SII-SWORD/CoKE huggingface dataset:
Pfam PF19555: Family of unknown function (DUF6078) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroidetes bacteria. Proteins in this family are approximately 150 amino acids in length. This family contains 4 conserved cysteines towards the N-terminus which may form a zinc-binding motif.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23410: Vps8 beta-propeller (repeat)
Vps8 is one of the Golgi complex components necessary for vacuolar sorting. It is the core component of the endosomal tethering complex CORVET (class C core vacuole/endosome tethering). Vps8 co-operates with Vps21-GTP to mediate endosomal clustering in a reaction that is dependent on Vps3. Vps8  is the only CORVET subunit that is enriched on late endosomes, suggesting that it is a marker for the maturation of late endosomes. These proteins consist of a beta-propeller at the N-terminal followed by a long, central TPR domain ([pfam:PF12816]) and a RING zinc finger at the C-terminal; this entry represents the beta-propeller domain.
Pfam PF17248: Family of unknown function (DUF5317) (family)
This is a family of unknown function found mainly in Bacteria. Members of this family have multiple trans-membrane domains with the majority typically constituted of 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 PF01968: Hydantoinase/oxoprolinase (family)
This family includes the enzymes hydantoinase and oxoprolinase [ec:3.5.2.9]. Both reactions involve the hydrolysis of 5-membered rings via hydrolysis of their internal imide bonds.
Pfam PF16171: Centromere kinetochore component CENP-T N-terminus (family)
CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore.  Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure.  The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This family represents the N-terminus of CENP-T.
Pfam PF18820: Bdellovibrio Beta-sandwich (domain)
A beta-sandwich domain exclusively found at the N-terminal of CHROMO domains in many Bdellovibrio proteins.
Pfam PF15218: Spermatogenesis-associated protein 25 (family)
This family of proteins may be involved in spermatogenesis.
Pfam PF05826: Phospholipase A2 (domain)
This family consists of several phospholipase A2 like proteins mostly from insects.
Pfam PF21863: Helix-turn-helix family (domain)
This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 270 and 293 amino acids in length. These proteins are composed of a large alpha-helical domain which appears to be related to MarR transcription factors.
Pfam PF16820: PKD-like domain (family)
This PKD-like family is found in various Bacteroidetes species.
Pfam PF08058: Nuclear pore complex component (domain)
Proteins containing this domain are components of the  nuclear pore complex.  One member of this family  is Nucleoporin POM34 (Swiss: Q12445) which is thought to have a role in anchoring peripheral Nups into the pore and mediating pore formation.
Pfam PF15735: Domain of unknown function (DUF4683) (family)
This domain family is found in eukaryotes, and is typically between 384 and 400 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 PF12144: Eukaryotic Mediator 12 catenin-binding domain (domain)
This domain is found in eukaryotes, and is typically between 325 and 354 amino acids in length. Both development and carcinogenesis are driven by signal transduction within the canonical Wnt/beta-catenin pathway through both programmed and unprogrammed changes in gene transcription. Beta-catenin physically and functionally targets this PQL (proline-, glutamine-, leucine-rich) region of the Med12 subunit of Mediator to activate transcription. The beta-catenin transactivation domain binds directly to isolated Med12 and intact Mediator both in vitro and in vivo, and Mediator is recruited to Wnt-responsive genes in a beta-catenin-dependent manner.
Wikipedia: Mediator is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes. It was discovered in 1990 in the lab of Roger D. Kornberg, recipient of the 2006 Nobel Prize in Chemistry. Mediator complexes interact with transcription factors and RNA polymerase II. The main function of mediator complexes is to transmit signals from the transcription factors to the polymerase.
Pfam PF06718: Protein of unknown function (DUF1203) (family)
This family consists of several hypothetical bacterial proteins of around 155 residues in length. Family members are present in Rhizobium, Agrobacterium and Streptomyces species.
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 PF18917: LiaI-LiaF-like transmembrane region (domain)
This entry represents a transmembrane region found in sequences related to LiaI-LiaF proteins. It is composed of two transmembrane helices that are often found in 2 or three copies in a protein. The members of this family are functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 40 amino acids in length. This entry is often associated with [pfam:PF09922] a putative adhesive domain that adopts a beta helix fold.
Pfam PF24867: Domain of unknown function (DUF7733) (domain)
This domain is found in uncharacterised proteins mainly from plants. It is predicted to fold into a structure consisting of six 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 PF13432: Tetratricopeptide repeat (repeat)
This family is found predominantly at the C-terminus of transglutaminase enzyme core regions.
Pfam PF04196: Bunyavirus RNA dependent RNA polymerase (family)
The bunyaviruses are enveloped viruses with a genome consisting of 3 ssRNA segments (called L, M and S). The nucleocapsid protein is encode on the small (S) genomic RNA. The L segment codes for an RNA polymerase. This family contains the RNA dependent RNA polymerase on the L segment.
Wikipedia: RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to typical DNA-dependent RNA polymerases, which all organisms use to catalyze the transcription of RNA from a DNA template.
Pfam PF14109: GldH lipoprotein (family)
Members of this protein family are predicted lipoproteins, exclusive to the Bacteroidetes phylum. Proteins in this family are typically between 155 and 167 amino acids in length. Members include GldH, a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family may have gliding motility.
Pfam PF21416: Inner layer core protein VP1-like, C-terminal (domain)
This entry includes capsid proteins from cypoviruses which form the icosahedral capsid through self-assembly (they are also known as inner layer core proteins). The capsid encapsulates and protects the genomic RNA. These viruses encode VP1, VP3 and VP5 as major capsid proteins, encoded by RNA segment 1 and 3 in the case of VP1 and VP3, respectively, whereas RNA segment encoding VP5 is still unclear. This entry represents the C-terminal domain of capsid proteins from cypovirusus.
Pfam PF13391: HNH endonuclease (domain)
This domain is found in HNH family of nucleases that includes yeast intron 1 protein, human DNA annealing helicase and endonuclease ZRANB3, bacterial CRISPR-associated endonuclease Cas9, colicins, pyocins and endonuclease HphI. Members in this group are found in all domains of life.
Pfam PF17150: C-terminal domain of two-partite extracellular sensor domain (family)
CHASE6 was originally described as a two-partite extracellular (periplasmic) sensor domain found in histidine kinases and HD-GYP-type c-di-GMP-specific phosphodiesterases and assigned to COG4250 in the COG database. Subsequently, its N-terminal part has been described as a separate DICT (DIguanylate Cyclases and Two-component systems) domain (PF10069) (Aravind L., Iyer LM, Anantharaman V. (2010) Natural history of sensor domains in the bacterial signalling systems. In: Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition ((Spiro S, Dixon R, eds)), pp. 1-38. Caister Academic Press, Norfolk, UK). The current entry contains only the C-terminal part of the original CHASE6 domain described in, which is found primarily in cyanobacteria.
Pfam PF20896: Tomato mosaic virus helicase, N-terminal domain (domain)
Tomato mosaic virus (ToMV) generates two large replication proteins in the host cell. The smaller one contains the methyltransferase domain and the helicase domain (Hel). This core helicase domain consists of two RecA domains and an N-terminal accessory domain (this entry) containing a flexible loop, a long alpha-helix and an antiparallel, six-stranded beta-sheet. This N-terminal domain plays a role in the binding of the host factors TOM1 and ARL8 required for viral replication. It is also found in proteins from related virus.
Pfam PF06417: ER membrane protein complex subunit 4 (family)
This entry includes ER membrane protein complex subunit 4 (EMC4 also known as TMEM85 in mammals) from animals and its orthologue Emc4 from budding yeasts. They inhibit hydrogen peroxide mediated cell death in yeast. Emc4 is part of the ER membrane complex (EMC) that enables the energy-independent insertion into endoplasmic reticulum membranes of newly synthesized membrane proteins.
Pfam PF09050: Stannin unstructured linker (disordered)
Members of this family are unstructured, acting as connectors of the stannin helical domains. They contain a conserved CXC metal-binding motif and a putative 14-3-3-zeta binding domain. Upon coordinating dimethytin, considerable structural or dynamic changes in the flexible loop region of SNN may take place, recruiting other binding partners such as 14-3-3-zeta, and thereby initiating the apoptotic cascade.
Pfam PF17670: Family of unknown function (DUF5530) (family)
This is a family of unknown function found in Chordata.
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 PF15587: Immunity protein 9 (family)
A predicted immunity protein with an alpha+beta fold and a conserved lysine residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-URI2 family. The protein is also found in heterogeneous poly-immunity loci.
Pfam PF08100: Plant O-methyltransferase dimerisation domain (domain)
This domain is found at the N-terminus of plant O-methyltransferases involved in phenylpropanoid metabolism, including caffeic acid O-methyltransferase (COMT), isoflavone O-methyltransferase (IOMT), and chalcone O-methyltransferase (ChOMT).  It mediates dimerisation of these enzymes, which is critical for their activity.  The dimerisation domain forms the central core of the homodimer, with the SAM-binding domains located peripherally. Dimerisation buries ~30% of the total surface area of the dimer. The domain also contributes to forming the back wall of the substrate binding cavity of the partner monomer.  Structurally, the dimerisation domain consists primarily of alpha-helices. Crystal structures reveal the domain is relatively rigid compared to the more mobile SAM-binding domain, which undergoes conformational changes upon substrate binding.
Pfam PF03424: Carbohydrate binding domain (family 17/28) (domain)
This entry represents two tandem carbohydrate binding domains from CBM17 and CBM28 families. CBM17 binds to amorphous cellulose and soluble beta-1,4-glucans. CBM28 does not compete with CBM17 modules when binding to non-crystalline cellulose and it is closely related to CBM17, according to sequence and structural  conservation which suggests that they have evolved through gene duplication and subsequent divergence.
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF17742: Fibronectin type III domain-containing protein 10 (domain)
This is a family of unknown function found in chordates. Family members carry one predicted transmembrane region. These proteins are known as Fibronectin type III domain-containing protein 10. This region represents the FN3 like domain.
Pfam PF19967: vWA-MoxR associated protein middle region (VMAP-M) 5 (family)
Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities.
Pfam PF09412: Endoribonuclease XendoU (family)
This is a family of endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini.
Wikipedia: In molecular biology, Endoribonuclease XendoU refers to a protein domain. This particular entry represents endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis. This protein domain belongs to a family of evolutionarily related proteins. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini.
Pfam PF21140: Translation initiation factor eIF4G-like, eIF4E-binding domain (domain)
This domain is found in proteins from animals, including Translation initiation factor eIF4G (eIF4G1) from Drosophila melanogaster. This domain shows a canonical helix, a linker and an elbow loop. It shows a conserved sequence YXR/KXXLXXXR/K/Q that plays a role in the interaction with eIF4E.
Pfam PF23005: Domain of unknown function (DUF7032) (domain)
This domain is found N-terminal in a group of uncharacterised proteins mainly from plants. This domain is predicted to adopt a globular structure that folds into a four helical bundle and has a significant sequence and structural similarity to MLKL executioner domain ([pfam:PF22215]).
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 PF20623: Sgo0707 N2 domain (domain)
This domain represents the N2 domain found in the Sgo0707 adhesin protein. This domain is closely related to [pfam:PF16569].
Pfam PF07272: Orthoreovirus P17 protein (family)
This family consists of several Orthoreovirus P17 proteins. P17 is specified be ORF2 of the S1 gene and represents a nonstructural protein which associate with cell membranes.
Pfam PF08416: Phosphotyrosine-binding domain (domain)
The phosphotyrosine-binding domain (PTB, also phosphotyrosine-interaction or PI domain) in the protein tensin tends to be found at the C-terminus.  Tensin is a multi-domain protein that binds to actin filaments and functions as a focal-adhesion molecule (focal adhesions are regions of plasma membrane through which cells attach to the extracellular matrix).  Human tensin has actin-binding sites, an SH2 ([pfam:PF00017]) domain and a region similar to the tumour suppressor PTEN.  The PTB domain interacts with the cytoplasmic tails of beta integrin by binding to an NPXY motif.
Wikipedia: In molecular biology, phosphotyrosine-binding domains  are protein domains which bind to phosphotyrosine.
Pfam PF03376: Adenovirus E3B protein (family)
Adenoviruses are medium-sized, non-enveloped viruses containing double-stranded DNA. They can cause a variety of diseases including pneumonia, cystitis, conjunctivitis and diarrhoea, all of which can be fatal to patients who are immunocompromised . These viruses have many mechanisms to evade the host immune response, including several proteins which are expressed as part of the early transcription unit 3 (E3) . One of the regions of E3, known as the E3B region, encodes three proteins known as 10.4K, 14.5K and 14.7K. Two of these proteins, 10.4K and 14.5K, form the RID complex (receptor internalisation and degradation) which protects the infected cell from host-induced lysis by clearing the the TNF and Fas receptors from the cell surface . Other receptors, such as the epidermal growth factor receptor, are also known to be cleared by RID .
Pfam PF20028: vWA-MoxR associated protein C-terminal domain (domain)
C-terminal region of the VMAP protein of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. Mixed alpha+beta domain with no apparent structural similarity to known protein folds. Contains several, nearly universally polar residues, suggesting a conserved interaction interface. Enzymatic function for VMAP-C though possible appears unlikely. Sensing of invasive elements by VMAP-Ms are predicted to trigger a sequence of conformational changes, which is communicated to the switch-component (MoxR) of the system via the more constant VMAP-C.
Pfam PF11074: Domain of unknown function(DUF2779) (domain)
This domain is conserved 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 PF03854: P-11 zinc finger (family)
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
This entry represents the RING zinc finger domain of 'RING finger protein Z', a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E . It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell . This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication .

The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions . There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known . The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is:

C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C

Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second.