SII-SWORD/CoKE huggingface dataset:
Pfam PF15539: CAF1 complex subunit p150, region binding to CAF1-p60 at C-term (domain)
CAF1-p150_C2 is part of the binding region of the CAF1 complex p150 subunit to the p60 subunit. The CAF1 complex is essential in human cells for the de novo deposition of histones H3 and H4 at the DNA replication fork.
Pfam PF07210: Protein of unknown function (DUF1416) (family)
This family consists of several hypothetical bacterial proteins of around 100 residues in length. Members of this family appear to be Actinomycete specific. 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 PF12122: Cytoplasmic N-terminal domain of rhomboid serine protease (domain)
Rhomboid_N is the N-terminal cytoplasmic domain of the rhomboid intra-membraneous serine protease, otherwise known as Peptidase_S54, [pfam:PF01694]. This N-terminal domain has similarity to other GlnB-like domains, some of which appear to have a binding role, eg to peptidoglycan.  It is not clear exactly what the function of this domain is in the protease, but its presence is critical for maintaining a catalytically competent state for the protein.
Pfam PF05718: Poxvirus intermediate transcription factor (family)
This family consists of several highly related Poxvirus sequences which are thought to be intermediate transcription factors.
Pfam PF23982: Putative phage cement protein (family)
This entry represents a family of uncharacterised phage proteins. Based on structural similarity These proteins form a trimeric arrangement which stabilises the phage capsid. The proteins have what is known as a beta-tulip fold.
Pfam PF12119: Protein of unknown function (DUF3581) (family)
This protein is found in bacteria. Proteins in this family are about 240 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 PF09858: Predicted membrane protein (DUF2085) (family)
This domain, found in various hypothetical prokaryotic proteins, has 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 PF20676: Herpesvirus envelope glycoprotein gp350, N-terminal B domain (domain)
This entry consists of the envelope glycoprotein gp350 from Epstein-Barr virus (also known as BLLF1 viral late glycoprotein). It is the most abundantly expressed glycoprotein in the viral envelope of Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. It is a 907 residues long gp350 polypeptide containing an 18-residue peptide at the C-terminal that is located inside the viral membrane, a membrane-spanning domain and a large N-terminal segment (860 residues) predicted to extend outside the viral membrane. The extreme N-terminal region (1-470) is sufficient to bind receptor CR2 (also known as CD21) and fold into three distinct domains (denoted as A, B and C) which organise into an "L-shape" structure. This is domain B.
Pfam PF04296: Protein of unknown function (DUF448) (family)
The YlxR family has been demonstrated to regulate metabolic gene expression.
Pfam PF25091: Domain of unknown function (DUF7806) (domain)
This domain is found in uncharacterised plant proteins. It is predicted to adopt a globular structure with similarity to members of the Kinetochore globular domain-like superfamily.
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 PF02517: Type II CAAX prenyl endopeptidase Rce1-like (family)
This family (also known as the ABI (abortive infection) family) contains putative IMPs and has homologues in all three domains of life, including Rce1 from S. cerevisiae. Rce1 is a type II CAAX prenyl protease that processes all farnesylated and geranylgeranylated CAAX proteins. It is an integral membrane endoprotease localized to the endoplasmic reticulum that mediates the cleavage of the carboxyl-terminal three amino acids from CaaX proteins. It is involved in processing the Ras family of small GTPases, the gamma-subunit of heterotrimeric GTPases, nuclear lamins, and protein kinases and phosphatases. Three residues of S. cerevisiae Rce1 -E156, H194 and H248- are critical for catalysis. The structure of Rce1 from the archaea Methanococcus (MmRce1) suggests that this group of proteins represents a novel IMP (intramembrane protease) family, the glutamate IMPs. There is a conserved sequence motif EExxxR.
Pfam PF21560: Long-tail fiber proximal subunit, C-terminal, second (domain)
This domain is found at the C-terminal end of Long-tail fiber proximal subunit from Bacteriophage T4 (Gp34), an structural component of the proximal-half of the long-tail fiber. This protein adopts a trimeric configuration. This domain shows a core antiparallel beta-sheet.
Pfam PF15087: Protein of unknown function (DUF4551) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in metazoa. This family includes human protein C12orf56.
Pfam PF10216: CO2 hydration protein (ChpXY) (family)
This small family of proteins includes paralogues ChpX and ChpY in Synechococcus sp. PCC7942 and other cyanobacteria, associated with distinct NAD(P)H dehydrogenase complexes. These proteins collectively enable light-dependent CO2 hydration and CO2 uptake; loss of both blocks growth at low CO2 concentrations.
Pfam PF09364: XFP N-terminal domain (family)
Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P [ec:4.1.2.9], [ec:4.1.2.22]. This family is distantly related to transketolases e.g. [pfam:PF02779].
Pfam PF14872: Hypothetical glycoside hydrolase 5 (family)
GHL5 is a family of hypothetical glycoside hydrolases.
Pfam PF14460: Prokaryotic E2 family D (family)
A member of the E2/UBC superfamily of proteins found in several bacteria. Members of this family lack the conserved histidine of the classical E2-fold. However, they have an absolutely conserved histidine carboxyl-terminal to the conserved cysteine. Members  of this family are usually present in a conserved gene neighborhood  with genes encoding members of the Ub modification pathway such as  the E1, Ub and JAB proteins. These neighborhoods also contain a  gene encoding a rapidly diverging alpha-helical protein.
Pfam PF10081: Alpha/beta-hydrolase family (family)
This is a family of alpha/beta hydrolases which may function as lipases. This domain is the catalytic domain and includes the catalytic triad and the GXSXG sequence motif which is a characteristic of these enzymes.
Pfam PF06901: RTX iron-regulated protein FrpC (family)
This family consists of several RTX iron-regulated FrpC proteins which appear to be found exclusively in Neisseria meningitidis. FrpC has been shown to be related to the RTX family of bacterial cytotoxins. FrpC is found in the meningococcal outer membrane. The function of this family is unknown although it is thought to be a virulence factor.
Pfam PF06753: Bradykinin (family)
This family consists of several bradykinin sequences. The skins of anuran amphibians, in addition to mucus glands, contain highly specialised poison glands, which, in reaction to stress or attack, exude a complex noxious cocktail of biologically active molecules. These secretions often contain a plethora of peptides among which bradykinin or structural variants have been identified.
Pfam PF16089: Domain of unknown function (DUF4818) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 176 and 214 amino acids in length. There is a single completely conserved residue W that may be functionally important.
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 PF02213: GYF domain (domain)
The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein [swissprot:O95400].
Wikipedia: In molecular biology, the GYF domain is an approximately 60-amino acid protein domain which contains a conserved GP[YF]xxxx[MV]xxWxxx[GN]YF motif. It was identified in the human intracellular protein termed CD2 binding protein 2 (CD2BP2), which binds to a site containing two tandem PPPGHR segments within the cytoplasmic region of CD2. Binding experiments and mutational analyses have demonstrated the critical importance of the GYF tripeptide in ligand binding. A GYF domain is also found in several other eukaryotic proteins of unknown function. It has been proposed that the GYF domain found in these proteins could also be involved in proline-rich sequence recognition. Resolution of the structure of the CD2BP2 GYF domain by NMR spectroscopy revealed a compact domain with a beta-beta-alpha-beta-beta topology, where the single alpha-helix is tilted away from the twisted, anti-parallel beta-sheet. The conserved residues of the GYF domain create a contiguous patch of predominantly hydrophobic nature which forms an integral part of the ligand-binding site. There is limited homology within the C-terminal 20-30 amino acids of various GYF domains, supporting the idea that this part of the domain is structurally but not functionally important.
Pfam PF06808: Tripartite ATP-independent periplasmic transporter, DctM component (domain)
This entry represents the transmembrane segments from a diverse range of transporter proteins from the tripartite ATP-independent periplasmic (TRAP) transport system, in which the driving force for solute accumulation is an electrochemical ion gradient and not ATP hydrolysis. The first TRAP transporter to be characterised was the high-affinity C4-dicarboxylate transport (Dct) system from Rhodobacter capsulatus which consists of ESR (DctP) and small (DctQ) and large (DctM) integral membrane proteins. In general, C4-dicarboxylate transport systems allow C4-dicarboxylates like succinate, fumarate, and malate to be taken up. This entry also includes SiaM (involved in sialic acid uptake) and YiaN (involved in the uptake of 2,3-diketo-L-gulonate).
Wikipedia: Tripartite ATP-independent periplasmic transporters are a large family of solute transporters found in bacteria and archaea, but not in eukaryotes, that appear to be specific for the uptake of organic acids or related molecules containing a carboxylate or sulfonate group. They are unique in that they utilize a substrate binding protein (SBP) in combination with a secondary transporter.
Pfam PF06163: Bacterial protein of unknown function (DUF977) (family)
This family consists of several hypothetical bacterial proteins from Escherichia coli and Salmonella typhi. 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 PF18715: Phage spike trimer (repeat)
Bacteriophages penetrate the host cell membrane using their tail to  inject genetic material into the host. In this penetration  process, they use central spike domain located beneath their  baseplate. The spike domain folds as a trimeric iron-binding  structure. This entry contains three copies of the repeat unit.
Pfam PF08761: dUTPase (domain)
2-Deoxyuridine 5-triphosphate nucleotidohydrolase (dUTPase) catalyses the hydrolysis of dUTP to dUMP and pyrophosphate ([ec:3.6.1.23]).  Members of this family have a novel all-alpha fold and are unrelated to the all-beta fold found in dUTPases of the majority of organisms.  This family contains both dUTPase homologues of dUTPase including dCTPase of phage T4.
Wikipedia: In Enzymology, a dUTP diphosphatase (EC 3.6.1.23) is an enzyme that catalyzes the chemical reactiondUTP + H2O  dUMP + diphosphate
Pfam PF13220: Protein of unknown function (DUF4028) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 67 and 93 amino acids in length. There are two conserved sequence motifs: IVKI and YVKKWF.
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 PF04510: Family of unknown function (DUF577) (family)
This domain is found in Arabidopsis thaliana proteins, which are specifically expressed during meiosis. Many of these members contain a repeated region.
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 PF22980: Myb-like DNA-binding domain (domain)
This entry represents a Myb-like domain. These domains are short DNA-binding domains.
Pfam PF14684: Tricorn protease C1 domain (domain)
This domain is the C1 core domain of tricorn protease. This is a mixed alpha-beta domain.
Pfam PF06086: Orthopoxvirus A26L/A30L protein (family)
This family consists of several Orthopoxvirus A26L and A30L proteins. The Vaccinia A30L gene is regulated by a late promoter and encodes a protein of approximately 9 kDa. It is thought that the A30L protein is needed for vaccinia virus morphogenesis, specifically the association of the dense viroplasm with viral membranes.
Pfam PF04928: Poly(A) polymerase central domain (domain)
In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. This entry represents the central domain.
Pfam PF04043: Plant invertase/pectin methylesterase inhibitor (domain)
This domain inhibits pectin methylesterases (PMEs) and invertases through formation of a non-covalent 1:1 complex. It has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension (see). It may also be involved in inhibiting microbial pathogen PMEs. It has been observed that it is often expressed as a large inactive preprotein. It is also found at the N-termini of PMEs predicted from DNA sequences (personal obs:C Yeats), suggesting that both PMEs and their inhibitor are expressed as a single polyprotein and subsequently processed. It has two disulphide bridges and is mainly alpha-helical.
Pfam PF22444: PaaX-like, ferredoxin-like domain (domain)
This entry represents a ferredoxin-like domain in PaaX-like protein from Jannaschia sp. (PDB:3l09). PaaX-like is a putative transcriptional regulator.
Pfam PF14884: Type I membrane glycoproteins cell-cell fusogen (family)
EFF-AFF was first identified when EFF1 mutants were found to block cell fusion in all epidermal and vulval epithelia in the worm. However, fusion between the anchor cell and the utse syncytium that establishes a continuous uterine-vulval tube proceeds normally in eff-1 mutants and thus Aff1 was established as necessary for this and the fusion of heterologous cells in C. elegans. The transmembrane forms of FF proteins, like most viral fusogens, possess an N-terminal signal sequence followed by a long extracellular portion, a predicted transmembrane domain, and a short intracellular tail. A striking conservation in the position and number of all 16 cysteines in the extracellular portion of FF proteins from different nematode species suggests that these proteins are folded in a similar 3D structure that is essential for their fusogenic activity. C. elegans AFF-1 and EFF-1 proteins are essential for developmental cell-to-cell fusion and can merge insect cells. Thus FFs comprise an ancient family of cellular fusogens that can promote fusion when expressed on a viral particle.
Wikipedia: Cell–cell fusogens are glycoproteins that facilitate the fusion of cell to cell membranes. Cell–cell fusion is critical for the merging of gamete genomes and the development of organs in multicellular organisms. Cell-cell fusion occurs when both actin cytoskeleton and fusogenic proteins properly rearrange across the cell membrane. This process is led by actin-propelled membrane protrusions.
Pfam PF14332: Domain of unknown function (DUF4388) (family)
This domain family is found in bacteria, and is typically between 102 and 135 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 PF03170: Bacterial cellulose synthase subunit (family)
This family includes bacterial proteins involved in cellulose synthesis. Cellulose synthesis has been identified in several bacteria. In Agrobacterium tumefaciens, for instance, cellulose has a pathogenic role: it allows the bacteria to bind tightly to their host plant cells.  While several enzymatic steps are involved in cellulose synthesis, potentially the only step unique to this pathway is that catalysed by cellulose synthase. This enzyme is a multi subunit complex. This family encodes a subunit that is thought to bind the positive effector cyclic di-GMP. This subunit is found in several different bacterial cellulose synthase enzymes. The first recognised sequence for this subunit is BcsB. In the AcsII cellulose synthase, this subunit and the subunit corresponding to BcsA are found in the same protein. Indeed, this alignment only includes the C-terminal half of the AcsAII synthase ([swissprot:Q59167]), which corresponds to BcsB.
Wikipedia: The UDP-forming form of cellulose synthase is the main enzyme that produces cellulose. Systematically, it is known as UDP-glucose:(1→4)-β-D-glucan 4-β-D-glucosyltransferase in enzymology. It catalyzes the chemical reaction:UDP-glucose + [(1→4)-β-D-glucosyl]n = UDP + [(1→4)-β-D-glucosyl]n+1
Pfam PF14433: SUKH-3 immunity protein (family)
This family belongs to the SUKH superfamily and functions as immunity proteins in bacterial toxin systems.
Pfam PF22047: Single-stranded-DNA-specific exonuclease RecJ C-terminal domain (domain)
This entry represents a C-terminal domain present in a set of RecJ proteins, such as RecJ from Thermus thermophilus. The RecJ protein of Escherichia coli plays an important role in a number of DNA repair and recombination pathways. RecJ catalyses processive degradation of single-stranded DNA in a 5'-to-3' direction. Sequences highly related to those encoding RecJ can be found in many of the eubacterial genomes sequenced to date.
Pfam PF13539: D-alanyl-D-alanine carboxypeptidase (family)
This family resembles VanY, [pfam:PF02557], which is part of the peptidase M15 family.
Pfam PF12355: Down syndrome cell adhesion molecule C terminal (family)
This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with [pfam:PF00047], [pfam:PF07679], [pfam:PF00041]. The Down syndrome cell adhesion molecule (Dscam) belongs to a family of cell membrane molecules involved in the differentiation of the nervous system. This is the C terminal cytoplasmic tail region of Dscam.
Pfam PF02070: Neuromedin U (family)
Neuromedin U (NmU)  is a vertebrate peptide which stimulates uterine smooth muscle contraction and causes selective vasoconstriction. Like most other active peptides, it is proteolytically processed from a larger precursor protein. The mature peptides are 8 (NmU-8) to 25 (NmU-25) residues long and C-terminally amidated.

This entry represents the sequence of the C-terminal extremity of NmU, which is extremely well conserved.
Pfam PF18003: Domain of unknown function (DUF3823_C) (domain)
This is a family of uncharacterised proteins from Bacteroidetes. This domain has an Ig-like fold.
Pfam PF02065: Melibiase (family)
Glycoside hydrolase families GH27, GH31 and GH36 form the glycoside hydrolase clan GH-D. Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K. This family includes enzymes from GH36A-B and GH36D-K and from GH27.
Wikipedia: In molecular biology, glycoside hydrolase family 27 is a family of glycoside hydrolases.
Pfam PF09643: YopX protein (domain)
YopX is a protein that is largely helical, with three identical chains probably complexing into a twelve-chain structure.
Pfam PF09479: Listeria-Bacteroides repeat domain (List_Bact_rpt) (domain)
This model describes a conserved core region of about 43 residues which occurs in more than 400 mostly secreted or cell surface-located proteins from over 300 eubacterial and few archaeal species. These proteins contain between one and 34 copies of the domain that often occur in tandem arrays with up to more than 20 copies.