SII-SWORD/CoKE huggingface dataset:
Pfam PF11253: Protein of unknown function (DUF3052) (family)
This family of proteins with unknown function appears to be restricted to 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 PF14676: FANCI solenoid 2 (repeat)
This is the solenoid 2 (S2) domain of the Fanconi anemia group I protein.
Pfam PF14481: Type 4 fimbrial biogenesis protein PilY2 (domain)
Members of this family were experimentally shown to be involved in fimbrial biogenesis, but its exact role appears to be unknown. This entry represents a structural domain with an OB-fold.
Pfam PF09271: LAG1, DNA binding (domain)
Members of this family are found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding.  This domain is also known as RHR-N (Rel-homology region) as it related to Rel domain proteins.
Pfam PF16951: Putative methionine and alanine importer, small subunit (family)
MaAIMP_sms is a family of hypothetical proteins from Proteobacteria that purported to be small subunits of a methionine and alanine importer.
Pfam PF19707: Family of unknown function (DUF6204) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001070) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the kirromycin biosynthetic  gene cluster from Streptomyces collinus Tu 365. This family appears to be predominantly found 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 PF11030: Nucleocapsid protein N (family)
This is the N protein of the nucleocapsid. The nucleocapsid functions to protect the RNA against nuclease degradation and to promote it's reverse transcription. The NC protein promotes viral RNA dimerisation and encapsidation and initiates reverse transcription by activating the annealing of the primer tRNA to the initiation site.
Pfam PF00576: HIUase/Transthyretin family (domain)
This family includes transthyretin that is a thyroid hormone-binding protein that transports thyroxine from the bloodstream to the brain.  However, most of the sequences listed in this family do not bind thyroid hormones. They are actually enzymes of the purine catabolism that catalyse the conversion of 5-hydroxyisourate (HIU) to OHCU.  HIU hydrolysis is the original function of the family and is conserved from bacteria to mammals; transthyretins arose by gene duplications in the vertebrate lineage. HIUases are distinguished in the alignment from the conserved C-terminal YRGS sequence.
Pfam PF11904: ANKRD13 C-terminal (domain)
This domain, and the associated ANK family repeat [pfam:PF00023] domain, are found in ANKRD13 of which at least 4 subtypes are known to exist, termed A-D. ANKRD13C act as a chaperone for biogenesis and folding of the DP receptor for prostaglandin D2. ANKRD13A/B/D are ubiquitin-binding proteins that specifically  recognise and bind Lys-63-linked ubiquitin. They positively regulate the internalisation of ligand-activated EGFR by binding to the Ub moiety of ubiquitinated EGFR at the cell membrane.
Pfam PF11972: HTH DNA binding domain (domain)
This is a helix-turn-helix DNA binding domain.
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 PF17623: Domain of unknown function (family)
This is a family of unknown function, however family members such as B277 have been suggested to play a role in viral 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 PF18812: phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3 (domain)
A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements. The predicted active site contains a conserved histidine and threonine residues.
Pfam PF21242: ECT2, PH domain (domain)
ECT2 (Epithelial Cell Transforming Sequence 2) is a guanine nucleotide exchange factor (GEF) that catalyses the exchange of GDP for GTP. It is a cell cycle regulator that plays key roles in cytokinesis. ECT2 contains triple copies of the BRCT domain (BRCT0, BRCT1 ([pfam:PF12738]) and BRCT2 ([pfam:PF00533]) at the N-terminal, separated from the C-terminal DH ([pfam:PF00621]) and PH domains by a linker of about 100 residues. This entry represents the PH domain. The BRCT and DH-PH domains mediate intra-molecular interactions that restrains ETC2 activity during interphase.
Pfam PF10180: WKF domain (domain)
This is the C-terminal conserved region of a family of proteins found from fungi to humans. The domain is named WKF after a conserved sequence motif. This domain has been shown to bind RNA. This domain was previously known as DUF2373.
Pfam PF24933: Domain of unknown function (DUF7751) (domain)
This domain is found in a group of uncharacterised plant proteins with the AAA domain ([pfam:PF00004]). This domain is predicted to adopt an all alpha configuration.
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 PF17428: Family of unknown function (DUF5412) (family)
This is a family of unknown function found in Bacteria. Members of this family have one or two predicted trans-membrane regions.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09512: Thiamine-precursor transporter protein (ThiW) (family)
Levels of thiamine pyrophosphate (TPP) or thiamine regulate transcription or translation of a number of thiamine biosynthesis, salvage, or transport genes in a wide range of prokaryotes. The mechanism involves direct binding, with no protein involved, to a structural element called THI found in the untranslated upstream region of thiamine metabolism gene operons. This element is called a riboswitch and is seen also for other metabolites such as FMN and glycine. This protein family consists of proteins identified in operons controlled by the THI riboswitch and designated ThiW. The hydrophobic nature of this protein and reconstructed metabolic background suggests that this protein acts in transport of a thiazole precursor of thiamine.
Pfam PF17958: EF-hand domain (domain)
This entry represents an EF-hand domain found in one of the regulatory B subunits of PP2A.
Wikipedia: The EF hand is a helix–loop–helix structural domain or motif found in a large family of calcium-binding proteins.
Pfam PF23284: Transcription elongation factor SPT5, second KOW domain (domain)
This entry includes Transcription elongation factor SPT5, a component of the elongation factor DRB-sensitivity inducing factor (DSIF) that plays multiple roles during transcription. SPT5 is a multidomain protein consisting of an N-terminal NusG domain ([pfam:PF03439]), tandem of KOW domains and and a mobile C-terminal-repeat region. This entry represents the second KOW domain.
Pfam PF07507: WavE lipopolysaccharide synthesis (family)
These proteins are encoded by putative wav gene  clusters, which are responsible for the synthesis of the core oligosaccharide (OS) region of  Vibrio cholerae lipopolysaccharide.
Pfam PF06741: LsmAD domain (domain)
This domain is found associated with Lsm domain.
Pfam PF00243: Nerve growth factor family (domain)
During the development of the vertebrate nervous system, many neurons become redundant (because they have died, failed to connect to target cells, etc.) and are eliminated. At the same time, developing neurons send out axon outgrowths that contact their target cells . Such cells control their degree of innervation (the number of axon connections) by the secretion of various specific neurotrophic factors that are essential for neuron survival. One of these is nerve growth factor (NGF or beta-NGF), a vertebrate protein that stimulates division and differentiation of sympathetic and embryonic sensory neurons . NGF is mostly found outside the central nervous system (CNS), but slight traces have been detected in adult CNS tissues, although a physiological role for this is unknown ; it has also been found in several snake venoms .

NGF is a protein of about 120 residues that is cleaved from a larger precursor molecule. It contains six cysteines all involved in intrachain disulphide bonds. A schematic representation of the structure of NGF is shown below:

                                    +------------------------+
                                    |                        |
                                    |                        |
        xxxxxxCxxxxxxxxxxxxxxxxxxxxxCxxxxCxxxxxCxxxxxxxxxxxxxCxCxxxx
              |                          |     |               |
              +--------------------------|-----+               |
                                         +---------------------+


'C': conserved cysteine involved in a disulphide bond.

This entry also contains NGF-related proteins such as neutrophin 3, which promotes the survival of visceral and proprioceptive sensory neurons, and brain-derived neurotrophin, which promotes the survival of neuronal populations that are located either in the central nervous system or directly connected to it .
Wikipedia: Neurotrophins are a family of proteins that induce the survival, development, and function of neurons.
Pfam PF12172: ChsH2, rubredoxin-like zinc ribbon domain (domain)
This domain is found at the C-terminal end of the probable enoyl -CoA hydratase alpha subunit from Thermomonospora curvata (ChsH2) and similar archaeal and bacterial proteins. ChsH2 is likely to be involved in bile acid degradation. The C-terminal region of this protein is organised into two domains: an N-terminal zinc finger domain with a three-stranded antiparallel beta-sheet and an N-terminal alpha-helix (this entry) and a OB-fold domain ([pfam:PF01796]). The domain is duplicated in some members like [swissprot:O53566] from M.tuberculosis. The structure of [swissprot:Q97WQ4] from Saccharolobus solfataricus reveals two long N-terminal helices followed by a rubredoxin -like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment.
Pfam PF22853: Protelomerase TelK-like N-terminal domain (domain)
This entry represents the N-terminal domain of protelomerase TelK from Klebsiella phage phiKO2 and similar proteins from tailed bacteriophages and bacterial prophages. TelK is a hairpin telomere resolvase with DNA cleavage-rejoining activity that resolves the catenated circular dimer produced from the bidirectional replication of a chromosome. The core of the TelK monomer consists of an N-terminal domain and a catalytic domain connected by a long alpha- helical linker. However, there are two extensions of the protein: a C-terminal DNA binding domain named the stirrup ([pfam:PF20818]) and an N-terminal domain containing an insertion, called the muzzle domain ([pfam:PF20849]).
Pfam PF11595: Protein of unknown function (DUF3245) (family)
This is a family of proteins conserved in fungi. The function is not known, and there is no S. cerevisiae member.
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 PF09931: Bacteriophage phiJL001, Gp84, N-terminal (domain)
This domain is found in a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus (Rhodopseudomonas capsulata) gene transfer agent, which packages DNA.
Pfam PF21077: Glutamate dehydrogenase, ACT3 domain (domain)
Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia. The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises three ACT-like (ACT1-3) and PAS-type domains which could act as metabolic sensors for allosteric regulation. This entry represents ACT3 domain.
Pfam PF08668: HDOD domain (domain)
The HD domain, named after the conserved doublet of predicted catalytic residues, is found in a wide range of bacterial, archaeal and eukaryotic proteins. It defines a superfamily of phosphohydrolases that can catalyze both metal-dependent and -independent phosphomonoesterase and phosphodiesterase reactions for a broad range of substrates . The HD-domain proteins appear to be involved in nucleic acid and nucleotide metabolism, signal transduction and possibly other functions. They are diverse in terms of both domain architecture and phylogenetic distribution; each of the completely sequenced genomes encodes more than one version of this domain.

The HD domain is composed of a bundle of Î± helices with a 5-helix core. Although all HD domains share key design features, a striking diversity of catalytic centres have been identified, containing no metal, mono-, bi- or trinuclear metal binding sites .

The HD-related output domain (HDOD) is a protein domain of unknown function. Proteins containing the HDOD are widespread in diverse bacteria; it can be present as a stand-alone domain, and also associated with other domains, such as response regulatory (RR), GGDEF, and EAL, suggesting a role in regulation and signaling . Proteins containing this domain include CdgJ from Vibrio cholerae serotype O1. CdgJ is a phosphodiesterase (PDE) that catalyzes the hydrolysis of cyclic diguanylate (c-di-GMP) .
Pfam PF10707: PhoP regulatory network protein YrbL (family)
This is a family of proteins that are activated by PhoP. PhoP protein controls the expression of a large number of genes that mediate adaptation to low Mg2+ environments and/or virulence in several bacterial species. YbrL is proposed to be acting in a loop activity with PhoP and PrmA analogous to the multicomponent loop in Salmonella where the PhoP-dependent PmrD protein activates the regulatory protein PmrA, and the activated PmrA then represses transcription from the PmrD promoter which harbours binding sites for both the PhoP and PmrA proteins. Expression of YrbL is induced in low Mg2+ in a PhoP-dependent fashion and repressed by Fe3+ in a PmrA-dependent manner.
Pfam PF07198: Protein of unknown function (DUF1410) (domain)
This family represents a conserved domain approximately 100 residues long, multiple copies of which are found within hypothetical Ureaplasma parvum proteins of unknown function, as well as related species.
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 PF12759: InsA C-terminal domain (domain)
This short domain is found at the C-terminus of the InsA protein. This domain contains a helix-turn-helix domain.
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 PF23487: TMEM132 sixth domain (domain)
This is the sixth domain of TMEM132 family of proteins which includes TMEM132A-E, transmembrane proteins that regulate neuronal structure and function. In mammalian cells, they may regulate NAP1 in the WAVE regulatory complex (WRC) to finely modulate actin nucleation, cellular cytoskeletal and morphological changes. TMEM132D member has been associated with panic disorders, anxiety and major depressive disorders. These proteins consist of six domains: N-terminal [pfam:PF15705], 2nd [pfam:PF23481], 3rd [pfam:PF23039], forth [pfam:PF16070], a fifth and a sixth. The latter three are a tandem of Ig-like domains. [pfam:PF15706] represents the C-terminal region which includes the single transmembrane helix.
Pfam PF13301: Protein of unknown function (DUF4079) (family)
This is an uncharacterised family of proteins.
Pfam PF00553: Cellulose binding domain (domain)
Two tryptophan residues are involved in cellulose binding. Cellulose binding domain found in bacteria.
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 PF07390: Mycoplasma P30 protein (family)
This family consists of several P30 proteins which seem to be specific to Mycoplasma agalactiae. P30 is a 30-kDa immunodominant antigen and is known to be a transmembrane protein.
Pfam PF01710: Transposase (domain)
Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily.
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 PF24608: Phage putative PDDEXK endonuclease (domain)
This entry represents a family family of phage proteins that are structurally related to the PD-(D/E)XK nuclease superfamily. The highest structural similarity is to Holliday junction resolvase Hjc proteins. The exact function of this protein family is unknown.
Pfam PF20443: Lamina-associated polypeptide 1, N-terminal (domain)
Torsin-1A-interacting proteins 1 and 2 (TOIP 1/2) also known as LAP1 proteins (Lamina-associated polypeptide 1) are type 2 integral membrane proteins with a single membrane-spanning region of the inner nuclear membrane. These proteins interact with and activate Torsin A, an AAA+ ATPase localised to the endoplasmic reticulum (ER) through a perinuclear domain, and forms a heterohexameric (LAP1-Torsin)3 ring that targets Torsin to the nuclear envelope. LAP1 has an atypical AAA+ fold and provides an arginine finger to the Torsin A active site to promote its ATPase activity. A single mutation in Torsin A causes early onset primary dystonia, a painful and severely disabling neuromuscular disease. This entry represents the N-terminal domain of LAP1 which contains transmembrane helices.
Pfam PF21906: NrtR DNA-binding winged helix domain (domain)
This entry represents the C-terminal DNA-binding domain of bacterial transcriptional regulator NrtR which is involved in regulating the transcription of NAD biosynthetic genes. This domain has a winged helix-turn-helix structure.
Pfam PF01453: D-mannose binding lectin (repeat)
These proteins include mannose-specific lectins from plants as well as bacteriocins from bacteria.
Pfam PF15975: Flotillin (family)
Flotillin is a family of lipid-membrane-associated proteins found in bacteria, archaea and eukaryotes.  The family is found in association with [pfam:PF01145], another integral membrane-associated domain. Flotillins in vertebrates are associated with sphingolipids and cholesterol-enriched membrane microdomains known as lipid-rafts. These rafts along with other membrane components are important in cell-signalling. Flotillins in other organisms have roles in viral pathogenesis, endocytosis, and membrane shaping.
Pfam PF19245: Family of unknown function (DUF5893) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Marseillevirus.
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.