SII-SWORD/CoKE huggingface dataset:
Pfam PF06515: Borna disease virus P10 protein (family)
This family consists of several Borna disease virus P10 (or X) proteins. Borna disease virus (BDV) is unique among the non-segmented negative-strand RNA viruses of animals and man because it transcribes and replicates its genome in the nucleus of the infected cell. It has been suggested that the p10 protein plays a role in viral RNA synthesis or ribonucleoprotein transport.
Wikipedia: The Borna disease viruses 1 and 2 are members of the species Mammalian 1 orthobornavirus and cause Borna disease in mammals.
Pfam PF23607: Tyrosine-protein kinase Wzc, N-terminal domain (domain)
This domain is found in the homologues of Tyrosine-protein kinases Wzc and Etk. The later are expressed only in enteropathogenic strains. Wzc is required for the extracellular polysaccharide colanic acid synthesis. The autophosphorylated form of this enzyme is inactive. This domain folds into a beta-sandwich.
Pfam PF09919: Uncharacterized conserved protein (DUF2149) (family)
This domain, found in various hypothetical prokaryotic proteins, has 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 PF04057: Replication factor-A protein 1, N-terminal domain (domain)
Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication .
Pfam PF03740: Pyridoxal phosphate biosynthesis protein PdxJ (domain)
Members of this family belong to the PdxJ family that catalyses the condensation of 1-deoxy-d-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxine 5'-phosphate (PNP). This reaction is involved in de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate.
Pfam PF16996: Accessory secretory protein Sec Asp4 (family)
Asp4 and Asp5 are putative accessory components of the SecY2 channel of the SecA2-SecY2 mediated export system, but they are not present in all SecA2-SecY2 systems. This family of Asp4 is found in Firmicutes.
Pfam PF07464: Apolipophorin-III precursor (apoLp-III) (family)
This family consists of several insect apolipoprotein-III sequences. Exchangeable apolipoproteins constitute a functionally important family of proteins that play critical roles in lipid transport and lipoprotein metabolism. Apolipophorin III (apoLp-III) is a prototypical exchangeable apolipoprotein found in many insect species that functions in transport of diacylglycerol (DAG) from the fat body lipid storage depot to flight muscles in the adult life stage.
Wikipedia: In molecular biology, the apolipophorin III family of proteins are a family of exchangeable apolipoproteins. Exchangeable apolipoproteins constitute a functionally important family of proteins that play critical roles in lipid transport and lipoprotein metabolism. Apolipophorin III (apoLp-III) is a prototypical exchangeable apolipoprotein found in many insect species that functions in transport of diacylglycerol (DAG) from the fat body lipid storage depot to flight muscles in the adult life stage. The special lipoproteins they form are called lipophorins. High-density lipophorin is characterized by its association with a lower proportion of lipid. It interacts with more lipid and stabilize by Apolipophorin III to form low-density lipophorin. This transformation occurs through tightly regulated and precisely timed processes.
Pfam PF01542: Hepatitis C virus core protein (family)
The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.
Pfam PF09623: CRISPR-associated protein NE0113 (Cas_NE0113) (family)
Members of this minor CRISPR-associated (Cas) protein family are encoded in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum.
Pfam PF15748: Centriole, cilia and spindle-associated (family)
This family of microtubule-binding proteins may play a role in embryonic brain development and cilia beating.
Pfam PF03672: Uncharacterised protein family (UPF0154) (family)
This family contains a set of short bacterial proteins of unknown function.
Pfam PF20317: Helix-turn-helix domain (domain)
This family of proteins contains a likely DNA-binding helix-turn-helix but is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 128 and 151 amino acids in length.
Pfam PF17572: Family of unknown function (DUF5478) (family)
This is a family of unknown function found in Alphabaculovirus.
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 PF14991: Protein melan-A (family)
Melan-A, also known as melanoma antigen recognised by T-cells 1, or MART-1, is a protein that in humans is encoded by the MLANA gene. It is required for the function of the melanosomal matrix protein PMEL17/GP100 and thus plays an important role in regulating mammalian pigmentation . Melan-A is a member of the MAGE gene family  and is a tumour associated antigen. Clinically, the protein may serve as an anti-cancer vaccine .
Wikipedia: Protein melan-A also known as melanoma antigen recognized by T cells 1 or MART-1 is a protein that in humans is encoded by the MLANA or "MALENA" gene. A fragment of the protein, usually consisting of the nine amino acids 27 to 35, is bound by MHC class I complexes which present it to T cells of the immune system. These complexes can be found on the surface of melanoma cells. Decameric peptides (26-35) are being investigated as cancer vaccines.
Pfam PF23525: AprA MT2-like domain (domain)
This entry represents a methyltransferase domain found in the homologues of AprA Methyltransferase 1. AprA is an S-adenosylmethionine and Fe3+-dependent dimethyltransferase that acts in the initiation steps of apratoxin A biosynthesis.
Pfam PF18388: Atg29 N-terminal domain (domain)
This is the N-terminal domain found in fungal Atg proteins such as Atg29. In yeast, the induction of autophagy begins at a single perivacuolar site that is proximal to the vacuole, called the phagophore assembly site (PAS). Atg17-Atg29-Atg31 complex (Atg1 complex) formation is a prerequisite for PAS assembly. Functional analysis indicate that the N-terminal half Atg29 can bind Atg31.
Pfam PF02759: RUN domain (family)
This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.
Wikipedia: The RUN domain is an evolutionary conserved protein–protein binding protein domain. They often interact with GTPases and could play a role in multiple Ras-like GTPase signalling pathways.
Pfam PF18647: Alpha-galactosyl-binding fungal lectin (domain)
This domain can be found in alpha-galactosyl binding Lyophyllum decastes lectin (LDL). It is composed of five-stranded anti-parallel beta-sheet and two alpha-helices and contain conserved cysteines responsible for disulfide bridges. The protein with the highest similarity is ginkbilobin-2, a protein with apparent anti-fungal properties isolated from the seeds of the ginkgo biloba tree. Homologous sequences can be divided into two groups, where the proteins in the group with closest homology to LDL only consist of a single LDL-like domain. In the second group of sequences, the LDL-like domain is found at the C-terminal end of a larger domain with homology to members of the Ser, Gly, Asn, His consensus sequence (SGNH)-hydrolase family, which is part of the Gly, Asp, Ser, Leu motif-esterase/lipase superfamily.
Pfam PF14892: Piercer of microtubule wall 1/2 (family)
This family of proteins is found in eukaryotes and includes Piercer of microtubule wall 1/2 proteins (PIRC1/2). In mice PIRC1 expression is induced by p53 may play a role in DNA damage response and has been shown to function at the initial step of left-right asymmetry specification of the visceral organs. PIRC1/2 are microtubule inner proteins involved in the attachment of outer dynein arms (ODAs) to dynein-decorated doublet microtubules (DMTs) in cilia axoneme.
Pfam PF13230: Glutamine amidotransferases class-II (domain)
This family captures members that are not found in [pfam:PF00310].
Pfam PF05798: Bacteriophage FRD3 protein (family)
This family consists of bacteriophage FRD3 proteins.
Pfam PF17310: Family of unknown function (DUF5357) (family)
This is a family of unknown function found in Cyanobacteria. Most of the family members are predicted to have several 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 PF17024: Putative DMAP1-like (family)
This is a family of microsporidia-specific sequences that may have distant homology to the family DMAP1, [pfam:PF05499].
Pfam PF23214: Mitochondrial protein cyt-4 SH3 domain (domain)
This entry represents a SH3 domain found in mitochondrial protein CYT4 from Neurospora crassa and related fungal sequences. CYT4 is required for RNA 5'- and 3'-end processing and splicing.
Pfam PF18508: Zinc finger domain (domain)
The SAGA (Spt-Ada-Gcn5-acetyltransferase) complex performs multiple functions in transcription activation including deubiquitinating histone H2B, which is mediated by a subcomplex called the deubiquitinating module (DUBm). The yeast DUBm comprises a catalytic subunit, Ubp8, and three additional subunits, Sgf11, Sus1 and Sgf73, all of which are required for DUBm activity. A portion of the non-globular Sgf73 subunit lies between the Ubp8 catalytic domain and the zinc finger (ZnF)-UBP domain and has been proposed to contribute to deubiquitinating activity by maintaining the catalytic domain in an active conformation. Sgf73 contributes to maintaining both the organization and ubiquitin-binding conformation of Ubp8, thereby contributing to overall DUBm activity. This domain is a Sgf73 fragment in the DUB module. It is a zinc finger (ZnF) domain whose integrity is essential for the incorporation of this subunit into DUBm as well as for the catalytic activity of Ubp8, as either a short deletion or point mutations in Sgf73 zinc-coordinating residues disrupt the association of Sgf73 with the rest of the DUBm.
Pfam PF00019: Transforming growth factor beta like domain (domain)
Transforming growth factor-beta (TGF-beta) is a multifunctional peptide that controls proliferation, differentiation and other functions in many cell types. TGF-beta-1 is a peptide of 112 amino acid residues derived by proteolytic cleavage from the C-terminal of a precursor protein .

A number of proteins are known to be related to TGF-beta-1 . Proteins from the TGF-beta family are only active as homo- or heterodimer; the two chains being linked by a single disulphide bond. From X-ray studies of TGF-beta-2 , it is known that all the other cysteines are involved in intrachain disulphide bonds. There are four disulphide bonds in the TGF-beta and in inhibin beta chains, while the other members of this family lack the first bond.

The regulatory cytokine TGFbeta exerts tumour-suppressive effects, but also modulates cell invasion and immune regulation . Misregulation of the TGF-beta signalling pathway can result in tumour development.
Wikipedia: The transforming growth factor beta (TGF-β) superfamily is a large group of structurally related cell regulatory proteins that was named after its first member, TGF-β1, originally described in 1983. They interact with TGF-beta receptors.
Pfam PF03352: Methyladenine glycosylase (family)
The DNA-3-methyladenine glycosylase I is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.
Pfam PF18851: Bacterial archaeo-eukaryotic release factor family 8 (family)
Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome.
Pfam PF22313: DIP0205-like, N-terminal domain (domain)
This domain is found at the N-terminal end of DIP0205 from Corynebacterium diphtheriae and other putative phage capsid proteins found in tailed bacteriophages and bacterial prophages. This domain shows an alpha-helical configuration. It is often found associated to [pfam:PF05065].
Pfam PF03559: NDP-hexose 2,3-dehydratase (domain)
This family includes a range of proteins from antibiotic production pathways. The family includes gra-ORF27 [swissprot:Q9ZA32] product that probably functions at an early step, most likely as a dTDP-4-keto-6- deoxyglucose-2,3-dehydratase. Its homologues include dnmT from the daunorubicin biosynthetic gene cluster in S. peucetius, a similar gene from the daunomycin biosynthetic cluster in Streptomyces sp. strain C5 [swissprot:Q53880] , eryBVI from the erythromycin cluster in S. erythraea and snoH from the nogalamycin cluster in S. nogalater. The proteins in this family are composed of two copies of a 200 amino acid long unit that may be a structural domain.
Pfam PF19525: Ets1 N-terminal flanking region of Ets domain (domain)
Ets1 is a member of the Ets family of transcription factors in which the DNA-binding activity is in an autoinhibited state. The autoinhibition of Ets1 is mediated by structural coupling of the regions flanking the Ets domain. The inhibitory regions are folded as helices HI1 and HI2 N-terminal to the ETS domain and as H4 C-terminal to the ETS domain, which are packed together to form an inhibitory module. This domain represents the N-terminal flanking region of Ets domain which contains the residues forming HI1 and HI2 helices and additional residues(244-301) N-terminal to HI1. HI1 and HI2 exert the autoinhibitory function by directing the inhibitory residues N-terminal to HI1 to mask the Ets domain DNA-binding surface. These residues are flexible and function by masking the DNA-binding surface of the Ets domain. Phosphorylation of serine residues present in this region enhances autoinhibition dramatically. These inhibitory sequences are required for cooperative DNA binding.
Pfam PF00609: Diacylglycerol kinase accessory domain (family)
Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown.
Wikipedia: Diacylglycerol kinase is a family of enzymes that catalyzes the conversion of diacylglycerol (DAG) to phosphatidic acid (PA), utilizing ATP as a source of the phosphate. In non-stimulated cells, DGK activity is low, allowing DAG to be used for glycerophospholipid biosynthesis, but on receptor activation of the phosphoinositide pathway, DGK activity increases, driving the conversion of DAG to PA. As both lipids are thought to function as bioactive lipid signaling molecules with distinct cellular targets, DGK therefore occupies an important position, effectively serving as a switch by terminating the signalling of one lipid while simultaneously activating signalling by another.
Pfam PF01561: Hantavirus glycoprotein Gc, N-terminal (domain)
The medium (M) genome segment of hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins Gn and Gc (also known as G1 and G2, respectively) as a polyprotein precursor. Gn and Gc forms homotetramers at the surface of the virion, which attach the virion to host cell receptors including integrin beta3/ITGB3 and induce internalisation, predominantly through clathrin-dependent endocytosis. Gc protein has a typical class II fusion protein fold consisting of a central beta-sandwich domain (termed domain I) made of eight beta-strands arranged in two antiparallel beta-sheets, domain II which has an elongated shape with two subdomains (central, opened beta-barrel proximal to domain I and a distal beta-sandwich 'tip') and and domain III, which has an Ig-like fold. This entry represents the N-terminal region of Gc containing the central and dimerisation domains (which includes domain I and II). This region has a conserved CNP motif, suggested to be an integrin-binding motif.
Pfam PF22876: SBE2, N-terminal domain (domain)
This entry represents a domain found N-terminal in Sbe2 and its paralogue, Sbe22 from budding yeast. These proteins are involved in bud growth and yeast cell wall formation. They may be also involved in the transport of cell wall components from the Golgi apparatus to the cell surface periphery.
Pfam PF03393: Pneumovirus matrix protein N-terminal domain (domain)
This entry represents the N-terminal domain of the pneumoviral matrix protein. The N-terminal domain of the RSV M protein (residues 1-126) adopts a twisted beta-sandwich fold comprised of two nearly perpendicular beta-sheets - one with 3 strands and one with 4 strands. The overall topology is a curved horseshoe-like arrangement with the 3-stranded beta-sheet forming the concave inner face flanked by loop regions, and the 4-stranded beta-sheet forming the convex outer face. This domain is loosely associated with the C-terminal domain via weak hydrophobic interactions. The N-terminal domain contains a distinctive negatively charged surface lobe that may direct interactions with binding partners. Sequence alignments indicate that regions of diversity between RSV and other pneumoviruses map to external loop regions and sheet edges in this domain, likely mediating species-specific protein or RNA interactions.
Pfam PF22999: LTN1 family HEAT repeat region (repeat)
This entry represents a series of HEAT repeats from the LTN1 family of proteins.  The LTN1 family consists of E3 ubiquitin-protein ligases that are integral components of the ribosome quality control complex (RQC). The RQC is a ribosome-associated complex responsible for the ubiquitination and subsequent extraction of incompletely synthesized nascent polypeptides for proteasomal degradation. Members of the LTN1 family are recruited to stalled 60S ribosomal subunits, often by NEMF, to mediate the ubiquitination of stalled nascent chains. This ubiquitination event is crucial for the recruitment of VCP/p97 or CDC48, which facilitates the extraction and degradation of the incomplete translation products. In some species, LTN1 proteins also ubiquitinate proteins derived from mRNAs lacking stop codons or translation arrest products induced by specific sequences. Additionally, they may play a role in chromatin function and transcription regulation indirectly.
Pfam PF00885: 6,7-dimethyl-8-ribityllumazine synthase (domain)
This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase [ec:2.5.1.9], an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example [swissprot:O28856]. The family contains a number of different subsets including a family of proteins comprising archaeal lumazine and riboflavin synthases, type I lumazine synthases, and the eubacterial type II lumazine synthases. It has been established that lumazine synthase catalyses the penultimate step in the biosynthesis of riboflavin in plants and microorganisms.  The type I lumazine synthases area active in pentameric or icosahedral quaternary assemblies, whereas the type II are decameric.  Brucella, a bacterial genus that causes brucellosis, and other Rhizobiales have an atypical riboflavin metabolic pathway. Brucella spp code for both a type-I and a type-II lumazine synthase, and it has been shown that at least one of these two has to be present in order for Brucella to be viable, showing that in the case of Brucella flavin metabolism is implicated in bacterial virulence.
Wikipedia: Riboflavin synthase is an enzyme that catalyzes the final reaction of riboflavin biosynthesis. It catalyzes the transfer of a four-carbon unit from one molecule of 6,7-dimethyl-8-ribityllumazine onto another, resulting in the synthesis of riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione:(2) 6,7-dimethyl-8-ribityllumazine → riboflavin + 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione
Pfam PF05419: GUN4-like (domain)
In Arabidopsis, GUN4 is required for the functioning of the plastid mediated repression of nuclear transcription that is involved in controlling the levels of magnesium- protoporphyrin IX.  GUN4 binds the product and substrate of Mg-chelatase, an enzyme that produces Mg-Proto, and activates  Mg-chelatase. GUN4 is thought to participates in plastid-to-nucleus  signaling by regulating magnesium-protoporphyrin IX synthesis or trafficking.
Pfam PF24484: ADAMTSL1 domain (domain)
This domain is found in human ADAMTS-like protein 1 (ADAMTSL1) and in similar proteins mainly found in vertebrates. This domain is predicted to adopt a mainly alpha-helical structure.
Pfam PF16477: Domain of unknown function (DUF5054) (family)
This family consists of Glycosyl hydrolase family 38 proteins around 700 residues in length and is mainly found in various Clostridium and Rhizobium species. 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 PF22580: Kynureninase C-terminal domain (domain)
This entry represents de C-terminal domain of kynureninase, a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyse the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases..