SII-SWORD/CoKE huggingface dataset:
Pfam PF06938: Domain of unknown function (DUF1285), N-terminal domain (domain)
This domain is found at the N-terminal end of several hypothetical bacterial proteins, including SPO0140 from Ruegeria pomeroyi ([swissprot:Q5LWU5]). It folds into a a beta-meander-alpha-helix- beta-meander core bound to a twisted mixed six-stranded beta-sheet. Its specific function is unknown.
Pfam PF22892: MRPL44 dsRNA-binding domain (domain)
This double stranded RNA-binding domain is found in the Large ribosomal subunit protein mL44 protein.
Pfam PF05680: ATP synthase E chain (family)
This family consists of several ATP synthase E chain sequences which are components of the CF(0) subunit.
Wikipedia: ATP synthase subunit e, mitochondrial is an enzyme that in humans is encoded by the ATP5ME gene.
Pfam PF15457: Type III T3SS secreted effector HopW1-1/HopPmaA (family)
HopW1-1 is a family of bacterial modular P. syringae Avr effectors that induce accumulation of the signal molecule salicylic acid (SA) and the transcripts of HWI1 (HOPW1-1-INDUCED GENE1) in Arabidopsis. Thus HopW1-1 elicits a resistance response in Arabidopsis.
Pfam PF18549: Nitrosopumilus output domain 1 (domain)
NitrOD1 (Nitrosopumilus output domain 1) is found in thaumarchaea, either in stand-alone form or in combination with the Response_reg [pfam:PF00072] domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems).
Pfam PF19253: Family of unknown function (DUF5900) (family)
This is a family of uncharacterised proteins of unknown function found in viruses. These proteins are thought to include F-box domain containing proteins, a conserved domain present in numerous proteins, involved in protein- protein interaction.
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 PF03337: Poxvirus F12L protein (family)
The vaccinia virus F12L gene encodes a 65kDa protein called Protein OPG056 that is expressed late during infection and is important for plaque formation, EEV production and virulence. The F12L protein is located on intracellular enveloped virus (IEV) particles, but is absent from immature virions, intracellular mature virus and cell-associated enveloped virus. F12L shows co-localization with endosomal compartments and microtubules and appears to play a role in the the transport of IEV particles to the cell surface on microtubules. Together with protein OPG064/E2, forms a complex that interacts with host KLC2 (kinesin light chain isoform 2) to engage the kinesin-1 complex and thereby promote IEV trafficking .
Pfam PF19512: Domain of unknown function (DUF6046) (domain)
This family of presumed domains is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 196 and 222 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 PF08652: RAI1 like PD-(D/E)XK nuclease (family)
RAI1 is homologous to Caenorhabditis elegans DOM-3 and human DOM3Z and binds to a nuclear exoribonuclease.  It is required for 5.8S rRNA processing. Profile-profile comparison tools demonstrate this to be a PD-(D/E)XK nuclease, with a full set of canonical active site signature motifs characteristic to the PD-(D/E)XK nuclease superfamily.
Pfam PF17588: Family of unknown function (DUF5486) (family)
This is a family of unknown function found in Myoviridae.
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 PF17581: Family of unknown function (DUF5483) (family)
This is a family of unknown function found in Saccharomycetaceae.
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 PF11841: ELMO, armadillo-like helical domain (repeat)
This domain is found in eukaryotes and predominantly in ELMO (Elongation and Cell motility) proteins and corresponds to the armadillo repeats domain (ARR). It may play an important role in defining the functions of the ELMO family members and may be functionally linked to the ELMO domain in these proteins, being involved in protein-protein interactions.
Pfam PF03402: Vomeronasal organ pheromone receptor family, V1R (family)
This family represents one of two known vomeronasal organ receptor families, the V1R family (after).
Wikipedia: Vomeronasal receptors are a class of olfactory receptors that putatively function as receptors for pheromones. Pheromones have evolved in all animal phyla, to signal sex and dominance status, and are responsible for stereotypical social and sexual behaviour among members of the same species. In mammals, these chemical signals are believed to be detected primarily by the vomeronasal organ (VNO), a chemosensory organ located at the base of the nasal septum.
Pfam PF11685: Protein of unknown function (DUF3281) (family)
This family of bacterial 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 PF18685: Family of unknown function (DUF5635) (domain)
This is a domain of unknown function which is found at the C-terminal region of [pfam:PF13749] in actinobacteria.
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 PF05833: NFACT N-terminal and middle domains (family)
This family contains the N-terminal and middle domains of NFACT (NEMF, FbpA, Caliban, and Tae2) proteins from eukaryotes, archaea and bacteria. Many members of this family act in ribosome quality control (RQC), including RqcH, which are involved in the addition of a poly-Ala tail to defective translated proteins to tag them for degradation. This process is analogous to the ssrA/tmRNA bacterial system. However, some other NFACT family members, such as bacterial proteins FbpA in Listeria or PavA in Streptococcus, are exported (despite lack of a classical signal peptide) and behave as fibronectin-binding adhesins associated with virulence.
Pfam PF11906: Protein of unknown function (DUF3426) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 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 PF20755: Domain of unknown function (DUF6834), C-terminal domain (domain)
This presumed domain is found at the C terminus of Uncharacterized protein AF_2093 from Archaeoglobus fulgidus and similar proteins of unknown function from archaea.
Pfam PF06325: Ribosomal protein L11 methyltransferase (PrmA) (family)
This family consists of several Ribosomal protein L11 methyltransferase ([ec:2.1.1.-]) sequences.
Pfam PF10581: Synapsin N-terminal (domain)
This highly conserved domain of synapsin proteins has a serine at position 9 or 10 which is a phosphorylation site. The domain appears to be the part of the molecule that binds to calmodulin.
Pfam PF12343: DeaD helicase C-terminal disordered region (disordered)
This region family is found at the C-terminus of the DeaD helicase, which are involved in various cellular processes such as transcription, translation and DNA recombination. This region contains several repeats which contain an ERRE sequence motif.
Pfam PF24731: Domain of unknown function (DUF7683) (domain)
This family represents uncharacterised proteins found in bacteria. These proteins are related to members of [pfam:PF03513] which are described as immunity proteins. They are predicted to adopt similar structure composed of a four-stranded antiparallel beta-sheet with alpha-helices packed on one side of it.
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 PF00293: NUDIX domain (domain)
The Nudix superfamily is widespread among eukaryotes, bacteria, archaea and viruses and consists mainly of pyrophosphohydrolases that act upon substrates of general structure NUcleoside DIphosphate linked to another moiety, X (NDP-X) to yield NMP plus P-X. Such substrates include (d)NTPs (both canonical and oxidised derivatives), nucleotide sugars and alcohols, dinucleoside polyphosphates (NpnN), dinucleotide coenzymes and capped RNAs. However, phosphohydrolase activity, including activity towards NDPs themselves, and non-nucleotide substrates such as diphosphoinositol polyphosphates (DIPs), 5-phosphoribosyl 1-pyrophosphate (PRPP), thiamine pyrophosphate (TPP) and dihydroneopterin triphosphate (DHNTP) have also been described. Some superfamily members, such as Escherichia coli MutT, have the ability to degrade potentially mutagenic, oxidised nucleotides while others control the levels of metabolic intermediates and signalling compounds. In procaryotes and simple eukaryotes, the number of Nudix genes varies from 0 to over 30, reflecting the metabolic complexity and adaptability of the organism. Nudix hydrolases are typically small proteins, larger ones having additional domains with interactive or other catalytic functions .
Wikipedia: NUDIX hydrolases are a superfamily of hydrolytic enzymes capable of cleaving nucleoside diphosphates linked to x, hence their name. The reaction yields nucleoside monophosphate (NMP) plus X-P. Substrates hydrolysed by nudix enzymes comprise a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, dinucleoside and diphosphoinositol polyphosphates, nucleotide sugars and RNA caps, with varying degrees of substrate specificity. Enzymes of the NUDIX superfamily are found in all types of organisms, including eukaryotes, bacteria and archaea.
Pfam PF06067: Domain of unknown function (DUF932) (family)
Family of prokaryotic proteins with unknown function. Contains a number of highly conserved polar residues that could suggest an enzymatic activity.
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 PF18782: Novel AID APOBEC clade 2 (family)
A distnct family of AID/APOBEC deaminases found only in Amphibians.
Pfam PF08324: PUL domain (repeat)
The PUL (PLAP, Ufd3p and Lub1p) domain is a novel alpha-helical Ub-associated domain.  It directly binds to Cdc48, a chaperone-like AAA ATPase that collects ubiquitylated substrates.
Pfam PF06781: Cell division protein CrgA (family)
CrgA is a trans-membrane (TM) protein, first described in Streptomyces as being required for sporulation through the coordination of several aspects of reproductive growth. In Mtb (Mycobacterium tuberculosis ) CrgA is a central component of the divisome, and consists of 93 residues with two predicted TM helices (TM1: residues 29-51; and TM2: residues 66-88). CrgA facilitates the recruitment of the proteins essential for peptidoglycan synthesis to the divisome and also stabilizes the divisome. Reduced production of CrgA results in elongated cells and reduced growth rate, and loss of CrgA impairs peptidoglycan synthesis. CrgA has homologs in other actinomycetes.
Pfam PF00835: SNAP-25 family (family)
SNAP-25 (synaptosome-associated protein 25 kDa) proteins are components of SNARE complexes. Members of this family contain a cluster of cysteine residues that can be palmitoylated for membrane attachment.
Wikipedia: Synaptosomal-Associated Protein, 25kDa (SNAP-25) is a Target Soluble NSF (N-ethylmaleimide-sensitive factor) Attachment Protein Receptor (t-SNARE) protein encoded by the SNAP25 gene found on chromosome 20p12.2 in humans. SNAP-25 is a component of the trans-SNARE complex, which accounts for membrane fusion specificity and directly executes fusion by forming a tight complex that brings the synaptic vesicle and plasma membranes together.
Pfam PF13645: L,D-transpeptidase catalytic domain (domain)
This family is related to [pfam:PF03734].
Pfam PF14526: Integron-associated effector binding protein (domain)
This family contains Cass2 from Vibrio cholerae, an integron-associated protein that has been shown to bind cationic drug compounds with submicromolar affinity. Cass2 has been proposed to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and other closely-related species.
Pfam PF02682: Carboxyltransferase domain, subdomain C and D (family)
Urea carboxylase (UC) catalyses a two-step, ATP- and biotin-dependent carboxylation reaction of urea. It is composed of biotin carboxylase (BC), carboxyltransferase (CT), and biotin carboxyl carrier protein  (BCCP) domains. The CT domain of UC consists of four subdomains, named A, B, C and D. This domain covers the C and D subdomains of the CT domain. This domain covers the whole length of kipI (kinase A inhibitor) from Bacillus subtilis. It can also be found in S. cerevisiae urea  amidolyase Dur1,2, which is a multifunctional biotin-dependent enzyme with domains for urea carboxylase and allophanate (urea carboxylate) hydrolase activity.
Pfam PF08446: PAS fold (domain)
The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Wikipedia: A Per-Arnt-Sim (PAS) domain is a protein domain found in all kingdoms of life. Generally, the PAS domain acts as a molecular sensor, whereby small molecules and other proteins associate via binding of the PAS domain. Due to this sensing capability, the PAS domain has been shown as the key structural motif involved in protein-protein interactions of the circadian clock, and it is also a common motif found in signaling proteins, where it functions as a signaling sensor.
Pfam PF03422: Carbohydrate binding module (family 6) (family)
This entry represents CBM6 which was previously known as cellulose-binding domain family VI (CBD VI). CBM6 bind to amorphous cellulose, xylan, mixed beta-(1,3)(1,4)glucan and beta-1,3-glucan .

CBM6 adopts a classic lectin-like Î²-jelly roll fold, predominantly consisting of five antiparallel Î²-strands on one face and four antiparallel Î²-strands on the other face. It contains two potential ligand binding sites, named respectively cleft A and B. These clefts include aromatic residues which are probably involved in the substrate binding. The cleft B is located on the concave surface of one Î²-sheet, and the cleft A on one edge of the protein between the loop that connects the inner and outer Î²-sheets of the jellyroll fold . The multiple binding clefts confer the extensive range of specificities displayed by the domain .
A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins.

CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose . However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology.

Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see .
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF14600: Cellulose-binding domain (domain)
This C-terminal domain belongs to the CAZy family of carbohydrate-binding domains that are associated with glycosyl-hydrolases. It is suggested to bind cellulose.
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF14048: C-terminal domain of methyl-CpG binding protein 2 and 3 (family)
CpG-methylation is a frequently occurring epigenetic modification of vertebrate genomes resulting in transcriptional repression. This domain was found at the C-terminus of the methyl-CpG-binding domain (MBD) containing proteins MBD2 and MBD3, the latter was shown to not bind directly to methyl-CpG DNA but rather interact with components of the NuRD/Mi2 complex, an abundant deacetylase complex. The domain is subject to structure determination by the Joint Center of Structural Genomics.
Pfam PF21322: Lysine-specific demethylase 6/UTY, C-terminal helical domain (domain)
Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry incudes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also known as JMJD3) and the related histone demethylase UTY [. This is the C-terminal helical domain localised adjacent the JmjC domain.
Pfam PF24887: Stabilin-1/2, EGF-like domain (domain)
This entry represents EGF-like domains found in Stabilin-1 and 2 (STAB1/2), proteins that act as a scavenger receptor for acetylated low density lipoprotein. They bind Gram-positive and Gram-negative bacteria and may play a role in defense against bacterial infection. These proteins are also involved in the delivery of newly synthesized CHID1/SI-CLP (stabilin-1 interacting chitinase-like protein) from he biosynthetic compartment to the endosomal/lysosomal system.
Pfam PF00135: Carboxylesterase family (domain)
Higher eukaryotes have many distinct esterases. Among the different types are those which act on carboxylic esters (3.1.1). Carboxyl-esterases have been classified into three categories (A, B and C) on the basis of differential patterns of inhibition by organophosphates. The sequence of a number of type-B carboxylesterases indicates  that the majority are evolutionary related. As is the case for lipases and serine proteases, the catalytic apparatus of esterases involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.
Wikipedia: Carboxylesterase, type B is a family of evolutionarily related proteins that belongs to the superfamily of proteins with the Alpha/beta hydrolase fold.
Pfam PF17383: Uncharacterized KorC regulated protein A (family)
This is a family of unknown function found in Proteobacteria.
Pfam PF15402: MELT motif (conserved_site)
This entry represents MELT motifs found in the SPC7 and related proteins.
Pfam PF02196: Raf-like Ras-binding domain (domain)
Ras and heterotrimeric G proteins' alpha subunits are signal-transducing GTPases that cycle between inactive GDP-bound and active GTP-bound forms. The activities of these GTPases are regulated in part by GTPase-activating protein (GAPs) that stimulate hydrolysis of GTP, and guanine nucleotide exchange factors (GEFs) that stimulate GDP release. Ras and G alpha GTPases are prolific signalling molecules interacting with a spectrum of effector molecules and acting through more than one signalling pathway. The Ras-binding domain (RBD) is an independent domain of about 75 residues, which is sufficient for GTP-dependent binding of Ras and other G alpha GTPases. The RBD domain can be present singly or in tandem and it can be found associated with many other domains, such as PDZ, RGS, PID, PH, C1, DH, or protein kinase .

Structurally, the RBD domain of Raf-1 consists of a five-stranded mixed beta- sheet with an interrupted Î±-helix and two additional small Î±-helices. The structure of the RBD domain belongs to the ubiquitin Î±/Î² roll superfold and is similar to that of the RA domain despite the lack of significant sequence identity. The major interaction between Ras and Raf-1 RBD domain occurs between two antiparallel Î²-strands: Î²2 of Ras and Î²2 of RBD .

This entry represents the entire RBD domain.
Wikipedia: Raf-like Ras-binding domain is an evolutionary conserved protein domain. This is the Ras-binding domain found in proteins related to Ras.