SII-SWORD/CoKE huggingface dataset:
Pfam PF07314: Protein of unknown function (DUF1461) (family)
This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long. These are possibly integral membrane proteins.
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 PF01049: Cadherin, Y-type LIR-motif (family)
LC3 Interacting Regions (LIRs), also known as ATG8-interacting motifs (AIMs), are short-linear motifs (SLiMs) of autophagy receptors and adaptor proteins that facilitates the selective recruitment of autophagy substrates to the autophagosome. LIRs are characterised by degenerated sequences with a four-residue core central sequence involved in ATG8-binding, with the W/Y/FxxL/I/V pattern. Based on the aromatic amino acid in position 1 they can be classified into W-type, Y-type and F-type. This entry includes three conserved LIR motifs of CADHs, which two are Y-type (YDxL/I) and one F-type (FKKL), while a fourth LIR (YGGV) is only present in CADH6 members. Cadherins (CADH) have a crucial role in epithelial-to-mesenchymal transition (EMT), involved in migration properties of tumour cells. CADH6 is an EMT marker in thyroid cancer that interacts with the ATG8 family members GABARAP, BNIP3 and BNIP3L restraining autophagy through LIR domains, a common feature among many cadherin family members.
Wikipedia: In molecular biology, the cadherin cytoplasmic region is a conserved region found at the C-terminus of cadherin proteins. A key determinant to the strength of the binding that it is mediated by cadherins is the juxtamembrane region of the cadherin. This region induces clustering and also binds to the protein catenin (p120ctn). The cytoplasmic region is highly conserved in sequence and has been shown experimentally to regulate the cell-cell binding function of the extracellular domain of E-cadherin, possibly through interaction with the cytoskeleton.
Pfam PF23003: Fibronectin type I domain (domain)
This entry represents a domain that structurally resembles the fibronectin type 1 repeat.
Pfam PF19925: Family of unknown function (DUF6388) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001859) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular fosfomycin biosynthetic gene cluster from Pseudomonas syringae. This family is predominantly found in proteobacteria. Some members  of this family have been putatively identified as DNA repair proteins.
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 PF01053: Cys/Met metabolism PLP-dependent enzyme (domain)
This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP (pyridoxal-5'-phosphate) as a cofactor.
Wikipedia: In molecular biology, the Cys/Met metabolism PLP-dependent enzyme family is a family of proteins including enzymes involved in cysteine and methionine metabolism which use PLP (pyridoxal-5'-phosphate) as a cofactor.
Pfam PF19567: Capsular polysaccharide synthesis, CpsB/CapC (domain)
Capsular polysaccharide biosynthesis proteins are critical for the production of a mature capsule in vitro. Members of Streptococcus pneumoniae have variable capsules, with about 90 known capsular serotypes that all have their own polysaccharide structure. cps14B to cps14H products are similar to other proteins involved in bacterial polysaccharide biosynthesis in both Gram-negative and -positive bacteria . CpsA to cpsD are common to most serotypes. CpsD is an autophosphorylating protein-tyrosine kinase. CpsC is required for CpsD tyrosine-phosphorylation, and CpsB is required for dephosphorylation of CpsD. CpsB is a novel manganese-dependent phosphotyrosine-protein phosphatase that belongs to the PHP (polymerase and histidinol phosphatase) family of phosphoesterases . Phosphorylation of proteins on hydroxyl amino acids (serine, threonine, tyrosine) occurs at different stages of pathenogenesis, including cell-cell interaction and adherence, translocation of bacterial effectors into host cells, and changes in host cellular structure and function induced by infection . CpsB, CpsC, CpsD, and ATP form a stable complex that enhances capsule synthesis and acts to regulate it .
Pfam PF19411: Cell cycle link protein Clink (family)
This entry represents the cell cycle link protein Clink from Banana bunchy top virus (BBTV) which was identified as a suppressor of RNA silencing. It interacts with retinoblastoma-related proteins (pRB) and S-phase kinase-associated protein 1 (SKP1). Clink contains LxCxE and F-box motifs that mediate the interactions with the respective proteins and the capacity of Clink to bind pRB correlates with its ability to stimulate viral replication. pRB is a key cell cycle regulator, which represses onset and progression into S-phase by interacting with a wide range of cell cycle-related proteins.
Pfam PF24115: Domain of unknown function (DUF7389) (domain)
This is a domain of unknown function found in a group of archaeal sequences.
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 PF19562: Family of unknown function (DUF6084) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a  protein from the herboxidiene biosynthetic gene cluster from  Streptomyces chromofuscus and appears to be predominantly found in Actinobacteria.
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 PF20453: Family of unknown function (DUF6707) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 190 and 350 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 PF09798: DNA damage checkpoint protein (family)
This is a family of proteins which regulate checkpoint kinases. In Schizosaccharomyces pombe this protein is called Rad26 and in Saccharomyces cerevisiae it is called LCD1.
Pfam PF12110: Nuclear protein 96 (domain)
Nup96 (often known by the name of its yeast homolog Nup145C) is part of the Nup84 heptameric complex in the nuclear pore complex. Nup96 complexes with Sec13 in the middle of the heptamer. The function of the heptamer is to coat the curvature of the nuclear pore complex between the inner and outer nuclear membranes. Nup96 is predicted to be an alpha helical solenoid. The interaction between Nup96 and Sec13 is the point of curvature in the heptameric complex.
Pfam PF08400: Prophage tail fibre N-terminal (family)
This domain is found at the N-terminus of prophage tail fibre proteins.
Pfam PF04996: Succinylarginine dihydrolase (family)
This enzyme transforms N(2)-succinylglutamate into succinate and glutamate. This is the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway.
Pfam PF04687: Microvirus H protein (pilot protein) (family)
A single molecule of H protein is found on each of the 12 spikes on the microvirus shell.  H is involved in the ejection of the phage DNA, and at least one copy is injected into the host's periplasmic space along with the ssDNA viral genome. Part of H is thought to lie outside the shell, where it recognises lipopolysaccharide from virus-sensitive strains.  Part of H may lie within the capsid, since mutations in H can influence the DNA ejection mechanism by affecting the DNA-protein interactions.  H may span the capsid through the hydrophilic channels formed by G proteins. Elucidation of the DNA-ejection mechanism from the crystal structure of part of the H protein shows that this tail-less icosahedral, single-stranded DNA phiX174-like coliphage bacteriophage requires H as a pilot protein for its DNA-delivery. H oligomerises to form a tube the function of which seems to be the delivery of the DNA genome across the host's periplasmic space into the host cytoplasm. The tube is constructed of ten alpha-helices with their amino termini arrayed in a right-handed super-helical coiled-coil and their carboxy termini arrayed in a left-handed super-helical coiled-coil. The tube spans the periplasmic space and is present while the genome is being delivered into the host cell's cytoplasm.
Pfam PF08911: NUP50 (Nucleoporin 50 kDa) (domain)
Nucleoporin 50 kDa (NUP50) acts as a cofactor for the importin-alpha:importin-beta heterodimer, which in turn allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. The C terminus of NUP50 binds importin-beta through RAN-GTP, the N terminus binds the C terminus of importin-alpha, while a central domain binds importin-beta. NUP50:importin-alpha:importin-beta then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to actively displace nuclear localisation signals from importin-alpha.
Pfam PF22242: 6-phosphogluconate dehydrogenase C-terminal domain-like (domain)
This alpha helical domain is found at the C-terminus of proteins that contain an N-terminal Rossmann domain. This domain belongs to the 6-phosphogluconate dehydrogenase C-terminal domain-like superfamily.
Pfam PF24081: SLA1-like, PH domain-like (domain)
This domain is found in Actin cytoskeleton-regulatory complex protein SLA1 from Saccharomyces cerevisiae and similar proteins mainly found in fungi. SLA1 is a component of the PAN1 actin cytoskeleton-regulatory complex required for the internalisation of endosomes during actin-coupled endocytosis. This domain is predicted to adopt a PH domain-like fold.
Pfam PF10065: Uncharacterized conserved protein (DUF2303) (family)
Members of this family of hypothetical bacterial proteins have 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 PF10472: eIF2-alpha phosphatase phosphorylation constitutive repressor (domain)
This is the conserved N-terminal domain of CReP, constitutive repressor of eIF2-alpha phosphorylation/protein phosphatase 1, catalytic subunit. It functions in the dephosphorylation of eIF2-alpha under basal conditions in the absence of stress. In response to translation inhibition, there is reduced synthesis of the labile CReP that contributes to elevated levels of eIF2-alpha phosphorylation. The C-terminus, family PP1c, is shared with the apoptosis-associated protein Gadd34 and herpes simplex virus.
Pfam PF11320: Protein of unknown function (DUF3122) (family)
This family of proteins with unknown function appear to be restricted to Cyanobacteria.
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 PF12399: Branched-chain amino acid ATP-binding cassette transporter (domain)
This domain family is found in bacteria, archaea and eukaryotes, and is approximately 30 amino acids in length. The family is found in association with [pfam:PF00005]. There is a conserved AYLG sequence motif. This family is the C terminal of an ATP dependent branched-chain amino acid transporter. This domain is essential for LPS transport, through critical interactions with Walker A and switch helix domains.
Pfam PF02163: Peptidase family M50 (family)
Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role. Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .
This entry contains metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM).
Wikipedia: A metalloproteinase, or metalloprotease, is any protease enzyme whose catalytic mechanism involves a metal. An example is ADAM12 which plays a significant role in the fusion of muscle cells during embryo development, in a process known as myogenesis.
Pfam PF11788: 39S mitochondrial ribosomal protein L46 (family)
This is the L46 subunit of the mammalian mitochondrial ribosome, conserved from plants and fungi.
Pfam PF04490: Poxvirus T4 protein, C terminus (family)
This family of poxvirus proteins are thought to be retained in the endoplasmic reticulum.  M-T4 of myxoma virus ([swissprot:O55698]) is thought to protect infected lymphocytes from apoptosis and modulate the inflammatory response to virus infection.
Pfam PF01290: Thymosin beta-4 family (family)
This entry represents beta-thymosin family. Its members include thymosin beta-4, -10, -15 from humans and their homologues (such as thymosin beta 11/12) from fish.

Thymosin beta-4 (Tbeta) is a small protein that sequesters actin monomers to help maintain the high concentrations of unpolymerised actin in higher eukaryotic cells. Its structure has been resolved . It is a multiple function protein that plays important roles in cellular processes such as wound healing, embryonic organ development and the pathogeneses of disease . It plays a role in anti-apoptotic response to an external stress , paclitaxel-resistance via ROS production  and HIF-1alpha stabilisation via Erk activation . It also regulates cancer cell migration through various signalling pathways, and hence plays a role in malignant progression and invasion in colon adenocarcinoma .
Wikipedia: Beta thymosins are a family of proteins which have in common a sequence of about 40 amino acids similar to the small protein thymosin β4. They are found almost exclusively in multicellular animals. Thymosin β4 was originally obtained from the thymus in company with several other small proteins which although named collectively "thymosins" are now known to be structurally and genetically unrelated and present in many different animal tissues.
Pfam PF19976: GTPase-associated adaptor domain (domain)
Adaptor domain in the GTPase-centric systems of NTP-dependent conflict systems that directly couples the effector to the GAP1 component.
Pfam PF09545: AccI restriction endonuclease (family)
This family includes the AccI (recognises and cleaves GT^MKAC) restriction endonuclease.
Pfam PF14839: DOR family (family)
This family of proteins regulate autophagy and gene transcription.
Pfam PF12222: Peptide N-acetyl-beta-D-glucosaminyl asparaginase amidase A (domain)
This domain is found in bacteria, archaea and eukaryotes (mainly fungi and plants). This entry includes Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase A, a protein capable of hydrolysing glycopeptides with an alpha-1,3-fucosylated asparagine-bound N-acetylglucosamine. This domain is related to Peptide-N-glycosidases.
Pfam PF22681: Lmo2446-like, N-terminal (domain)
This domain is found at the N-terminal end of a group of bacterial proteins, including Lmo2446 protein from Listeria monocytogenes, a functionally uncharacterised extracellular lipidated protein. Lmo2446 contains a glycoside hydrolase 31 family (GH31) catalytic domain ([pfam:PF01055]) flanked by three structural beta-domains. This domain folds into a carbohydrate binding module (CBM)-like beta-sandwich.
Pfam PF13833: EF-hand domain pair (domain)
Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue Î±-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand). Ca2 binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers .
Wikipedia: The EF hand is a helix–loop–helix structural domain or motif found in a large family of calcium-binding proteins.
Pfam PF23875: Domain of unknown function (DUF7229) (domain)
This small helical domain is found a small family of phage proteins.
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 PF02989: Lyme disease proteins of unknown function (family)
This group comprises proteins of unknown function from Borrelia burgdorferi, the causitive organism of Lyme disease.
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 PF15319: RAD9, RAD1, HUS1-interacting nuclear orphan protein (family)
RHINO, or RAD9, RAD1, HUS1-interacting nuclear orphan, is a family of eukaryotic proteins. Under genotoxic stresses such as ionizing radiation during the S phase, RHINO plays a role in DNA damage response signalling. It is recruited to sites of DNA damage through interaction with the 9-1-1 cell-cycle checkpoint response complex and TOPBP1 in a ATR-dependent (ataxia telangiectasia and Rad3-related) manner. It is required for the progression of the G1 to S phase transition of breast cancer cells, and it is known to play a role in the stimulation of CHEK1 phosphorylation. It interacts with RAD9A, RAD18, TOPBP1 and UBE2N.
Pfam PF00038: Intermediate filament protein (coiled_coil)
Intermediate filaments (IF)  are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in six types:


 * Type I: Acidic cytokeratins.
 * Type II: Basic cytokeratins.
 * Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin.
 * Type IV: Neurofilaments L, H and M, alpha-internexin and nestin.
 * Type V: Nuclear lamins A, B1, B2 and C.
 * Type VI: 'Orphan' IF proteins, which are more distant in terms of their amino acid sequences.


All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled- coiled Î±-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins.

While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. The IF rod domain is approximately 310 residues long in all cytoplasmic IF proteins and close to 350 residues in the nuclear ones. The IF rod domain exhibits an interrupted Î±-helical conformation and reveals a pronounced seven-residue periodicity in the distribution of apolar residues. The heptad periodicity within the rod domain is interrupted in several places, which generates four consecutive Î±-helical segments: 1A and 1B, which together form the so-called coil 1, and 2A and 2B, which form coil 2. The four Î±-helical segments are interconnected by relatively short, variable linkers L1, L12 and L2 .

IF proteins have a very strong tendency to dimerize via the formation of an Î±-helical coiled coil (CC) by their rod domains .
Wikipedia: Intermediate filaments (IFs) are cytoskeletal structural components found in the cells of vertebrates, and many invertebrates. Homologues of the IF protein have been noted in an invertebrate, the cephalochordate Branchiostoma.
Pfam PF15600: Immunity protein 64 (family)
A predicted immunity protein with an alpha+beta fold and a conserved DxEA motif and arginine residue. 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-ColD family.