SII-SWORD/CoKE huggingface dataset:
Pfam PF01849: NAC domain (family)
In eukaryotes, the Nascent polypeptide-Associated Complex (NAC) is a heterodimeric cytosolic protein complex composed of NAC alpha (NACA) and NAC beta (BTF3) . NAC binds reversibly to the ribosome where it is in contact with nascent chains as they emerge from the ribosome. But the cellular function of NAC seems to be much more diverse as it is also involved in transcription regulation and mitochondrial translocation . Alpha and beta NACs share homology with each other, both contain a NAC A/B domain. In archaea no beta NAC proteins are found; the complex is an homodimer of NAC alpha .

The crystal structure of an archeal NAC has been solved . The NAC A/B domain consists of six strands arranged in a Î²-barrel structure similar to the OB fold. Various OB folds interact with ribosomal RNA which could suggest a similar role for the NAC A/B domain.
Pfam PF17781: RPN1 N-terminal domain (repeat)
This domain is found at the N-terminus of the 26S proteasome regulatory subunits RPN1 (also known as 26S proteasome non-ATPase  regulatory subunit 2 (PMSD2). The domain is formed by an array of  alpha helices.
Pfam PF22919: C-terminal domain of V and A type ATP synthase (domain)
This entry represents a small alpha helical domain found at the C-terminus of a variety of ATP synthases.
Pfam PF06693: Protein of unknown function (DUF1190) (family)
This family consists of several hypothetical Enterobacterial proteins of around 212 residues in length and is known as YjfM in Escherichia coli. 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 PF23560: Hemicentin galactose-binding domain-like (domain)
This entry represents a galactose-binding domain-like found in hemicentin and Willebrand factor A domain-containing proteins. The Hemicentin and von Willebrand factor A domain-containing protein family is involved in various cellular and developmental processes. Members of this family play a crucial role in the rearrangement of the podocyte cytoskeleton, influenced by transforming growth factor beta, which includes the modulation of F-actin fibers and changes in podocyte morphology. They are also implicated in the organisation of the basement membrane and may contribute to cleavage furrow maturation during cytokinesis in embryos. Additionally, they are involved in the structural integrity of adhesive and flexible epithelial cell junctions and may influence cardiac fibroblast migration during myocardial remodeling.
Pfam PF15401: Tryptophan-ring motif of head of Trimeric autotransporter adhesin (domain)
TAA-head_Trp-ring is the tryptophan-ring motif of some Gram-negative Enterobacteriaceae. The Trp-ring folds into a beta-meander type on the top of the head domain of its trimeric autotransporter adhesin proteins. In conjunction with the GIN domain it is thought to be the region of the head that adheres to fibronectin.
Wikipedia: In molecular biology, trimeric autotransporter adhesins (TAAs), are proteins found on the outer membrane of Gram-negative bacteria. Bacteria use TAAs in order to infect their host cells via a process called cell adhesion. TAAs also go by another name, oligomeric coiled-coil adhesins, which is shortened to OCAs. In essence, they are virulence factors, factors that make the bacteria harmful and infective to the host organism.
Pfam PF15025: C5orf34-like, N-terminal (domain)
This entry represents the N-terminal domain of a family of eukaryotic proteins, including the human uncharacterised protein C5orf34, which has been reported to be correlated with an unfavourable prognosis of patients from a variety of human malignancies. This domain is predicted to show an alpha-beta structure with high structural similarity to a polo box.
Pfam PF16632: C-terminal region of Caskin (disordered)
This region is found at the C-terminus of Caskin proteins. Caskins are CASK-binding synaptic scaffolding proteins. Part of this region is predicted to be in coiled-coil conformation. Its function is not known.
Pfam PF02046: Cytochrome c oxidase subunit VIa (family)
Cytochrome c oxidase (1.9.3.1) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen . In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane.

In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as VIa in vertebrates and fungi. Mammals have two tissue-specific isoforms of VIa, a liver (VIa-L) and a heart and skeletal muscle isoform (VIa-H). Mammalian VIa-H induces a slip in CcO (decrease in proton/electron stoichiometry) at high intramitochondrial ATP/ADP ratios, while VIa-L induces a permanent slip in CcO, depending on the presence of cardiolipin and palmitate . Only one form is found in fish .
Pfam PF11693: Protein of unknown function (DUF2990) (family)
This family of proteins represents a fungal protein with unknown 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 PF07842: GC-rich sequence DNA-binding factor-like protein (family)
This entry describes a domain found in a number of GC-rich sequence  DNA-binding factor proteins and homologues, as well as in a  number of other proteins including Tuftelin-interacting protein 11. While the function of the domain is unknown, some of the  proteins it is found in are reported to be involved in pre-mRNA  splicing. This domain is also found in Sip1, a septin  interacting protein.
Pfam PF15843: Domain of unknown function (DUF4719) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 67 and 240 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 PF22035: Lpg0393 VPS9-like domain (domain)
Lpg0393 consists of two domains both of which composed of alpha- helices. The N-terminal domain contains seven helices and makes roughly a 90-degree angle with the C-terminal domain that forms a helical bundle structure. The N-terminal domain is similar to Vps9 domain of Rabex-5. Lpg0393 exhibits a GEF activity toward Rab5, Rab21 and Rab22, and this activity is associated with a VPS9-like domain of the protein.
Pfam PF11419: Protein of unknown function (DUF3194) (family)
This family of proteins has no known function however the structure has been determined. The protein consists of two alpha-helices packed on the same side of a central beta-hairpin.
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 PF15270: Metallo-carboxypeptidase inhibitor (family)
ACI44, a metallo-carboxypeptidase inhibitor, is one member of a battery of selective inhibitors protecting roundworms of the genus Ascaris, common parasites of the human gastrointestinal tract, from host enzymes and the immune system.
Pfam PF06648: Autographa californica nuclear polyhedrosis virus (AcMNPV), Ac75 (family)
This family is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV) protein Ac75, which is required for the egress of nucleocapsids from the nucleus, formation of intranuclear microvesicles and subsequent budded virion formation, in addition to protein Ac93. Ac75 is not an integral membrane protein, but it interacts with integral membrane protein Ac76 and is associated with the nuclear membrane.
Pfam PF20041: Domain of unknown function (DUF6443) (domain)
This presumed domain is functionally uncharacterised. This domain family is predominantly found in Bacteroidetes, and is about 100 amino acids in length. This domain contains a highly conserved YDxxGR motif which suggests that it is related the RHS repeats, that appear to be involved in ligand binding. RHS repeats share structural similarity with the eukaryotic tyrosine-aspartate (YD) repeat.
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 PF00232: Glycosyl hydrolase family 1 (domain)
O-Glycosyl hydrolases (3.2.1.) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Glycoside hydrolase family 1 GH1 comprises enzymes with a number of known activities; beta-glucosidase (3.2.1.21); beta-galactosidase (3.2.1.23); 6-phospho-beta-galactosidase (3.2.1.85); 6-phospho-beta-glucosidase (3.2.1.86); lactase-phlorizin hydrolase (3.2.1.62), (3.2.1.108); beta-mannosidase (3.2.1.25); myrosinase (3.2.1.147).
Wikipedia: Glycoside hydrolase family 1 is a family of glycoside hydrolases. Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of &gt;100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Pfam PF03307: Adenovirus 15.3kD protein in E3 region (family)
Adenoviruses have evolved multiple mechanisms to evade the host immune response. Several of the immunomodulatory proteins are encoded in early transcription unit 3 (E3) of human adenoviruses (Ads). These proteins appear to control viral interactions with the host . This entry represents the E3_15 family, including proteins from the E3 region which may protect virus-infected cells from TNF-induced cytolysis .
Pfam PF10281: Putative nuclear envelope organisation protein (repeat)
This entry represents a repeat found in the fungal protein Ish1, a protein which has a role in nuclear membrane organisation.
Pfam PF01929: Ribosomal protein L14 (family)
This family includes the eukaryotic ribosomal protein L14.
Pfam PF19670: Family of unknown function (DUF6173) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 139 and 154 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 PF00784: MyTH4 domain (family)
Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins.
Pfam PF23299: Domain of unknown function (DUF7081) (domain)
This presumed domain is found in a group of plant sequences related to Oberon-like proteins. According to structure predictions this domain may consist of mainly three beta-sheets and two alpha-helices.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF08629: PDE8 phosphodiesterase (family)
This region is found in members of the PDE8 phosphodiesterase family.  It is found with [pfam:PF00233].
Pfam PF02072: Prepro-orexin (family)
Orexins (also known as hypocretins) are neuropeptides that are specifically localised to the hypothalamus. They are thought to interact with autonomic, neurendocrine and neuroregulatory systems, and play an important role in the regulation of feeding behaviour . When applied to hypothalamic neurones, these peptides are neuroexcitatory, which action is probably mediated by their binding to a new family of G-protein-coupled receptors (orexin receptors 1 and 2), which were previously orphan .

To date, two orexins have been characterised (orexin-A and -B), both encoded by a single mRNA transcript (prepro-orexin or hypocretin neuropeptide precursor, whose product is represented in this entry): orexin-A is a 33-residue peptide with two intramolecular disulphide bonds in the N-terminal region; and orexin-B is a linear 28-residue peptide. These peptides have 46% identity at the amino acid sequence level, and show some similarity to the glucagon/vasoactive intestinal polypeptide/secretin peptide family.
Wikipedia: Orexin, also known as hypocretin, is a neuropeptide that regulates arousal, wakefulness, and appetite. It exists in the forms of orexin-A and orexin-B. The most common form of narcolepsy, type 1, in which the individual experiences brief losses of muscle tone, is caused by a lack of orexin in the brain due to destruction of the cells that produce it.
Pfam PF24932: Next to BRCA1 gene 1 protein-like, C-terminal UBA domain (domain)
This UBA domain is found at the C-terminal end of human Next to BRCA1 gene 1 protein (NBR1) and similar eukaryotic proteins. NBR1 is an ubiquitin-binding autophagy adapter that participates in different processes including host defense or intracellular homeostasis.
Pfam PF10902: WYL_2, Sm-like SH3 beta-barrel fold (family)
WYL_2 is a family of Sm-like SH3 beta-barrel fold containing domains. WYL is named for three conserved amino acids found in a subset of domains of this superfamily. These residues are not strongly conserved throughout the family. Rather, the conservation pattern includes four basic residues and a position often occupied by a cysteine, which are predicted to line a  ligand-binding groove typical of the Sm-like SH3 beta-barrels.  It is predicted to be a ligand-sensing domain that could   bind negatively charged ligands, such as nucleotides or nucleic acid fragments, to regulate CRISPR-Cas and other defense   systems such as the abortive infection AbiG system
Pfam PF05355: Apolipoprotein C-II (family)
Apolipoprotein C-II (ApoC-II) is the major activator of lipoprotein lipase, a key enzyme in the regulation of triglyceride levels in human serum.
Wikipedia: Apolipoprotein C-II, or apolipoprotein C2 is a protein that in humans is encoded by the APOC2 gene.
Pfam PF11389: Leptospira porin protein OmpL1 (family)
OmpL1 is a member of the outer membrane (OM) proteins in the mammalian pathogen Leptospira. Specifically, it is a porin.
Pfam PF11485: STK_08120-like (family)
This family of proteins specific to thermoacidophile archaea includes STK_08120 from Sulfurisphaera tokodaii. This protein shows three alpha-helices and a seven-stranded beta-sheet. It may function as a carrier of fatty acids in their biosynthesis, metabolism, and/or intracellular transport processes.
Pfam PF05981: CreA protein (family)
This family consists of several bacterial CreA proteins, the function of which is unknown.
Pfam PF14452: Multiubiquitin (family)
A ubiquitin superfamily domain that is often present in multiple tandem copies in the same polypeptide. Members of this family are associated in gene neighborhoods, or on occasions fused to, bacterial homologs of components of ubiquitin-dependent modification  system such as the E1, E2 and JAB metallopeptidase enzymes and a distinct metal-binding domain. The E2/UBC fold domain appears to be  inactive. The JAB domain in these operons is usually fused to  the E1 domain.
Pfam PF13652: Putative quorum-sensing-regulated virulence factor (domain)
This is a family of short ~14 kDa proteins from Psuedomonas. The structure of UniProtKB:Q9HY15 a secreted protein has been solved and deposited as PDB:3npd.  It comprises one structural domain with five beta-strands and five alpha-helices. Various comparative structural prediction methods plus its genomic location point to the protein forming a functional dimer with its adjacent genomic partner, UniProtKB:Q9HY14, in [pfam:PF12843]. Together these might be regulated by the other product from the PotABCD operon, namely the putrescine-binding periplasmic protein UniProtKB:Q9HY16. which has been implicated in quorum-sensing. QSregVF is certainly up-regulated in quorum-sensing, and is predicted to be a virulence factor.
Pfam PF10743: Regulatory phage protein cox (family)
This family of phage Cox proteins is expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes.
Pfam PF11677: Protein of unknown function (DUF3273) (family)
Some members in this family of proteins are annotated as multi-transmembrane proteins however this cannot be confirmed. Currently this family 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 PF00943: Alphavirus E2 glycoprotein (family)
E2 forms a heterodimer with E1.  The virus spikes are made up of 80 trimers of these heterodimers (sindbis virus).
Wikipedia: Alphavirus is a genus of RNA viruses, the sole genus in the Togaviridae family. Alphaviruses belong to group IV of the Baltimore classification of viruses, with a positive-sense, single-stranded RNA genome. There are 32 alphavirus species, which infect various vertebrates such as humans, rodents, fish, birds, and larger mammals such as horses, as well as invertebrates. Alphaviruses that can infect both vertebrates and arthropods are referred dual-host alphaviruses, while insect-specific alphaviruses such as Eilat virus and Yada yada virus are restricted to their competent arthropod vector. Transmission between species and their vertebrate hosts occurs mainly via mosquitoes, making the alphaviruses a member of the collection of arboviruses – or arthropod-borne viruses. Alphavirus particles are enveloped, have a 70 nm diameter, tend to be spherical, and have a 40 nm isometric nucleocapsid.
Pfam PF11668: HCMV glycoprotein pUL130 (family)
This family of proteins represents pUL130 from Human cytomegalovirus, a glycoprotein secreted from infected cells that is incorporated into the virion envelope as a Golgi-matured form. The protein promotes endothelial cell infection through a producer cell modification of the virion.
Pfam PF14999: Shadow of prion protein, neuroprotective (family)
This protein family is a Prion-like protein and its function is neuroprotective and similar to PrP(C)-like. Shadoo is mainly expressed in the brain, and highly expressed in the hippocampus, the area of the brain which co-ordinates memory as well as spatial memory and navigation. This protein may also alter the biological actions of normal and abnormal Prion Protein (PrP) which lead to lethal neurodegenerative diseases. This family of proteins is found in eukaryotes. Proteins in this family are approximately 150 amino acids in length, of which the first 90 are alanine rich.
Pfam PF23931: Terminase small subunit (domain)
The small subunit of terminase, a DNA packaging enzyme of bacteriophages, plays a role in binding and cutting the phage DNA during packaging into the capsid. This entry represents diverse small subunits from a wide range of actinobacteriophages and some Bacillota phages. The domain is often found at the N-terminus of proteins, followed by a disordered or low complexity region at the C-terminus. In some larger proteins, additional C-terminal domains may also be present.
Pfam PF06596: Photosystem II reaction centre X protein (PsbX) (family)
This family consists of several photosystem II reaction centre X protein (PsbX) sequences from both prokaryotes and eukaryotes.
Pfam PF17416: Herpesvirus Glycoprotein B (domain)
This domain has a PH-like fold.
Wikipedia: Herpesvirus glycoprotein B is a viral glycoprotein that is involved in the viral cell entry of Herpes simplex virus (HSV). Herpesviruses have a lipid bilayer, called the envelope, which contains twelve surface glycoproteins. For infectivity to be attained, the double stranded DNA genome of HSV must enter the host cell through means of fusion of its envelope with the cellular membrane or via endocytosis. Other viral glycoproteins involved in the process of viral cell entry include gC, gB, gD, gH, and gL, but only gC, gB, gD, and gH are required for the fusion of the HSV's envelope with the cellular membrane. It can be noted that all herpesviruses have glycoproteins gB, gH, and gL.
Pfam PF24673: Divisome-associated membrane protein Blr family (family)
This entry represents the Blr family, which consists of proteins that are components of the cell division machinery. These proteins are likely involved in the stabilization of the divisome, particularly under certain stress conditions. Blr is a short membrane protein that interacts with the essential cell division protein FtsL. Mutations in Blr have been shown to increase the sensitivity of bacteria to beta-lactam antibiotics or their resistance to cell envelope stress.