SII-SWORD/CoKE huggingface dataset:
Pfam PF19665: Family of unknown function (DUF6168) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 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 PF02250: Viral chemokine binding protein (domain)
This family of orthopoxvirus secreted proteins (also known as T1 and  A41) interact with members of both the CC and CXC superfamilies of  chemokines. It has been suggested that these secreted proteins  modulate leukocyte influx into virus-infected tissues.
Pfam PF13741: Mitochondrial ribosomal protein S25 (family)
This is the family of fungal 37S mitochondrial ribosomal S25 proteins.
Pfam PF21361: Sina, zinc finger (domain)
Sina is a RING-type E3 ubiquitin ligase first identified in Drosophila, a protein essential for the determination of the R7 pathway in photoreceptor cell development. Murine and human homologues of Sina have also been identified, namely Siah1 and Siah2, and also in Arabidopsis, SINAT3. These proteins have a RING-type zinc finger at the N-terminal followed by two zinc fingers and a C-terminal TRAF-like domain ([pfam:PF03145]). This entry represents the central C2H2 zinc finger domains.
Pfam PF16550: UCH-binding domain (domain)
RPN13_C is a family of all-helical domains that forms the binding-surface for the proteasome-ubiquitn-receptor protein Rpn13 to UCH37, one of the three de-ubiquitinating enzymes of the proteasome.
Pfam PF11548: Protein-tyrosine phosphatase receptor IA-2 (family)
IA-2 is a protein-tyrosine phosphatase receptor that upon exocytosis, the cytoplasmic domain is cleaved and moves to the nucleus where it enhances transcription of the insulin gene. The mature exodomain of IA-2 participates in adhesion to the extracellular matrix and is self-proteolyzed in vitro by reactive oxygen species which may be a new shedding mechanism.
Pfam PF09348: Domain of unknown function (DUF1990) (domain)
This family of proteins are functionally uncharacterised.
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 PF18678: Allene oxide cyclase barrel like domain (domain)
This is an allene oxide cyclase barrel like domain found in spirotetronate cyclases such as AbyU, a Diels-Alderase enzyme. It is comprised of two eight-stranded antiparallel beta-barrels.
Pfam PF22039: Imidazolonepropionase-like composite domain, bacteria (domain)
This entry represents the composite domain usually found in metal-dependent hydrolases which is interrupted by the catalytic alpha/beta barrel domain ([pfam:PF01979]). This domain has a pseudo-barrel fold. This model covers the N-terminal segment of the composite domain of bacterial proteins, such as imidazolonepropionases.
Pfam PF20576: HEWD domain (domain)
This small domain is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are approximately 60 amino acids in length. There is a conserved HEWD sequence after which the domain is named.
Pfam PF21206: Roquin 1/2-like, ROQ domain (domain)
This domain is found in Roquin-1/2 from humans and in other eukaryotic RING-E3 ubiquitin ligases and transferases. These paralogous proteins Roquin-1/2 recruit the deadenylation and decapping machineries to initiate mRNA degradation. They play a central role in repressing autoimmunity. The ROQ domain, highly conserved, is required for RNA binding and shows a mostly helical structure with a small three-stranded beta-sheet. It bears a winged helix-turn-helix motif, which is involved in the binding of constitutive decay elements-containing stem-loop mRNAs.
Pfam PF02758: PAAD/DAPIN/Pyrin domain (domain)
This domain is predicted to contain 6 alpha helices and to have the same fold as the [pfam:PF00531] domain.  This similarity may mean that this is a protein-protein interaction domain.
Wikipedia: A pyrin domain is a protein domain and a subclass of protein motif known as the death fold, the 4th and most recently discovered member of the death domain superfamily (DDF). It was originally discovered in the pyrin protein, or marenostrin, encoded by MEFV. The mutation of the MEFV gene is the cause of the disease known as Familial Mediterranean Fever. The domain is encoded in 23 human proteins and at least 31 mouse genes.
Pfam PF14524: Wzt C-terminal domain (domain)
This domain is found at the C-terminus of the Wzt protein. The crystal structure of C-Wzt(O9a) reveals a beta sandwich with an immunoglobulin-like topology that contains the O-antigenic polysaccharide binding pocket. This domain is often associated with  the ABC-transporter domain.
Pfam PF12523: Protein of unknown function (DUF3725) (family)
This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with [pfam:PF01577]. There is a conserved FLE sequence 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 PF24397: VNG_1110C-like (family)
This entry represents a family of archaeal uncharacterised proteins, including VNG_1110C protein from Halobacterium salinarum. These proteins are predicted to adopt a globular structure consisting of three-stranded antiparallel beta-sheet and two alpha- helices packed on one side of the sheet. They contain two semi-conserved RDSTQ and RIIGSP sequence motifs.
Pfam PF10967: Protein of unknown function (DUF2769) (family)
This family of 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 PF12490: BCAS3 microtubule associated cell migration factor, C-terminal (domain)
BCAS3 microtubule associated cell migration factor (BCSA3, also known as Rudhira in mice) has been shown to be involved in angiogenesis and metastasis, and to be implicated in the development of breast cancer. BCAS3 plays also a role in regulation of autophagy; it forms a complex with PHAF1 (C16orf70) which associates with the preautophagosomal structure during both non-selective and selective autophagy. This entry represents the C-terminal domain which seems to be important for PHAF1 interactions. This domain is also found in ATG18-like proteins from plants.
Pfam PF13946: Domain of unknown function (DUF4214) (domain)
This domain is found on a variety of different proteins including transferases, and allergen V5/Tpx-1 related 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 PF03266: NTPase (domain)
This domain is found across all species from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue.
Pfam PF07736: Chorismate mutase type I (domain)
Chorismate mutase (CM) [ec:5.4.99.5] catalyses the the conversion of  chorismate to prephenate in the shikimate pathway of tyrosine  and phenylalanine biosynthesis in bacteria, fungi and plants.  The three types of CM are AroH class, AroQ class, prokaryotic  type and AroQ class, eukaryotic type. Structurally CMs can be  divided into two main groups: type I (AroH) class and type II  (AroQ). Type I (AroH) CMs include CMs characterised by a  trimeric pseudo alpha/beta barrel structure. The two types  of the AroQ structural class (the Escherichia coli CM dimer and  the yeast CM monomer) can be structurally superimposed, and the topology of the four-helix bundle forming the active site is  conserved. CMs can be monofunctional or bifunctional  (generally fused to another shikimate pathway member). Despite  the structural differences, all CMs perform the same basic  reaction. This entry represents chorismate mutases of the  AroH class predominantly from Terrabacteria.
Wikipedia: In enzymology, chorismate mutase is an enzyme that catalyzes the chemical reaction for the conversion of chorismate to prephenate in the pathway to the production of phenylalanine and tyrosine, also known as the shikimate pathway.
Hence, this enzyme has one substrate, chorismate, and one product, prephenate. Chorismate mutase is found at a branch point in the pathway. The enzyme channels the substrate, chorismate to the biosynthesis of tyrosine and phenylalanine and away from tryptophan. Its role in maintaining the balance of these aromatic amino acids in the cell is vital. This is the single known example of a naturally occurring enzyme catalyzing a pericyclic reaction. Chorismate mutase is only found in fungi, bacteria, and higher plants. Some varieties of this protein may use the morpheein model of allosteric regulation.
Pfam PF00995: Sec1 family (family)
Sec1-like molecules have been implicated in a variety of eukaryotic vesicle transport processes including neurotransmitter release by exocytosis . They regulate vesicle transport by binding to a t-SNARE from the syntaxin family. This process is thought to prevent SNARE complex formation, a protein complex required for membrane fusion. Whereas Sec1 molecules are essential for neurotransmitter release and other secretory events, their interaction with syntaxin molecules seems to represent a negative regulatory step in secretion .
Pfam PF18780: Homing endonuclease associated repeat (repeat)
This entry represents a 60 residue repeat of unknown function found associated with homing endonuclease domains.
Pfam PF03614: Repressor of phase-1 flagellin (family)
Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.
Pfam PF16147: Domain of unknown function (DUF4855) (family)
This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various Bacteroides species. Several proteins are annotated as glycerophosphodiester phosphodiesterases,  but the origin of this annotation is not clear.
Pfam PF14166: YueH-like protein (family)
The YueH-like protein family includes the B. subtilis YueH protein [swissprot:O32093], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.
Pfam PF00059: Lectin C-type domain (domain)
This family includes both long and short form C-type
Wikipedia: A C-type lectin (CLEC) is a type of carbohydrate-binding protein known as a lectin. The C-type designation is from their requirement for calcium for binding. Proteins that contain C-type lectin domains have a diverse range of functions including cell-cell adhesion, immune response to pathogens and apoptosis.
Pfam PF21922: Penicillin binding protein A dimerisation domain (domain)
This domain is found in peptidoglycan D,D-transpeptidase also known as penicillin-binding protein A (PBPA). This domain consists of a four-stranded mixed beta-sheet with three short helices packed on one side. Compared to the N-terminal domains of other class B High Molecular Mass (HMM) PBPs, the NTD of PBPA is relatively small because it contains only the so-called inter-domain linker region.
Pfam PF23815: Family of unknown function (DUF7186) (family)
This entry represents a small transmembrane protein found in Lactococcus 936-type phages. The function of this protein is unknown.  It contains a single transmembrane helix.
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 PF17304: Mitochondrial outer membrane protein OM14, C-terminal (domain)
This entry includes Mitochondrial outer membrane protein OM14 from yeast and similar fungal sequences. OM14 is a mitochondrial membrane receptor for cytosolic ribosomes. It interacts with the nascent chain-associated complex (NAC) bound to ribosomes, contributing to co-translational mitochondrial import. This entry represents two transmembrane found at the C-terminal of OM14.
Pfam PF04807: Geminivirus AC4/5 conserved region (family)
This entry represents a conserved domain found in Gemini virus AC4 and AC5 proteins .
Pfam PF12455: Dynein associated protein (family)
This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with [pfam:PF01302]. There is a single completely conserved residue E that may be functionally important. Dynactin has been associated with Dynein, a kinesin protein which is involved in organelle transport, mitotic spindle assembly and chromosome segregation. Dynactin anchors Dynein to specific subcellular structures.
Wikipedia: Dynactin is a 23 subunit protein complex that acts as a co-factor for the microtubule motor cytoplasmic dynein-1. It is built around a short filament of actin related protein-1 (Arp1).
Pfam PF03206: Nitrogen fixation protein NifW (family)
Nitrogenase is a complex metalloenzyme composed of two proteins designated the Fe-protein and the MoFe-protein. Apart from these two proteins, a number of accessory proteins are essential for the maturation and assembly of nitrogenase. Even though experimental evidence suggests that these accessory proteins are required for nitrogenase activity, the exact roles played by many of these proteins in the functions of nitrogenase are unclear.      Using yeast two-hybrid screening it has been shown that NifW can interact with itself as well as NifZ.
Pfam PF16789: YscO-like protein (coiled_coil)
This family of proteins is similar to the type III secretion protein YscO. The family includes Chlamydia trachomatis CT670 which is found in a type III secretion gene cluster. CT670 interacts with CT671, a putative YscP homologue and CT670 and CT671 may form a chaperone-effector pair.
Pfam PF12583: Tripeptidyl peptidase II, C-terminal (repeat)
Tripeptidyl peptidase II (TPPII) is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. It consists of three main parts: the N-terminal subtilisin-like domain ([pfam:PF00082]), a central domain and a C-terminal domain. The central domain consists of Ig-like subdomain ([pfam:PF12580]) and a GBD-like one. This is the C-terminal domain with adopts an ARM repeat fold.
Pfam PF19121: Family of unknown function (DUF5805) (family)
This is a family of proteins of unknown function predominantly found in Halobacteria.
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 PF14618: Domain of unknown function (DUF4452) (family)
This fungal family has no known function. However, it is rich in paired, as CXXC, cysteines and histidines, but these do not fall in the conformation that might suggest zinc-binding.
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 PF07162: Ciliary basal body-associated, B9 protein (domain)
The B9-C2 domain is found in proteins associated with the ciliary basal body. B9 domains were identified as a specific family of C2 domains.  There are three sub-families represented by this family, notably, Mks1-Xbx7, Stumpy-Tza1 and Tza2 groups of proteins. Mutations in human Mks1 result in the developmental disorder Mechler-Gruber syndrome; mutations in mouse Stumpy lead to perinatal hydrocephalus and severe polycystic kidney disease. All the three distinct types of B9-C2 proteins cooperatively localise to the basal body or centrosome of cilia.
Pfam PF11622: Protein of unknown function (DUF3251) (domain)
This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. This domain is found in a group of bacterial lipoproteins such as YajI from E.coli and SadB from Salmonella typhimurium. SadB is required for proper surface expression of the autotransporter adhesin SadA.
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 PF13460: NAD(P)H-binding (domain)
This entry represents NAD- and NADP-binding domains with a core Rossmann-type fold, which consists of 3-layers Î±/Î²/Î±, where the six Î²-strands are parallel in the order 321456. Many different enzymes contain an NAD/NADP-binding domain, including:


 * C-terminal domain of alcohol dehydrogenases 
 * Tyrosine-dependent oxidoreductases (also known as short-chain dehydrogenases) 
 * N-terminal domain of glyceraldehyde-3-phosphate dehydrogenase 
 * NAD-binding domain of formate/glycerate dehydrogenases 
 * N-terminal domain of sirohaem synthase 
 * N-terminal domain of lactate dehydrogenase 
 * N-terminal domain of 6-phosphogluconate dehydrogenase (the Î²-sheet is extended to 8 strands) 
 * C-terminal domain of amino acid dehydrogenases (an extra N-terminal helix displaces the C-terminal helix 
 * NAD-binding domain of certain potassium channels 
 * C-terminal domain of the transcriptional repressor Rex 
 * Ornithine cyclodeaminase 
 * CoA-binding N-terminal domain of the alpha chain of succinyl-CoA synthetase
Pfam PF20505: Family of unknown function (DUF6731) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 297 and 311 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 PF15602: Immunity protein 71 (family)
A predicted immunity protein with a mostly alpha-helical fold and conserved arginine and phenylalanine residues. 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 Ntox48 family. This domain is often fused to the Imm72 immunity domain.
Pfam PF24499: TMEM131L fourth Ig-like domain (domain)
Transmembrane protein 131-like (TMEM131L) was identified as a negative regulator of thymocyte proliferation that acts through mixed Wnt-dependent and independent mechanisms. It has two isoforms, L and S, which have different subcellular localisation. L isoform, the membrane-associated form, inhibits canonical Wnt/beta-catenin signalling through the induction of lysosome-dependent degradation of the active phosphorylated form of the LRP6 coreceptor. This protein was firstly described as containing three conserved homology domains (CHD1, 2 and 3), a transmembrane region and a C-terminal serine-rich region. Using structure prediction models from AlphaFold, it has been possible to identify the CHDs as Ig-like domains. This entry represents the fourth Ig-like domain of TMEM131L while in TMEM131 represents the seventh one. TMEM131 is a collagen binding transmembrane protein involved in collagen secretion by recruiting the ER-to-Golgi transport complex TRAPPIII.
Pfam PF04678: Mitochondrial calcium uniporter (family)
MCU functions with MICU1, an essential gatekeeper component of calcium-channel transport, to facilitate Ca2+ uptake into the mitochondrion.
Wikipedia: The mitochondrial calcium uniporter (MCU) is a transmembrane protein that allows the passage of calcium ions from a cell's cytosol into mitochondria. Its activity is regulated by MICU1 and MICU2, which together with the MCU make up the mitochondrial calcium uniporter complex.
Pfam PF15337: Vascular protein family Vasculin-like 1 (family)
GC-rich promoter-binding protein 1-like 1 or Vasculin-like protein family 1, is likely to be a transcription factor. The domain family is found in eukaryotes, and is approximately 90 amino acids in length.
Pfam PF17004: Putative TPR-like repeat (repeat)
This is a family of microsporidial sequences that are likely to fold into a TPR-like structure. Many sequences are annotated as being signal recognition proteins.
Pfam PF01506: Hepatitis C virus non-structural 5a protein membrane anchor (family)
The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR, [swissprot:P19525]. The N-terminal region of the NS5a protein has been used in the construction of the alignment for this family.  The C-terminal region has not been included because it is too heterogeneous.