SII-SWORD/CoKE huggingface dataset:
Pfam PF09147: Carbapenam-3-carboxylate synthase, N-terminal (domain)
This domain is found in the N-terminal of carbapenam-3-carboxylate synthase (carA), and is composed of two antiparallel six-stranded beta-sheets that form a sandwich, flanked on each side by two alpha-helices. carA is involved in the biosynthesis of carbapenam-3-carboxylate, a beta-lactam antibiotic of the carbapenem class. It catalyses the ATP-dependent formation of (3S,5S)-carbapenam-3-carboxylate from (2S,5S)-5-carboxymethylproline.
Pfam PF17544: Family of unknown function (DUF5460) (family)
This is a family of unknown function found in Rickettsia. Family members are predicted to contain one trans-membrane region.
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 PF13236: Clustered mitochondria (domain)
The CLU domain (CLUstered mitochondria) is a eukaryotic domain found in proteins from fungi, protozoa, plants to humans. It is required for correct functioning of the mitochondria and mitochondrial transport although the exact function of the domain is unknown. In Dictyostelium the full-length protein is required for a very late step in fission of the outer mitochondrial membrane suggesting that mitochondria are transported along microtubules, as in mammalian cells, rather than along actin filaments, as in budding yeast. Disruption of the protein-impaired cytokinesis and caused mitochondria to cluster at the cell centre. It is likely that CLU functions in a novel pathway that positions mitochondria within the cell based on their physiological state. Disruption of the CLU pathway may enhance oxidative damage, alter gene expression, cause mitochondria to cluster at microtubule plus ends, and lead eventually to mitochondrial failure.
Pfam PF13373: DSC E3 ubiquitin ligase complex subunit 3, C-terminal domain (domain)
This is the C-terminal domain of DSC E3 ubiquitin ligase complex subunit 3 (Dsc3), which contains two transmembrane helices and a characteristic GFDRL sequence motif. Dsc3 is a component of the DSC E3 ubiquitin ligase complex (a Golgi-specific protein ubiquitination system) that functions in protein homeostasis under non-stress conditions, playing a role in protein quality control. Yeast DSC E3 ubiquitin ligase complex is the homologue of Hrd1 E3 ligase complex from mammals, in which Dsc1, Dsc2 and Dsc3 corresponds to Hrd1, Der1, and Usa1, respectively. Dsc3 is a Herp-like protein that acts as a bridge between Dsc1 and Dsc2 for their interaction.
Pfam PF23076: PH domain found in tandem in fungal proteins (domain)
This PH domain is found as the C-terminal one of a pair that is found in a family of uncharacterised fungal proteins.
Pfam PF14583: Oligogalacturonate lyase (repeat)
This is a family of oligogalacturonate lyases, referred to more generally as pectate lyase family 22.  These proteins fold into 7-bladed beta-propellers.
Wikipedia: The WD40 repeat is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide. Tandem copies of these repeats typically fold together to form a type of circular solenoid protein domain called the WD40 domain.
Pfam PF07322: Seadornavirus Vp10 (family)
This family consists of several Seadornavirus Vp10 proteins found in the Banna and Kadipiro viruses. Members of this family are typically around 240 residues in length. The function of this family is unknown.
Pfam PF09228: Prokaryotic Transcriptional repressor TraM (domain)
Members of this family of transcriptional repressors adopt a T-shaped structure, with a core composed of two antiparallel alpha-helices. These proteins can be divided into two parts, a 'globular head' and an 'elongated tail', and they negatively regulate conjugation and the expression of tra genes by antagonising traR/AAI-dependent activation.
Pfam PF17483: C-lobe handle domain of Tf-binding protein B (domain)
Bacterial lipoproteins represent a large group of specialised membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialised uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a 'handle' domain made up of four (N lobe) or eight (C lobe) beta strands. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf. This domain family is found in the handle domain of the C lobe (domain C) of TbpB proteins. It consists of a squashed six-stranded beta sheet flanked by two antiparallel beta strands and has no supporting alpha helix as in the N lobe.
Pfam PF17421: Family of unknown function (DUF5409) (family)
This domain of unknown function is found in Poxviridae.
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 PF10242: Lipoma HMGIC fusion partner-like protein (family)
This is a group of proteins expressed from a series of genes referred to as Lipoma HMGIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans and hypospadias, and LHFPL1 is transcribed in six liver tumour cell lines.
Pfam PF14693: Ribosomal protein TL5, C-terminal domain (domain)
This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, [pfam:PF01386]. Full length (N- and C-terminal domain) homologues of TL5 are also known as CTC proteins. TL5 or CTC are not found in Eukarya or Archaea. In some Bacteria, including E. coli, this ribosomal subunit occurs as a single domain protein (named Ribosomal subunit L25), where the only domain is homologous to TL5 N-terminal domain (hence included in family [pfam:PF01386]). The function of the C-terminal domain of TLC is at present unknown.
Pfam PF11176: Translation machinery-associated protein 16 (family)
Proteins in this family localise to the nucleus.  Their function is not clear.
Pfam PF10599: Retro-transposon transporting motif (domain)
This is the highly conserved C-terminal motif GRKIxxxxxRRKx of nucleoporins that plays a critical and unique role in the nuclear import of retro-transposons in both yeasts and higher organisms. It would appear that the arginine residues at positions 2 and 9-10 constitute a bipartite nuclear localisation signal, with two basic peptide motifs separated by an interchangeable spacer sequence, that is crucial for the retro-transposon activity.
Pfam PF05483: Synaptonemal complex protein 1 (SCP-1) (coiled_coil)
Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.
Pfam PF13903: PMP-22/EMP/MP20/Claudin tight junction (family)
Members of this family are claudins, that form tight junctions between cells.
Wikipedia: Claudins are a family of proteins which, along with occludin, are the most important components of the tight junctions. Tight junctions establish the paracellular barrier that controls the flow of molecules in the intercellular space between the cells of an epithelium. They have four transmembrane domains, with the N-terminus and the C-terminus in the cytoplasm.
Pfam PF09076: Beta/Gamma crystallin (domain)
Members of this family assume a beta-gamma-crystallin fold, wherein nine beta-strands are connected by loop, and are separated into two sheets, each sheet forming the Greek key motif. The two Greek key motifs face each other in the global topology. The three-dimensional structure of the molecule is a 'sandwich'-shaped beta-barrel structure: hydrophobic side-chains are packed in the large interface area of the beta-sheets. In Streptomyces killer toxin-like protein domain confers a cytocidal effect to the toxin, causing cell death in both budding and fission yeasts, and morphological changes in yeasts and filamentous fungi.  This family also includes chitin-biding antifungal proteins.
Pfam PF20950: Influenza RNA polymerase PB2 helical domain (domain)
Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching. This entry represents the helical domain of Flu PB2 protein.
Pfam PF05133: Phage portal protein, SPP1 Gp6-like (family)
This bacteriophage protein forms a gateway that enables DNA passage during packaging and ejection of the phage genome. It also  forms the junction between the phage head (capsid) and the tail  proteins. During SPP1 morphogenesis, the portal protein, Gp6,  participates in the procapsid assembly reaction. In the  mature SPP1 virion, Gp6 exists as a dodecamer, while recombinant  SPP1 Gp6 has been shown to form 13-subunit assemblies. This  protein is common to Siphoviridae (phages with long non-contractile tails) and  Myoviridae (phages with contractile tails). It is also  found in a number of bacterial species. This family also includes  the old Pfam family Phage_min_cap (PF:PF05126). RC   Paper  describing PDB structure 2jes
Pfam PF13510: 2Fe-2S iron-sulfur cluster binding domain (domain)
The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins.
Pfam PF11242: Protein of unknown function (DUF2774) (family)
This is a viral family of proteins 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 PF16667: Unstructured region 10 on multiple PDZ protein (disordered)
MPDZ_u10 is a region of natively unstructured but highly conserved sequence on multiple-PDZ-containing domain proteins in higher eukaryotes. It lies between two PDZ domains, [pfam:PF00595]. The function is not known.
Pfam PF21220: RecQ-1-like, helix-turn-helix domain (domain)
This domain is found in a group of bacterial DNA helicases, including RecQ-1 from Porphyromonas gingivalis, which shows an all-helical structure. This entry represents the helix-turn-helix (HTH) domain.
Pfam PF01708: Geminivirus putative movement protein (family)
This family consists of putative movement proteins from Maize streak and wheat dwarf virus.
Pfam PF10516: SHNi-TPR (repeat)
SHNi-TPR family members contain a reiterated sequence motif that is an interrupted form of TPR repeat.
Pfam PF14128: Domain of unknown function (DUF4295) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There are two completely conserved residues (K and Y) that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF20511: Phosphomannose isomerase type I, catalytic domain (domain)
This entry represents the catalytic domain of Phosphomannose isomerase type I enzymes (EC 5.3.1.8) which contains a zinc-binding site. It is composed of beta-strands connected by long loops in a jelly roll conformation.
Pfam PF23823: Family of unknown function (DUF7193) (family)
This entry represents a family of viral proteins that are found in various bacteriophages infecting Gram-negative bacteria, such as Pseudomonas, Vibrio, Erwinia, Ralstonia, and Klebsiella. The family members are typically 800-1200 residues in length. Many are annotated as putative virion structural proteins, suggesting they may play a role in phage particle structure or assembly. However, the precise function of this family remains 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 PF08098: Anemonia sulcata toxin III family (family)
This family consists of the Anemonia sulcata toxin III  (ATX III) neurotoxin family. ATX III is a neurotoxin  that is produced by sea anemone; it adopts a compact  structure containing four reverse turns and two other  chain reversals, but no regular alpha-helix or beta-sheet.  A hydrophobic patch found on the surface of the peptide may  constitute part of the sodium channel binding surface.
Pfam PF11602: ATPase P4 of dsRNA bacteriophage phi-12 (family)
P4 is a packaging motor which is involved in the packaging of phi-12 genome into preformed capsids using ATP. P4 is located at the vertices of the icosahedral capsid. ATP drives RNA translocation through cooperative conformational changes.
Pfam PF05203: Hom_end-associated Hint (domain)
Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a second domain containing the protein-splicing active site. This Domain corresponds to the latter protein-splicing domain.
Wikipedia: The homing endonucleases are a collection of endonucleases encoded either as freestanding genes within introns, as fusions with host proteins, or as self-splicing inteins. They catalyze the hydrolysis of genomic DNA within the cells that synthesize them, but do so at very few, or even singular, locations. Repair of the hydrolyzed DNA by the host cell frequently results in the gene encoding the homing endonuclease having been copied into the cleavage site, hence the term 'homing' to describe the movement of these genes. Homing endonucleases can thereby transmit their genes horizontally within a host population, increasing their allele frequency at greater than Mendelian rates.
Pfam PF16894: Domain of unknown function (DUF5084) (family)
This protein is believed to be involved in the type VII secretion system.
Pfam PF22019: alpha-1,4-glucan branching enzyme GlgB, N-terminal domain (domain)
This is the N-terminal beta-sandwich domain of alpha-1,4-glucan branching enzyme GlgB and related proteins. This domain has a differential preference in substrate recognition and binding during amylase activity, when amylose is used as a substrate.
Pfam PF17720: RNA ligase 1 (domain)
This entry includes RNA ligase 1 from animals (RLIG1), which functions as an RNA ligase in vitro. This protein catalyses ATP-dependent RNA ligation via a three-step mechanism, involving tandem auto- and RNA AMPylation. It exhibits selectivity for single-stranded RNA substrates. RLIG1 may play a role in maintaining RNA integrity under stress conditions, such as in response to reactive oxygen species (ROS).
Pfam PF02122: Peptidase S39 (family)
This family contains polyprotein processing endopeptidases from RNA viruses.
Pfam PF18478: PIN like domain (domain)
This is a bacterial domain of unknown function suggested to resemble PIN like domains.
Pfam PF10080: Membrane iron-sulfur containing protein FtrD-like (family)
Members of this family are bacterial membrane proteins associated with the FTR1 protein, an homologous to FtrC in the FtrABCD complex. This complex is a ferric iron transporter in which the ferric iron is generated by ferrous oxidation that requires the electron transfer by iron-sulfur cluster-containing FrtD. Proteins in this family are part of the iron-sulfur-containing Rieske superfamily and are likely to have an analogous function to FtrD in iron transport.
Pfam PF01636: Phosphotransferase enzyme family (family)
This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides they include: aminoglycoside 3'-phosphotransferase or kanamycin kinase / neomycin-kanamycin phosphotransferase and streptomycin 3''-kinase or streptomycin 3''-phosphotransferase. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation. This family also includes homoserine kinase. This family is related to fructosamine kinase [pfam:PF03881].
Pfam PF21932: MIC2-associated protein, central beta-domain (domain)
This domain is found in MIC2-associated protein from Toxoplasma gondii (M2AP), which is necessary for the proper trafficking and secretion of MIC2 and thus involved in parasite invasion. M2AP is a soluble protein with an N-terminal propeptide, a central beta-domain (this entry), and a predicted C-terminal coil domain. This domain folds into a a compact beta-sandwich comprising 13 antiparallel beta-strands.
Pfam PF10450: POC1 chaperone (family)
In yeast, POC1 is a chaperone of the 20S proteasome which functions in early 20S proteasome assembly.
Pfam PF21040: Centrosomal protein CEP104-like, TOG domain (repeat)
Centrosomal protein CEP104 localises to the distal end of centrioles that interacts through its N- and C-terminal region, respectively, with the distal end proteins Cep97 and CP110. It is required for ciliogenesis and for structural integrity at the ciliary tip, being involved in regulating microtubule length in cilia. This is a multidomain protein that consists of an N-terminal all-beta domain, a central all-alpha-helical TOG domain and a C-terminal array of four zinc fingers domain. This entry represents the central tubulin-binding TOG domain, consisting of HEAT repeats. The sequence of TOG domains is quite divergent but the structure is conserved with some variation at the N and C-terminal. This entry also includes MEKK1 which has a TOG domain more closely related to that in CEP104, as they share a similar pair of arginine-rich C-terminal helices relative to canonical TOGs. MEKK1 TOG preferentially binds curved tubulin heterodimers.
Pfam PF23601: Domain of unknown function (DUF7140) (domain)
This entry represents a likely zinc-binding domain found at the C-terminus of a set of archaebacterial proteins. AlphaFold prediction show a structure forming 2-3 beta strands.
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 PF14136: Domain of unknown function (DUF4303) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 169 and 192 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 PF11985: Bacteriophage Mu, Gp27 (family)
This family is represented by Bacteriophage Mu, Gp27. It is probably the small subunit of terminase, which recognises viral DNA, binding to the packaging initiation site (pac) and regulates the ATPase activity of the terminase large subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Pfam PF17075: Regular of rDNA transcription protein 14 (family)
Regulator of rDNA transcription protein14 (RRT14) is a nucleolar protein that is involved in ribosome biogenensis.
Pfam PF21342: SoxA/TsdA, cytochrome c domain (domain)
This entry represents the first cytochrome c domain of SoxA and TsdA proteins, heme proteins involved in sulfur oxidation.
Pfam PF14467: Domain of unknown function (DUF4426) (domain)
Members of this entry are found mostly  in g-proteobacteria, especially in Vibrio. Strangely enough, there seems to be one eukaryotic homolog in Nematostella vectensis (NEMVEDRAFT_v1g226006), where the PA0388-like domain is fused with a domain homogous to the Methionine biosynthesis protein MetW (see below). In several Pseudomonas species, but also in Vibrio vulnificus and Azotobacter vinelandii PA0388 homologs are genomic neighbors of Nucleoside 5-triphosphatase  RdgB (dHAPTP, dITP, XTP-specific) (EC 3.6.1.15) and Methionine  biosynthesis protein MetW. On the other hand, in most Vibrio  species it appears as a part of a conserved operon involved in possible response to stress.
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.