SII-SWORD/CoKE huggingface dataset:
Pfam PF01476: LysM domain (domain)
The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation.  This domain may have a general peptidoglycan binding function. The structure of this domain is known.
Wikipedia: In molecular biology the LysM domain is a protein domain found in a wide variety of extracellular proteins and receptors. The LysM domain is named after the Lysin Motif which was the original name given to the sequence motif identified in bacterial proteins. The region was originally identified as a C-terminal repeat found in the Enterococcus hirae muramidase. The LysM domain is found in a wide range of microbial extracellular proteins, where the LysM domain is thought to provide an anchoring to extracellular polysaccharides such as peptidoglycan and chitin. LysM domains are also found in plant receptors, including NFP, the receptor for Nod factor which is necessary for the root nodule symbiosis between legumes and symbiotic bacteria. The LysM domain is typically between 44 and 65 amino acid residues in length. The structure of the LysM domain showed that it is composed of a pair of antiparallel beta strands separated by a pair of short alpha helices.
Pfam PF09738: LRRFIP family (family)
LRRFIP1 is a transcriptional repressor which preferentially binds to the GC-rich consensus sequence (5'- AGCCCCCGGCG-3') and may regulate expression of TNF,  EGFR and PDGFA.  LRRFIP2 may function as activator  of the canonical Wnt signalling pathway, in association with DVL3, upstream of CTNNB1/beta-catenin.
Pfam PF16907: Proline rich region of Caskin proteins (family)
This proline rich region is found in Caskin proteins. Caskins are CASK-binding synaptic scaffolding proteins. This region is predicted to be natively unstructured.  Its function is not known.
Pfam PF24756: CWZF3-5-7 THD domain (domain)
This domain is found in Cysteine-tryptophan domain-containing zinc finger proteins 3, 5 and 7 from Oryza sativa and related plant proteins. These proteins are involved in chromatin modification and gene expression regulation. They can bind to specific methylated forms of histone H3, facilitating the recruitment of various effectors to mediate gene expression. This domain has a significant similarity to the THD domain (TPRL with Handle Region Dimerization Domain) of AFF4, which is a scaffold protein that recruits other components of Super elongation complex. The THD domain is composed of alpha-helices and is involved in dimerisation. The domain represented by this entry is predicted to adopt similar structure and similarly could be involved in dimer formation.
Pfam PF14386: Domain of unknown function (DUF4417) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 220 and 340 amino acids in length. There is a single completely conserved residue G 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 PF15371: Domain of unknown function (DUF4599) (family)
The function of this family of eukaryotic proteins is not known.
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 PF22413: Methylated DNA-protein cysteine MeTransferase OGT N-terminal domain (domain)
This entry represents the N-terminal of methylated DNA-protein cysteine methyltransferase (MGMT, also known as 6-O- methylguanine-DNA methyltransferase and  MJ1529/OGT) from Methanocaldococcus jannaschii and similar sequences. This entry corresponds to the ribonuclease-like domain associated with 6-O-methylguanine DNA methyltransferase activity.
Pfam PF00764: Arginosuccinate synthase N-terminal HUP domain (domain)
This entry represents the N-terminal domain of the Arginosuccinate synthase enzyme. This domain is part of the HUP superfamily.
Wikipedia: Argininosuccinate synthase or synthetase is an enzyme that catalyzes the synthesis of argininosuccinate from citrulline and aspartate. In humans, argininosuccinate synthase is encoded by the ASS gene located on chromosome 9.
Pfam PF01678: Diaminopimelate epimerase (domain)
Diaminopimelate epimerase contains two domains of the same alpha/beta fold, both contained in this family.
Wikipedia: In enzymology, a diaminopimelate epimerase is an enzyme that catalyzes the chemical reactionLL-2,6-diaminoheptanedioate  meso-diaminoheptanedioate
Pfam PF22502: tRNA-intron endonuclease SEN2-like, N-terminal domain (domain)
This entry represents a tRNA-intron endonuclease SEN2-like N-terminal domain in a splicing endonuclease from Aeropyrum pernix.
Pfam PF16591: Helical bimodular sensor domain (family)
The HBM sensor domain has been identified primarily in bacterial chemoreceptors but is also present on histidine kinases. Characteristic features of this domain are its size of approximately 250 amino acids and its location in the bacterial periplasm. The McpS chemoreceptor of Pseudomonas putida KT2440 was found to possess an HBM sensor domain and its 3D structure in complex with physiologically relevant ligands has been reported. This domain is composed of 2 long and 4 short helices that form two modules each composed of a 4-helix bundle. The McpS chemoreceptor mediates chemotaxis towards a number of organic acids. Both modules of the McpS HBM domain contain a ligand binding site. Chemo-attractants binds to each of these sites and their binding was shown to trigger a chemotactic response. This domain is primarily found in different proteobacteria but also in archaea. Interestingly, amino acids in both ligand binding sites showed a high degree of conservation suggesting that members of this family sense similar ligands. This domain recognises Multiple TCA cycle intermediates, citrate and alpha-ketoglutarate (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF09339: IclR helix-turn-helix domain (domain)
The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including:
 * gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces.


 * iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium.


These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins .
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF08816: Inhibitor of vertebrate lysozyme (Ivy) (family)
This bacterial family is a strong inhibitor of vertebrate lysozyme.
Pfam PF11898: Domain of unknown function (DUF3418) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 582 to 594 amino acids in length. This domain is found associated with [pfam:PF07717], [pfam:PF00271], [pfam:PF04408].
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 PF13746: 4Fe-4S dicluster domain (domain)
This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.
Wikipedia: 
Iron–sulfur proteins are proteins characterized by the presence of iron–sulfur clusters containing sulfide-linked di-, tri-, and tetrairon centers in variable oxidation states. Iron–sulfur clusters are found in a variety of metalloproteins, such as the ferredoxins, as well as NADH dehydrogenase, hydrogenases, coenzyme Q – cytochrome c reductase, succinate – coenzyme Q reductase and nitrogenase. Iron–sulfur clusters are best known for their role in the oxidation-reduction reactions of electron transport in mitochondria and chloroplasts. Both Complex I and Complex II of oxidative phosphorylation have multiple Fe–S clusters. They have many other functions including catalysis as illustrated by aconitase, generation of radicals as illustrated by SAM-dependent enzymes, and as sulfur donors in the biosynthesis of lipoic acid and biotin. Additionally, some Fe–S proteins regulate gene expression. Fe–S proteins are vulnerable to attack by biogenic nitric oxide, forming dinitrosyl iron complexes. In most Fe–S proteins, the terminal ligands on Fe are thiolate, but exceptions exist.
Pfam PF00749: tRNA synthetases class I (E and Q), catalytic domain (domain)
Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).
Wikipedia: The aminoacyl-tRNA synthetases catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossmann fold catalytic domain and are mostly monomeric. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices, and are mostly dimeric or multimeric, containing at least three conserved regions. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases.
Pfam PF09853: Putative transposon-encoded protein (DUF2080) (family)
This domain, found in various hypothetical archaeal 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 PF14562: Restriction endonuclease BglI (domain)
This restriction endonuclease binds DNA as a dimer. BglI recognises and cleaves the interrupted DNA sequence GCCNNNNNGGC and cleaves between the fourth and fifth unspecified base pair to produce 3' overhanging ends.
Pfam PF10169: LLP homolog (family)
This is a family of LLP homolog (LLPH) proteins found in metazoa. In ash-black slug this proteins was found to be involved  in the regulation of neuronal cell adhesion and/or movement and synapse attachment. Another member of this family from Aplysia kurodai was found to bind to the ApC/EBP (Aplysia CCAAT/enhancer binding protein) promoter and activates the transcription of ApC/EBP mRNA. In humans, LLPH plays a role in the ribosome biogenesis as one of the pre-60S assembly factors.
Pfam PF23041: Domain of unknown function (DUF7036) (domain)
This entry represents a predicted ferredoxin-like domain found in a family of uncharacterized plant proteins. This group of proteins typically has this domain duplicated.
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 PF19116: Domain of unknown function (DUF5801) (domain)
This entry contains a domain that is found as tandem repeats in a number of bacterial proteins. The domain is rich in negatively charged amino acids and contains multiple potential calcium binding sites.
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 PF19311: KELAA motif (conserved_site)
This short motif is found at the C-terminus of FHIP proteins, FAM160B proteins and UPF0518 family proteins. It has a conserved KELAA sequence for which it is named.
Pfam PF06795: Erythrovirus X protein (family)
This family consists of several Erythrovirus X proteins which seem to be found exclusively in human parvovirus and human erythrovirus. The function of this family is unknown.
Pfam PF00777: Glycosyltransferase family 29 (sialyltransferase) (family)
Members of this family belong to glycosyltransferase family 29.
Wikipedia: Sialyltransferases are enzymes that transfer sialic acid to nascent oligosaccharide. Each sialyltransferase is specific for a particular sugar substrate. Sialyltransferases add sialic acid to the terminal portions of the sialylated glycolipids (gangliosides) or to the N- or O-linked sugar chains of glycoproteins.
Pfam PF14706: Transposase DNA-binding (domain)
This domain occurs at the C-terminus of transposases including E. coli tnpA ([swissprot:Q46731]). TnpA encodes a transposase and an inhibitor protein, the inhibitor only differs from the transposase by the absence of the N-terminal 55 amino acids, which includes most of this domain. This domain consists of alpha helices and turns, and functions as a DNA-binding domain.
Pfam PF23364: MAX effector (family)
This entry represents a family of MAX effectors (for Magnaporthe Avrs and ToxB like) from Magnaporthe oryzae (Rice blast fungus) that share a conserved beta-sandwich structure.
Pfam PF23840: Phage tail terminator protein (domain)
This entry represents a family of phage tail terminator proteins. These proteins form a hexameric ring at the top of the phage tail tube in the neck of the phage.
Pfam PF13247: 4Fe-4S dicluster domain (domain)
Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.
Wikipedia: Nitrate reductases are molybdoenzymes that reduce nitrate to nitrite. This reaction is critical for the production of protein in most crop plants, as nitrate is the predominant source of nitrogen in fertilized soils.
Pfam PF22812: Plant cysteine-rich protein domain (domain)
This domain is found in a group of plant cysteine-rich proteins, including Cysteine-rich repeat secretory protein 1 from Arabidopsis thaliana. This domain is usually found C-terminal to two copies of [pfam:PF01657]. It is predicted to adopt an alpha -helical structure.
Pfam PF01681: C6 domain (family)
This domain of unknown function is found in the C. elegans protein [swissprot:Q19522]. It is presumed to be an extracellular domain.  The C6 domain contains six conserved cysteine residues in most copies of the domain. However some copies of the domain are missing cysteine residues 1 and 3 suggesting that these form a disulphide bridge.
Pfam PF07517: SecA DEAD-like domain (domain)
SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the [pfam:PF00270].
Wikipedia: The SecA protein is a cell membrane associated subunit of the bacterial Sec or Type II secretory pathway, a system which is responsible for the secretion of proteins through the cell membrane. Within this system the SecA ATPase forms a translocase complex with the SecYEG channel, thereby driving the movement of the protein substrate across the membrane.
Pfam PF05098: Late expression factor 4 (LEF-4) (family)
Late expression factor 4 (LEF-4) is one of the Baculovirus late expression factor proteins. LEF-4 carries out all the enzymatic functions related to  mRNA capping.
Pfam PF10505: NMDA receptor-regulated gene protein 2 C-terminus (domain)
The transition of neuronal cells from pre-cursor to mature state is regulated by the N-methyl-d-aspartate (NMDA) receptor, a glutamate-gated ion channel that is permeable to Ca2+. NMDA receptors probably mediate this activity by permitting expression of NARG2.  NARG2 is transiently expressed, being a regulatory protein that is present in the nucleus of dividing cells and then down-regulated as progenitors exit the cell cycle and begin to differentiate. NARG2 contains repeats of (S/T)PXX, (11 in mouse , six in human), a putative DNA-binding motif that is found in many gene-regulatory proteins including Kruppel, Hunchback and Antennapedi.
Pfam PF04794: YdjC-like protein (family)
Family of YdjC-like proteins.  This region is possibly involved in the the cleavage of cellobiose-phosphate.
Pfam PF06517: Orthopoxvirus A43R protein (family)
This family consists of several Orthopoxvirus A43R proteins. The function of this family is unknown.
Pfam PF18032: Photoprotection regulator fluorescence recovery protein (domain)
This family includes fluorescence recovery protein (FRP) domain, which is found in Synechocystis sp. PCC 6803 substr. Kazusa. FRP causes the dissociation of the orange carotenoid protein (OCP) from the phycobilisomes by interacting with the C-terminal domain of OCP, accelerating the conversion of the active red OCP to the inactive orange form. A patch of residues (W50, D54, H53, and R60), contributed by both chains of the FRP dimer cause the acceleration of the OCPr to OCPo conversion. Mutation of the absolutely conserved amino acids (R60) affect the activity of FRP.
Pfam PF00414: Neuraxin and MAP1B repeat (repeat)
In microtubule-associated protein 1B (MAP1B) the basic region containing the KKEE and KKEVI motifs is responsible for the interaction between MAP1B and microtubulesin vivo. This region bears no sequence relationship to the microtubule binding domains of kinesin, MAP2, or tau . Neuraxin is a putative structural protein of the rat central nervous system that is immunologically related to microtubule-associated protein 5 (MAP5). Neuraxin may be implicated in neuronal membrane-microtubule interactions .

Both proteins contain a region that consists of 12 tandem repeats of a 17 residues motif.
Pfam PF13526: Protein of unknown function (DUF4125) (family)
This family of proteins is functionally uncharacterised.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF05528: Accessory protein 5b, avian coronavirus (family)
Avian infectious bronchitis virus, a member of Coronaviridae family, has a single-stranded positive-sense RNA genome, which is 27 kb in length. Gene 5 contains two (5a and 5b) open reading frames. This entry represents the host translation inhibitor 5b (ORF 5b, also known as accessory protein 5b) which is involved in host translation shut off without degrading host RNA. It suppresses host gene expression which facilitates evasion from host type I interferon immune response.
Pfam PF03883: Peroxide stress protein YaaA (domain)
YaaA is a key element of the stress response to H2O2. It acts by reducing the level of intracellular iron levels after peroxide stress, thereby attenuating the Fenton reaction and the DNA damage that this would cause. The molecular mechanism of action is not known.
Pfam PF10247: Reactive mitochondrial oxygen species modulator 1 (family)
This is a family of small, approximately 100 amino acid, proteins found from yeasts to humans. The majority of endogenous reactive oxygen species (ROS) in cells are produced by the mitochondrial respiratory chain. An increase or imbalance in ROS alters the intracellular redox homeostasis, triggers DNA damage, and may contribute to cancer development and progression. Members of this family are mitochondrial reactive oxygen species modulator 1 (Romo1) proteins that are responsible for increasing the level of ROS in cells. Increased Romo1 expression can have a number of other effects including: inducing premature senescence of cultured human fibroblasts and increased resistance to 5-fluorouracil.
Pfam PF23726: RSE1/DDB1/CPSF1 second beta-propeller (repeat)
This entry represents the second beta-propeller found in RSE1/SF3B3/ DDB1/CPSF1/CFT1 proteins in eukaryotes, which share a domain architecture consisting of three beta-propellers. Members of the family have diverse functions, primarily related to RNA/DNA binding.  Pre-mRNA-splicing factor RSE1 plays an important role in the spliceosome, a complex that removes introns from pre-mRNAs. Its orthologue, splicing factor 3B subunit 3 (SF3B3) also forms part of the U2 small nuclear ribonucleoprotein particle (snRNP) and has been identified as part of the SAGA transcriptional coactivator complex in Drosophila melanogaster. Also included in this entry is DNA damage -binding protein 1 (DDB1), which is both involved in the recognition and repair of UV-induced DNA damage, as part of the UV-DDB complex, and in protein ubiquitination, as part of the DCX (DDB1-CUL4-X-box) complex. Additionally, this family includes cleavage and polyadenylation specificity factor subunit 1 (CPSF1) and its orthologue protein CFT1, both involved in the cleavage and polyadenylation of pre-mRNAs, for which this entry is a partial match.