SII-SWORD/CoKE huggingface dataset:
Pfam PF14879: Domain of unknown function (DUF4489) (family)
This family of uncharacterised proteins is found mainly in Clostridium.
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 PF15198: Dexamethasone-induced (family)
Dexamethasone is a member of the glucocorticoid group of steroid hormones; it functions as an anti-inflammatory and immunosuppressant. A differentially- expressed transcript of unknown function has been identified in emphysematous lungs  - this has been named Dexamethasone-Induced transcript (DEXI). It is suggested that the up-regulation of DEXI in emphysema patient's tissues may be a direct result of their treatment with corticosteroids.

The human DEXI protein is a 95-residue acidic polypeptide, predicted to contain a central transmembrane domain and a C-terminal leucine zipper . It is unclear how dexamethasone influences proteins within this family. However, the leucine zipper contains a predicted casein kinase II phosphorylation site, suggesting that interaction may possibly be regulated by phosphorylation. It is hoped that further studies will eventually help to elucidate the function of this protein and its role in emphysema and inflammatory-airway disease.
Pfam PF24479: Plexin A/B, PSI domain (domain)
This entry represents a PSI domain found in Plexin A, B and related proteins. These are neuronal receptors for the axon guidance regulators Semaphorins. Semaphorin-plexin interactions play central roles in regulating processes such as neuronal axon guidance, angiogenesis and immune responses.
Pfam PF03050: Transposase IS66 family (family)
Transposase proteins are necessary for efficient DNA transposition. This family includes IS66 from Agrobacterium tumefaciens.
Pfam PF19495: Family of unknown function (DUF6030) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000762) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a  protein from the exopolysaccharide biosynthetic gene cluster from  Rhizobium leguminosarum bv. viciae and appears to be predominantly  found in proteobacteria.
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 PF16709: Ig domain of plant-specific actin-binding protein (domain)
This family is an Ig-like domain found on plant-specific actin-binding proteins or SCABs. SCAB proteins bind, bundle and stabilise actin filaments and regulate stomatal movement. The Ig-PH fusion domain is at the C-terminus. This domain is an Ig beta-sandwich fold consisting of two antiparallel beta-sheets built from strands beta1 and beta2 and strands beta3-beta6, respectively.
Pfam PF01082: Copper type II ascorbate-dependent monooxygenase, N-terminal domain (domain)
The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.
Wikipedia: In molecular biology, the copper type II ascorbate-dependent monooxygenases are a class of enzymes that require copper as a cofactor and which use ascorbate as an electron donor. This family contains two related enzymes, dopamine beta-monooxygenase EC 1.14.17.1 and peptidylglycine alpha-amidating monooxygenase EC 1.14.17.3. There are a few regions of sequence similarities between these two enzymes, two of these regions contain clusters of conserved histidine residues which are most probably involved in binding copper.
Pfam PF20070: Family of unknown function (DUF6466) (family)
This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Bifidobacteria. Proteins in this family are approximately 190 amino acids in length. They contain the conserved motifs QQQQ, SxxLT and KPW. Members in this family are probably cell surface proteins, some of them are likely elastin binding 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 PF01880: Desulfoferrodoxin (domain)
Desulfoferrodoxins contains two types of iron: an Fe-S4 site very similar to that found in desulforedoxin from Desulfovibrio gigas and an octahedral coordinated high-spin ferrous site most probably with nitrogen/oxygen-containing ligands. Due to this rather unusual combination of active centres, this novel protein is named desulfoferrodoxin.
Pfam PF03727: Hexokinase (domain)
Hexokinase ([ec:2.7.1.1]) contains two structurally similar domains represented by this family and [pfam:PF00349]. Some members of the family have two copies of each of these domains.
Wikipedia: A hexokinase is an enzyme that irreversibly phosphorylates hexoses, forming hexose phosphate. In most organisms, glucose is the most important substrate for hexokinases, and glucose-6-phosphate is the most important product. Hexokinase possesses the ability to transfer an inorganic phosphate group from ATP to a substrate.
Pfam PF05337: Macrophage colony stimulating factor-1 (CSF-1) (domain)
Colony stimulating factor 1 (CSF-1) is a homodimeric polypeptide growth factor whose primary function is to regulate the survival, proliferation, differentiation, and function of cells of the mononuclear phagocytic lineage. This lineage includes mononuclear phagocytic precursors, blood monocytes, tissue macrophages, osteoclasts, and microglia of the brain, all of which possess cell surface receptors for CSF-1. The protein has also been linked with male fertility and mutations in the Csf-1 gene have been found to cause osteopetrosis and failure of tooth eruption. Structurally these are short-chain 4-helical cytokines.
Pfam PF23101: First Zinc fingers C2H2 type, ZNF451 (domain)
This entry represents a Zinc Finger C2H2 type found in the N-terminal of ZNF451 protein. E3 SUMO-protein ligase ZNF451 is a key enzyme involved in the sumoylation process, exhibiting a preference for SUMO2 and SUMO3 over SUMO1. It facilitates the UBE2I/UBC9-mediated sumoylation of target proteins, particularly in response to DNA damage and proteasome inhibitors. ZNF451 is essential for MCM4 sumoylation,  and it negatively regulates transcriptional activation mediated by the SMAD4 complex in the context of TGF-beta signaling. Additionally, it inhibits EP300-mediated acetylation of histone H3 at 'Lys-9'.
Pfam PF17761: DUF1016 N-terminal domain (family)
This family may include an HTH domain.
Pfam PF01480: PWI domain (family)
The PWI domain, named after a highly conserved PWI tri-peptide located within its N-terminal region, is a ~80 amino acid module, which is found either at the N terminus or at the C terminus of eukaryotic proteins involved in pre-mRNA processing . It is generally found in association with other domains such as RRM and RS. The PWI domain is a RNA/DNA-binding domain that has an equal preference for single- and double-stranded nucleic acids and is likely to have multiple important functions in pre-mRNA processing . Proteins containing this domain include the SR-related nuclear matrix protein of 160kDa (SRm160) splicing and 3'-end cleavage-stimulatory factor, and the mammalian splicing factor PRP3. This domain is also present in Rmn1 from S.pombe, a component of a MTREC submodule, which promotes degradation of meiotic mRNAs and regulatory ncRNAs, and is the major nuclear exosome targeting complex for cryptic unstable transcripts (CUTs) and unspliced pre-mRNAs . Rmn1 homologues from human RBM26/27 may be involved in turnover of nuclear polyadenylated RNA and are important for PAXT-mediated nuclear RNA decay .

The PWI domain is a soluble, globular and independently folded domain which consists of a four-helix bundle, with structured N- and C-terminal elements .
Pfam PF05666: YcgJ protein (domain)
This entry represents a domain that contains an internal duplication.  It contains the E. coli YcgJ protein [swissprot:P76001]. This protein contains 6 cysteines that may form disulphide bridges. It contains an N-terminal signal peptide suggesting these proteins are secreted.
Pfam PF17552: Family of unknown function (DUF5464) (family)
This is a family of unknown function found in Bacteriophages.
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 PF24711: YxiG-like protein (domain)
This family includes proteins related to B. subtilis YxiG [swissprot:P42299]. This protein forms a single compact all beta domain that is predicted to homodimerise.
Pfam PF10810: Protein of unknown function (DUF2545) (family)
This family of proteins with unknown function is restricted to Enterobacteriaceae. The sequence is highly conserved.
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 PF03547: Membrane transport protein (family)
This family includes auxin efflux carrier proteins and other transporter proteins from all domains of life.
Pfam PF03011: PFEMP1 DBL domain (domain)
PfEMP1 (Plasmodium falciparum erythrocyte membrane protein) has been identified as the rosetting ligand of the malaria parasite P.  falciparum.   Rosetting is the adhesion of infected erythrocytes with uninfected erythrocytes in the vasculature of the infected organ, and is associated with severe malaria. PfEMP1 interacts with Complement Receptor One on uninfected erythrocytes to form rosettes. The extreme variation within these proteins and the grouping of var genes implies that var gene recombination preferentially occurs within var gene groups. These groups reflect a functional diversification that has evolved to cope with the varying conditions of transmission and host immune response met by the parasite. A recombination hotspot was uncovered between Duffy-binding-like (DBL) subdomains. Solution of the crystal structure of the N-terminal and first DBL region of PfEMP1 from the VarO variant of the PfEMP1 protein is found to be directly implicated in rosetting as the heparin-binding site.
Wikipedia: Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is a family of proteins present on the membrane surface of red blood cells that are infected by the malarial parasite Plasmodium falciparum. PfEMP1 is synthesized during the parasite's blood stage inside the RBC, during which the clinical symptoms of falciparum malaria are manifested. Acting as both an antigen and adhesion protein, it is thought to play a key role in the high level of virulence associated with P. falciparum. It was discovered in 1984 when it was reported that infected RBCs had unusually large-sized cell membrane proteins, and these proteins had antibody-binding (antigenic) properties. An elusive protein, its chemical structure and molecular properties were revealed only after a decade, in 1995. It is now established that there is not one but a large family of PfEMP1 proteins, genetically regulated (encoded) by a group of about 60 genes called var. Each P. falciparum is able to switch on and off specific var genes to produce a functionally different protein, thereby evading the host's immune system. RBCs carrying PfEMP1 on their surface stick to endothelial cells, which facilitates further binding with uninfected RBCs, ultimately helping the parasite to both spread to other RBCs as well as bringing about the fatal symptoms of P. falciparum malaria.
Pfam PF18397: IQBAL scaffold dimerization domain (domain)
This is the C-terminal scaffold dimerization domain (SDD) found in inhibitor of nuclear factor kappa-B kinase subunit beta IKBKB ([ec:2.7.11.10]). IKK2 also known as IKBKB is one of the core component of IKB kinases (IKK). IKB kinase (IKK) is an enzyme that quickly becomes active in response to diverse stresses on a cell. The SDD consists primarily of two long alpha-helices.
Wikipedia: IKK-β also known as inhibitor of nuclear factor kappa-B kinase subunit beta is a protein that in humans is encoded by the IKBKB gene.
Pfam PF00360: Phytochrome region (domain)
Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to [pfam:PF01590], which is generally located immediately N-terminal to this domain.  Compared with [pfam:PF01590], this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilise the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue.
Wikipedia: Phytochromes are a class of photoreceptor proteins found in plants, bacteria and fungi. They respond to light in the red and far-red regions of the visible spectrum and can be classed as either Type I, which are activated by far-red light, or Type II that are activated by red light. Recent advances have suggested that phytochromes also act as temperature sensors, as warmer temperatures enhance their de-activation. All of these factors contribute to the plant's ability to germinate.
Pfam PF02033: Ribosome-binding factor A (family)
Ribosome-binding factor A  (gene rbfA) is a bacterial protein that associates with free 30S ribosomal subunits. It does not associate with 30S subunits that are part of 70S ribosomes or polysomes. It is essential for efficient processing of 16S rRNA. Ribosome-binding factor A is a protein of from 13 to 15 Kd which is found in most bacteria. A putative chloroplastic form seems to exist in plants.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF18297: NFACT protein RNA binding domain (domain)
NFACT-R RNA binding family found found in bacteria fused to the ThiI domain as a variant of the canonical tRNA 4-thiouridylation pathway.
Pfam PF17857: AAA+ lid domain (domain)
This domain represents the AAA lid domain from dynein heavy chain D3.
Pfam PF13325: N-terminal region of micro-spherule protein (family)
This domain is found in plants and higher eukaryotes, and is the N-terminal region of micro-spherule proteins which repress the transactivation activities of Nrf1 (p45 nuclear factor-erythroid 2 (p45 NF-E2)-related factor 1). In conjunction with DIPA the full-length protein acts as a transcription repressor. The exact function of the region is not known.
Pfam PF12179: I-kappa-kinase-beta NEMO binding domain (domain)
This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF00069]. These proteins are involved in inflammatory reactions. They cause release of NF-kappa-B into the nucleus of inflammatory cells and upregulation of transcription of proinflammatory cytokines. They perform this function by phosphorylating I-kappa-B proteins which are targeted for degradation to release NF-kappa-B. This kinase (I-kappa-kinase-beta) is found in association with IKK-alpha and NEMO (NF-kappa-B essential modulator). This domain is the binding site of IKK-beta for NEMO.
Pfam PF17233: Family of unknown function (DUF5308) (family)
This family of uncharacterised fungal proteins are primarily found in ascomycota.
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 PF22992: BIRD-IDD transcription factor, fourth C2HC zinc finger (domain)
This C2HC zinc finger domain is found in the BIRD/INDETERMINATE DOMAIN (IDD) transcription factor family. Members of this BIRD/IDD family such as JACKDAW (JKD)/IDD10, BALDIBIS (BIB), MAGPIE (MGP)/IDD3 are required for asymmetric cell division of ground tissue and QC specification by direct protein-protein interaction with SHR and/or SCR to control ground tissue patterning during root growth. SHR-SCR functions as a transcription cofactor by binding to the zinc finger domains of these transcription factors. Members of the BIRD/IDD family contain 4 zinc finger domains, two classical C2H2 followed by two C2HC zinc finger domains. This entry represents the fourth C2HC zinc finger domain that is involved in interaction with SHR-SCR.
Pfam PF12031: SWI/SNF-like complex subunit BAF250/Osa (repeat)
This entry represents the mammalian BAF250a/b and its homologue osa from fruit flies. They are part of the  SWI/SNF-like ATP-dependent chromatin remodelling  complex that regulates gene expression through regulating  nucleosome remodelling. In humans there are two BAF250 isoforms, BAF250a/ARID1a and BAF250b/ARID1b. BAF250a/b may be E3 ubiquitin ligases that target histone H2B.
Pfam PF11813: Protein of unknown function (DUF3334) (family)
This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 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 PF04253: Transferrin receptor-like dimerisation domain (domain)
This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure.
Pfam PF17330: SWR1 chromatin-remodelling complex, sub-unit Swc7 (family)
The SWR1 complex is involved in chromatin-remodeling by promoting the the ATP-dependent exchange of histone H2A for the H2A variant HZT1 in Saccharomyces cerevisiae or H2AZ in mammals. The SWR1 chromatin-remodeling complex is composed of at least 14 subunits and has a molecular mass of about 1.2 to 1.5 MDa. In S. cerevisiae there are core conserved subunits (ATPase; Swr1,RuvB-like; Rvb1 and Rvb2, Actin; Act1, Actin-related: Arp4 and Arp6, YEATS protein;) and non-conserved subunits (Vps71 (Swc6), Vps72 (Swc2), Swc3, Swc4, Swc5, Swc7, Bdf1). Seven of the SWR1 subunits are involved in maintaining complex integrity and H2AZ histone replacement activity: Swr1, Swc2, Swc3, Arp6, Swc5, Yaf9 and Swc6. Arp4 is required for the association of Bdf1, Yaf9, and Swc4 and Arp4 is also required for SWR1 H2AZ histone replacement activity in vitro. Furthermore the N-terminal region of the ATPase Swr1 provides the platform upon which Bdf1, Swc7, Arp4, Act1, Yaf9 and Swc4 associate. It also contains an additional H2AZ-H2B specific binding site, distinct from the binding site of the Swc2 subunit. In eukaryotes the deposition of variant histones into nucleosomes by the chromatin-remodeling complexes such as the SWR1 and INO80 complexes have many crucial functions including the control of gene regulation and expression, checkpoint regulation, DNA replication and repair, telomere maintenance and chromosomal segregation and as such represent critical components of pathways that maintain genomic integrity. This entry represents the subunit Swc7; the smallest subunit of the SWR1 complex. Swc7 is not required for H2AZ binding. It associates with the N terminus of Swr1, and the association of Bdf1 requires Swc7, Yaf9, and Arp4.
Pfam PF12933: FTO catalytic domain (domain)
This domain is the catalytic AlkB-like domain from the FTO protein. This domain catalyses a demethylase activity with a preference for 3-methylthymidine.
Wikipedia: Fat mass and obesity-associated protein, also known as alpha-ketoglutarate-dependent dioxygenase FTO, is an enzyme that in humans is encoded by the FTO gene located on chromosome 16. As one homolog in the AlkB family proteins, it is the first messenger RNA (mRNA) demethylase that has been identified. Certain alleles of the FTO gene appear to be correlated with obesity in humans.