoclast-mediated resorption. Expression of the gene is localised to chondrocyte, osteoblast, and osteocyte in the bone and to the hippocampus and Purkinje cell layer of cerebellum in the brain.
Wikipedia: Neurochondrin is a protein that in humans is encoded by the NCDN gene.
Pfam PF03230: Antirestriction protein (family)
This family includes various protein that are involved in antirestriction. The ArdB protein [swissprot:Q47057] efficiently inhibits restriction by members of the three known families of type I systems of E. coli.
Pfam PF22724: NACHT C-terminal Alpha/Beta 1 (domain)
This domain contains alpha-helices and beta-strands, found at the C-terminus of certain bacterial NACHT conflict systems.
Pfam PF13347: MFS/sugar transport protein (family)
This family is part of the major facilitator superfamily of membrane transport proteins.
Pfam PF17343: Family of unknown function (DUF5373) (family)
This family of unknown function is found in Caenorhabditis. Members of this family are predicted to contain 4 trans-membrane regions.
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 PF18281: BILBO1 N-terminal domain (domain)
This is the N-terminal domain of BIBLO1 present in Trypanosoma brucei. BILBO1 is a flagella pocket collar component. Depletion of BIBLO1 prevents flagella pocket and flagella pocket collar biogenesis and leads to cell death. This domain has a ubiquitin-like fold and has a conserved patch of four aromatic residues (Phe-12, Trp-71, Tyr-87, and Phe-89) and three basic residues (Lys-15, Lys-60, and Lys-62).
Pfam PF18214: STATa Immunoglobulin-like domain (domain)
This domain is found in signal transducer and activator of transcription A protein (STATa) present in Dictyostelium discoideum (dd). STATa is responsible for transcriptionally regulating cellular differentiation in Dictyostelium discoideum. ddSTATa is the only non-metazoan known to employ SH2 domain signaling. This domain adopts an Immunoglobulin-like fold.
Pfam PF19223: Chroparavirus methyltransferase (family)
This entry represents a family of chroparavirus proteins that is homologous to [pfam:PF01660]. These proteins are likely methytransferases involved in mRNA capping.
Pfam PF11609: Protein of unknown function (DUF3248) (family)
This family of proteins is thought to be the product of the gene TT1592 from Thermus thermophilus however this cannot be confirmed. Currently there is no known 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 PF22205: Csm6 6H domain (domain)
This entry represents the six-helix domain (6H) of Csm6 from Thermus termophilus and relates sequences. Csm6 is a ssRNA-specific endoribonuclease that provides an auxiliary RNA-targeting interference mechanism in type III-A CRISPR-Cas systems, working together with the RNA- and DNA-targeting endonuclease activities of the Csm effector complex. Csm6 consists of a CARF domain at the N-terminal, a 6H central domain and the HEPN domain ([pfam:PF09670]) at the C-terminal.
Pfam PF21269: Trehalose synthase, N-terminal domain (domain)
This domain is found at the N-terminal end of Trehalose synthase from Pyrococcus horikoshii (TreT) and similar proteins from prokaryotic organisms. TreT synthesises an alpha,alpha-trehalose from nucleoside diphosphate glucose and glucose. This protein has a typical GT-B glycosyltransferase structure with dual beta/alpha/ beta Rossmann-folds. The N-terminal domain shows a core of six beta-strands and seven associated helices.
Pfam PF20180: Complex III assembly factor UQCC2/CBP6 (family)
This family represents mitochondrial respiratory chain complex III (or cytochrome b-c1 complex) assembly factors, including Cbp6 from yeast and its human orthologue UQCC2 (Ubiquinol-Cytochrome c Reductase Complex Assembly Factor 2). These proteins have diverged significantly among eukaryotes and UQCC2/Cbp6 have an overall low amino acid conservation. UQCC2 interacts with UQCC1, the human orthologue of the Cbp6 binding partner Cbp3, to form a complex necessary for cytochrome b biogenesis. Cbp3-Cbp6 complex interacts with mitochondrial ribosomes for efficient translation of cytochrome b transcript and it also interacts with newly synthesized cytochrome b to assist its correct assembly. These proteins contain a LRY-like N-terminal sequence being related to the LYR superfamily of proteins, which function as subunits or assembly factors for respiratory complexes I, II, III, and V.
Pfam PF12741: Susd and RagB outer membrane lipoprotein (repeat)
This is a family of SusD-like proteins, one member of which, BT1043 ([swissprot:Q8A8X4]), is an outer membrane lipoprotein involved in host glycan metabolism. The structures of this and SusD-homologues in the family are dominated by tetratrico peptide repeats that may facilitate association with outer membrane beta-barrel transporters required for glycan uptake. The structure of BT1043 complexed with N-acetyllactosamine reveals that recognition is mediated via hydrogen bonding interactions with the reducing end of beta-N-acetylglucosamine, suggesting a role in binding glycans liberated from the mucin polypeptide. Mammalian distal gut bacteria have an expanded capacity to utilize glycans. In the absence of dietary sources, some species rely on host-derived mucosal glycans. The ability of Bacteroides thetaiotaomicron, a prominent human gut symbiont, to forage host glycans contributes to both its ability to persist within an individual host and its ability to be transmitted naturally to new hosts at birth.