SII-SWORD/CoKE huggingface dataset:
Pfam PF18292: Zinc transporter ZIP4 domain (domain)
This domain is found in ZRT1-IRT1-like protein 4 (ZIP4) present in Homo sapiens and Mus musculus. ZIP4 is a zinc transporter that allows uptake of the essential nutrient zinc. The domain is found before the N-terminal of ZIP Zinc transporter domain (Pfam: PF02535).
Pfam PF08118: Yeast mitochondrial distribution and morphology (MDM) proteins (family)
Proteins in this family are yeast mitochondrial inner membrane proteins MDM31 and MDM32.                    These proteins are required for the maintenance of mitochondrial morphology, and the stability of mitochondrial DNA.
Pfam PF07342: Protein of unknown function (DUF1474) (family)
This family consists of several bacterial proteins of around 100 residues in length. Members of this family seem to be found exclusively in Staphylococcus aureus. 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 PF23673: Domain of unknown function (DUF7154) (domain)
This domain is found in the Caenorhabditis elegans uncharacterised protein Clec-72 and related eukaryotic proteins. It is predicted to adopt a globular structure with similarity to Galactose-binding domains.
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 PF00340: Interleukin-1 / 18 (domain)
This family includes interleukin-1 and interleukin-18.
Pfam PF14515: Haem-oxygenase-associated N-terminal helices (domain)
This domain represents a pair of alpha helices, which are found at the N-terminus of some Haem-oxygenase globular domain.
Pfam PF21441: DUF3860-like (family)
This protein family includes [swissprot:Q6N4D8] from Rhodopseudomonas palustris, an uncharacterized protein that shows an alpha-beta structure and has some similarity with the structure predicted for members of [pfam:PF12976].
Pfam PF10250: GDP-fucose protein O-fucosyltransferase (family)
This is a family of conserved proteins representing the enzyme responsible for adding O-fucose to EGF (epidermal growth factor-like) repeats. Six highly conserved cysteines are present in O-FucT-1 as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and C. elegans. Both features are characteristic of several glycosyltransferase families. The enzyme is a membrane-bound protein released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese.
Pfam PF05801: Lagovirus minor capsid protein VP2 (family)
This entry includes minor capsid protein VP2 from Rabbit hemorrhagic disease virus and related lagoviruses. VP2 is minor structural protein that forms a portal-like structure at a unique three-fold axis of symmetry, following binding to the host receptor. The channel formed by VP2 may allow the delivery of the viral genome through the host endosomal membrane.
Pfam PF24572: RNA-dependent RNA polymerase 6, RNA-binding domain (domain)
This entry represents the RNA-binding domain (RBD) found at the N-terminal of RNA-dependent RNA polymerase 6 (RPR6) from Arabidopsis and related sequences from plants. RDR6 is involved in post-transcriptional gene silencing (PTGS) and natural virus resistance. It possess ssRNA and ssDNA-dependent polymerase activity. RDR6 is required for the production of trans-acting siRNA and other siRNA.
Pfam PF17968: Toll-like receptor 3 trans-membrane domain (domain)
Toll-like receptor (TLR) 3 is an endosomal TLR that mediates immune responses against viral infections upon activation by its ligand double-stranded RNA, a replication intermediate of most viruses. TLR3 is expressed widely in the body and activates both the innate and adaptive immune systems. This entry represents the Toll-like receptor 3 trans-membrane domain which has been shown to form dimers and trimers with different surfaces for helix-helix interaction.
Pfam PF24609: SCN5A-like, C-terminal IQ motif (domain)
Human Sodium channel protein type 5 subunit alpha (SCN5A) mediates the voltage-dependent sodium ion permeability of excitable membranes. Its C-terminal domain is organised into two regions: an IQ motif and an EF-hand domain. This entry represents the IQ motif, a key element in the calcium sensing apparatus.
Pfam PF19620: Family of unknown function (DUF6125) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 170 and 247 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 PF05011: Lariat debranching enzyme, C-terminal domain (domain)
This presumed domain is found at the C-terminus of lariat debranching enzyme. This domain is always found in association with [pfam:PF00149].
Pfam PF14638: Folliculin-interacting protein C-terminus (family)
This is the C-terminus of folliculin-interacting proteins. This region is responsible for binding to folliculin.
Pfam PF23794: Mycobacterium phage Gp84-like protein (domain)
This entry represents a family of phage proteins. One example is the Gp84 protein from Mycobacteriophage L5 [swissprot:Q05301]. An AlphaFold model of a family member:K5BEF7 has a compact fold of one alpha helix followed by a three stranded beta sheet. The function of these proteins is unknown.
Pfam PF08090: Heat stable E.coli enterotoxin 1 (family)
Heat-stable toxin 1 of entero-aggregative E.coli (EAST1) is a small toxin. It is not, however, solely associated with entero-aggregative E.coli but also with many other diarrhoaeic E. coli families. Some studies have established the role of EAST1 in some human outbreaks of diarrhoea. Isolates from farm animals have been shown to carry the astA gene coding for EAST1. However, the relation between the presence of EAST1 and disease is not conclusive.
Wikipedia: Heat-stable enterotoxins (STs) are secretory peptides produced by some bacterial strains, such as enterotoxigenic Escherichia coli which are in general toxic to animals.
Pfam PF01409: tRNA synthetases class II core domain (F) (domain)
Other tRNA synthetase sub-families are too dissimilar to be included.  This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain.
Pfam PF19162: Family of unknown function (DUF5844) (family)
This is a family of uncharacterised proteins of unknown function found in Iridoviridae.
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 PF24663: Domain of unknown function (DUF7651) (domain)
This domain is found in the Polycomb group protein EMBRYONIC FLOWER 2 (EMF2) from Arabidopsis thaliana and related proteins. EMF2 is involved in flowering processes by repressing unknown target genes and preventing reproductive development. This domain is predicted to adopt a globular structure that resembles barrel-sandwich hybrid. The beta-sandwich has a topology most similar to C2 domains found in diverse proteins such as CEP120, Dysferlin and Myoferlin.
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 PF11409: Smad anchor for receptor activation (SARA) (family)
Smad proteins mediate transforming growth factor-beta (TGF-beta) signaling from the transmembrane serine-threonine receptor kinases to the nucleus. SARA recruits Smad2 to the TGF-beta receptors for phosphorylation.
Pfam PF12686: Protein of unknown function (DUF3800) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses.  Proteins in this family are typically between 215 and 302 amino acids in length. There is a DE motif at the N-terminus and a QXXD motif at the C-terminus 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 PF21025: Formamidopyrimidine-DNA glycosylase C-terminal domain (domain)
This entry represents a small C-terminal zinc finger domain found in a small subset of Formamidopyrimidine-DNA glycosylase enzymes.
Pfam PF00544: Pectate lyase (repeat)
This enzyme forms a right handed beta helix structure. Pectate lyase is an enzyme involved in the maceration and  soft rotting of plant tissue.
Wikipedia: Pectate lyase is an enzyme involved in the maceration and soft rotting of plant tissue. Pectate lyase is responsible for the eliminative cleavage of pectate, yielding oligosaccharides with 4-deoxy-α-D-mann-4-enuronosyl groups at their non-reducing ends. The protein is maximally expressed late in pollen development. It has been suggested that the pollen expression of pectate lyase genes might relate to a requirement for pectin degradation during pollen tube growth.
Pfam PF16619: Unstructured region C-term to UIM in Ataxin3 (disordered)
SUIM_assoc is a natively unstructured region on Ataxin 3 proteins that lies immediately C-terminal to the second UIM domain linking it to a third when present.  The function is not known. It is rich in glutamine residues.
Pfam PF00026: Eukaryotic aspartyl protease (domain)
Aspartyl (acid) proteases include pepsins, cathepsins, and renins.  Two-domain structure, probably arising from ancestral duplication.  This family does not include the retroviral nor retrotransposon proteases ([pfam:PF00077]), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.
Wikipedia: Aspartic proteases are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. In general, they have two highly conserved aspartates in the active site and are optimally active at acidic pH. Nearly all known aspartyl proteases are inhibited by pepstatin.
Pfam PF11631: Protein of unknown function (DUF3255) (domain)
Members in this family of proteins are annotated as YxeF however no function is currently known. The family appears to be restricted to Bacillus.
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 PF15356: Psoriasis susceptibility locus 2 (disordered)
SPR1 is psoriasis susceptibility locus 2 protein family.
Pfam PF02079: Nuclear transition protein 1 (family)
Nuclear transition protein 1 (TP1) is one of the spermatid-specific proteins . TP1 is a basic protein well conserved in mammalian species. In mammals, the second stage of spermatogenesis is characterised by the conversion of nucleosomal chromatin to the compact, non-nucleosomal and transcriptionally inactive form found in the sperm nucleus. This condensation is associated with a double-protein transition. The first transition corresponds to the replacement of histones by several spermatid-specific proteins (also called transition proteins) which are themselves replaced by protamines during the second transition.
Pfam PF22435: MRM3-like substrate binding domain (domain)
MRM3 catalyses the formation of 2'-O-methylguanosine at position 1370 Gm1370) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a conserved modification in the peptidyl transferase domain of the mtLSU rRNA. This entry represents the substrate binding domain of MRM3 from animals and related sequences from bacteria.
Pfam PF08628: Sorting nexin C terminal (family)
This region is found a the C terminal of proteins belonging to the sorting nexin family.  It is found on proteins which also contain [pfam:PF00787].
Wikipedia: Sorting nexins are a large group of proteins that are localized in the cytoplasm and have the potential for membrane association either through their lipid-binding PX domain or through protein–protein interactions with membrane-associated protein complexes Some members of this family have been shown to facilitate protein sorting.
Pfam PF11070: Protein of unknown function (DUF2871) (family)
This is a family of short uncharacterised proteins predominantly found in bacteria. This model matches four of the twelve transmembrane helices of cytochrome c and quinol oxidase subunit I ([pfam:PF00115]) and contains the HxH motif conserved in both. A DALI search suggests that this family may be related to Cox1, however, there is no evidence for the involvement of this family in any Cox1-like assembly.
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 PF06258: Mitochondrial fission ELM1 (family)
In plants, this family is involved in mitochondrial fission. It binds to dynamin-related proteins and plays a role in their relocation from the cytosol to mitochondrial fission sites. Its function in bacteria is unknown.
Pfam PF03902: Gal4-like dimerisation domain (family)
The DNA binding domain (residues 1 to 147) of the yeast transcriptional activator GAL4 exists in solution in dimeric form, with the region responsible for dimerisation somewhere between residues 74 and 147. Experimental studies confirmed that the 'hydrophobic region' of the protein (residues 54-97, which contains a larger proportion of Î±-helix), is essential for dimerisation .
Pfam PF18635: Epithelial cell adhesion molecule, N-terminal domain (domain)
EpCAM (epithelial cell adhesion molecule), a stem and carcinoma cell marker, is a cell surface protein involved in homotypic cell-cell adhesion via intercellular oligomerization and proliferative signalling via proteolytic cleavage. Structure analysis indicate that it is composed of three domains: N-domain, Thyroglobulin type-1A (TY) domain and the C-terminal domain. This entry represents the small and compact disulphide-rich N-terminal domain of 39 amino-acid residues. Trop-2 (also known as tumor-associated calcium signal transducer 2, TACSTD2) is also included in this entry, as they are evolutionarily related and both are implicated in signaling triggered by proteolytic cleavage within the ectodomain. They share an overall similar structure but differ in their dimers formation.
Pfam PF06169: Protein of unknown function (DUF982) (family)
This family consists of several hypothetical proteins from Rhizobium meliloti, Rhizobium loti and Agrobacterium tumefaciens. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids.
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 PF09472: Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF) (family)
Many archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This domain is mostly found in MtrF, where it covers the entire length of the protein. This polypeptide is one of eight subunits of the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase complex found in methanogenic archaea. This is a membrane-associated enzyme complex that uses methyl-transfer reactions to drive a sodium-ion pump. MtrF itself is involved in the transfer of the methyl group from N5-methyltetrahydromethanopterin to coenzyme M. Subsequently, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase. In some organisms this domain is found at the C terminal region of what appears to be a fusion of the MtrA and MtrF proteins. The function of these proteins is unknown, though it is likely that they are involved in C1 metabolism.
Pfam PF05499: DNA methyltransferase 1-associated protein 1 (DMAP1) (family)
DNA methylation can contribute to transcriptional silencing through several transcriptionally repressive complexes, which include methyl-CpG binding domain proteins (MBDs) and histone deacetylases (HDACs). The chief enzyme that maintains mammalian DNA methylation, DNMT1, can also establish a repressive transcription complex. The non-catalytic amino terminus of DNMT1 binds to HDAC2 and DMAP1 (for DNMT1 associated protein), and can mediate transcriptional repression. DMAP1 has intrinsic transcription repressive activity, and binds to the transcriptional co-repressor TSG101. DMAP1 is targeted to replication foci through interaction with the far N terminus of DNMT1 throughout S phase, whereas HDAC2 joins DNMT1 and DMAP1 only during late S phase, providing a platform for how histones may become deacetylated in heterochromatin following replication.
Pfam PF05670: NFACT protein RNA binding domain (domain)
This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from [swissprot:O34693] where the N-terminal region is involved in this activity. It is an RNA binding domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins. This NFACT-R family is found in two eukaryotic gene contexts: fused to the NFACT-N and NFACT-C domains in the NFACT protein involved in the ribosomal quality control pathway which contributes to CAT-tailing and as a standalone domain. Additionally this domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.
Pfam PF01790: Prolipoprotein diacylglyceryl transferase (family)
Phosphatidylglycerol--prolipoprotein diacylglyceryl transferase lgt  is an integral membrane enzyme that catalyses the first reaction of the three-step post-translational lipid modification . It transfers the n-acyl diglyceride group onto what will become the N-terminal cysteine of membrane lipoproteins. This enzyme is an integral membrane protein.
Pfam PF15599: Immunity protein 63 (family)
A predicted immunity protein with an alpha+beta fold and a conserved E+G and ExxY motifs. 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 Ntox40, Tox-CdiAC and Tox-ARC families. The protein is also found in poly-immunity loci in polymorphic toxin systems.
Pfam PF17094: Uncharacterised protein family (UPF0715) (family)
This is a family of Bacilli transmembrane proteins. The function is unknown.
Pfam PF23221: MROH2B-like, HEAT repeats (repeat)
This entry represents HEAT repeats from maestro heat-like repeat-containing proteins, including Maestro heat-like repeat -containing protein family member 2B from mouse (MROH2B, also known as SPIF), which may play a role in the process of sperm capacitation.
Pfam PF21383: DPAGT1 insertion domain (domain)
DPAGT1 catalyses the initial step of dolichol-linked oligosaccharide biosynthesis in N-linked protein glycosylation pathway. This is the insertion domain of eukaryotic DPAGT1, a feature absent in prokaryotic counterparts. It referred to as CL9 in; it adopts a mixed alpha/beta fold and it forms part of the substrate recognition site in human DPAGT1.
Pfam PF04873: Ethylene insensitive 3, DNA-binding domain (domain)
Ethylene insensitive 3 (EIN3) proteins are a family of plant DNA-binding proteins that regulate transcription in response to the gaseous plant hormone ethylene, and are essential for ethylene-mediated responses including the triple response, cell growth inhibition, and accelerated senescence. This entry represents the DNA-binding domain of EIN3 and EIN3-like proteins.
Pfam PF12640: UPF0489 domain (domain)
This family is probably an enzyme which is related to the Arginase family.
Pfam PF18458: Xeroderma pigmentosum group B helicase damage recognition domain (domain)
This domain is found in the N-terminal region of xeroderma pigmentosum group B (XPB) helicase present in Archaeoglobus fulgidus. XPB is essential for transcription, nucleotide excision repair, and TFIIH functional assembly. The domain is a damage recognition domain (DRD) which allows XPB to unwind damaged DNA as needed for nucleotide excision repair.
Pfam PF22271: Family of unknown function (DUF6955) (family)
This is a family of small uncharacterised proteins found in bacteria and archaea. They are predicted to adopt an alpha/beta globular structure consisting of a cradle-like beta-sheet and alpha-helices packed on the convex side of the sheet.
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 PF06301: Bacteriophage lambda Kil protein (family)
This family consists of several Bacteriophage lambda Kil protein like sequences from both phages and bacteria. Induction of a lambda prophage causes the death of the host cell even in the absence of phage replication and lytic functions due to expression of the lambda kil gene.