SII-SWORD/CoKE huggingface dataset:
Pfam PF04007: Protein of unknown function (DUF354) (family)
Members of this family are around 350 amino acids in length. They are found in archaebacteria and have 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 PF17445: Mating factor A1 (disordered)
Many pathogenic fungi undergo morphological changes in order to infect their hosts. The Ustilago maydis pathogenic cycle starts when two mating compatible haploid yeast cells recognize each other via a pheromone-receptor system which is encoded by two sets of genes a and b. The a locus (a1 and a2) controls the cell fusion by encoding intercellular recognition system consisting of precursors (mfa1 and mfa2) and receptors (pra1 and pra2) of lipopeptide pheromones. The open reading frame codes for a 42-amino acid precursor, which is processed to a shorter peptide of 13 amino acids. The terminal CAAX motif is typical of farnesylated fungal pheromones, in which the last three amino acids are removed during farnesylation of the cysteine residue. This terminal cysteine is known to be Omethylated in several fungal pheromones. Mating leads to the formation of a dikaryon filament, whose apical tip differentiates into a specialized structure for plant penetration known as the appressorium. Once inside the plant, U. maydis proliferates, inducing the formation of tumours and eventually develops into diploid spores. This mating process requires cross-talk between cAMP and mitogen-activated protein kinase (MAPK) signaling. Upstream regulation of a locus has been demonstrated where Hos2 (Histone deacetylases (HDACs) plant homologue) directly regulates the expression of U. maydis mating-type genes downstream of the cAMP-PKA pathway. Furthermore, pheromone recognition blocks cell cycle progression in U. maydis cells in order to prepare mating partners for conjugation where cells undergo arrest in G2 phase. This entry relates to the domain found in Mfa1 proteins in Ustilgo maydis and U. hordei.
Pfam PF09191: CD4, extracellular (domain)
Members of this family adopt an immunoglobulin-like beta-sandwich, with seven strands in 2 beta sheets, in a Greek key topology. They are predominantly found in the extracellular portion of CD4 proteins, where they enable interaction with major histocompatibility complex class II antigens.
Wikipedia: In molecular biology, CD4 is a glycoprotein that serves as a co-receptor for the T-cell receptor (TCR). CD4 is found on the surface of immune cells such as helper T cells, monocytes, macrophages, and dendritic cells. It was discovered in the late 1970s and was originally known as leu-3 and T4 before being named CD4 in 1984. In humans, the CD4 protein is encoded by the CD4 gene.
Pfam PF13991: BssS protein family (family)
The BssS protein family is a group of proteins that are involved in regulation of biofilm formation.  Proteins in this family are approximately 80 amino acids in length.
Pfam PF06737: Transglycosylase-like domain (domain)
This family of proteins are very likely to act as transglycosylase enzymes related to [pfam:PF00062] and [pfam:PF01464]. These other families are weakly matched by this family, and include the known active site residues.
Pfam PF24675: 16S rRNA (adenine(1408)-N(1))-methyltransferase (family)
This entry represents the 16S rRNA (adenine(1408)-N(1))-methyltransferase.
Pfam PF01263: Aldose 1-epimerase (family)
Aldose 1-epimerase (5.1.3.3) (mutarotase) is the enzyme responsible for the anomeric interconversion of D-glucose and other aldoses between their alpha- and beta-forms. Glucose-6-phosphate 1-epimerase (5.1.3.3) has been shown to catalyse the interconversion between the alpha and beta anomers from at least three hexose 6-phosphate sugars (Glc6P, Gal6P, and Man6P) .
Pfam PF08363: Glucan-binding protein C (family)
This domain is found in the Streptococcus Glucan-binding protein C (GbpC) and also in surface protein antigen (Spa)-family proteins which show sequence similarity to GbpC.
Pfam PF02110: Hydroxyethylthiazole kinase family (domain)
Most microorganisms and plants can synthesise thiamin de novo . In this de novo pathway, the thiazole and pyrimidine moieties of thiamin are made separately and coupled together to form thiamin phosphate. For the thiazole moiety, 4-methyl-5-(2-hydroxyethyl)thiazole (THZ), the key salvage step is phosphorylation to give 4-methyl-5-(2-phosphonooxyethyl)thiazole (THZ-P). The enzyme hydoxyethylthiazole kinase (2.7.1.50) is responsible for this step. Hydoxyethylthiazole kinase is encoded by thiM in Escherichia coli  and other bacteria , and by the C-terminal region of bifunctional proteins in some cases, such as Saccharomyces cerevisiae, in which the N-terminal domain corresponds to the bacterial thiamine-phosphate pyrophosphorylase (2.5.1.3), ThiE . ThiM constitutes a potential target for pro-drug compounds for antibacterial drug development.

The Arabidopsis and maize genomes encode homologues of ThiM .
Wikipedia: In enzymology, a hydroxyethylthiazole kinase is an enzyme that catalyzes the chemical reactionATP + 4-methyl-5-(2-hydroxyethyl)thiazole  ADP + 4-methyl-5-(2-phosphonooxyethyl)thiazole
Pfam PF05728: Uncharacterised protein family (UPF0227) (domain)
Despite being classed as uncharacterised proteins, the members of this family are almost certainly enzymes that are distantly related to the [pfam:PF00561].
Pfam PF02769: AIR synthase related protein, C-terminal domain (domain)
This family includes Hydrogen expression/formation protein  HypE [swissprot:P24193], AIR synthases [swissprot:P08178] [ec:6.3.3.1], FGAM synthase [swissprot:P35852] [ec:6.3.5.3] and selenide, water dikinase [swissprot:P16456] [ec:2.7.9.3]. The function of the C-terminal domain of AIR synthase is unclear, but the cleft formed between N and C domains is postulated as a sulphate binding site.
Pfam PF12012: Domain of unknown function (DUF3504) (family)
This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 156 to 173 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 PF21763: DHH-CID domain (domain)
DHH-CID (CMG Interacting Domain) domain is found in proteins that are members of DHH phosphatase family. This domain is located between the catalytic domains and consists of array of four helices with two 'kissing' loops. The DHH-CID domain contains H2TH motif and is structurally very similar to proteins members of S13-like H2TH superfamily.
Pfam PF17590: Family of unknown function (DUF5488) (family)
This is a family of unknown function found in Orthopoxvirus.
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 PF04236: Tc5 transposase C-terminal domain (domain)
This family corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA binding (pers. obs. A Bateman).
Pfam PF04930: FUN14 family (family)
This family of short proteins are found in eukaryotes and some archaea.  Although the function of these proteins is not known they may contain transmembrane helices.
Pfam PF03763: Remorin, C-terminal region (family)
Remorins are plant-specific plasma membrane-associated proteins. In tobacco remorin co-purifies with lipid rafts. Most remorins have a variable, proline-rich N-half and a more conserved C-half that is predicted to form coiled coils. Consistent with this, circular dichroism studies have demonstrated that much of the protein is alpha-helical. Remorins exist in plasma membrane preparations as oligomeric structures and form filaments in vitro. The proteins can bind polyanions including the extracellular matrix component oligogalacturonic acid (OGA). In vitro, remorin in plasma membrane preparations is phosphorylated (principally on threonine residues) in the presence of OGA and thus co-purifies with a protein kinases(s). The biological functions of remorins are unknown but roles as components of the membrane/cytoskeleton are possible.
Pfam PF22845: DUF3097, N-terminal domain (domain)
This entry represents an N-terminal Tudor-like domain found in DUF3097 proteins. This family of proteins with unknown function appears to be restricted to Actinobacteria.
Pfam PF19049: SidE DUB domain (domain)
This entry represents the N-terminal deubiquitinating domain from the SidE protein. The SidE protein is a bacterial effector protein that can ubiquitinate and presumably deubiquitinate host proteins.
Pfam PF23264: Domain of unknown function (DUF7073) (domain)
This domain is found in Histone-lysine N-methyltransferase, H3 lysine-4 specific from Plasmodium falciparum ([swissprot:W4J2P1]) and similar sequences from alveolates. In some proteins this domain is found associated with [pfam:PF00628]. It shows a conserved motif LLxxYKxKI/LxDLL.
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 PF08002: Protein of unknown function (DUF1697) (family)
This family contains many hypothetical bacterial proteins.
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 PF21810: Family of unknown function (DUF6880) (repeat)
This entry represents a family of proteins that form an alpha-helical solenoid structure of HEAT-like repeats. Proteins in this family are found in various bacterial species, but most commonly in proteobacteria.
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 PF22303: Protein kinase OspG, kinase domain (domain)
This entry represents the kinase domain of protein kinase OspG which is involved in down-regulation of the host innate response induced by invasive bacteria. OspG is a an effector kinase that binds host E2 ubiquitin-conjugating enzymes activated with ubiquitin, which enhances its kinase activity, playing a role to suppress the host inflammatory response during invasion and colonization.
Pfam PF08230: CW_7 repeat (domain)
This domain was originally found in the C-terminal moiety of the Cpl-7 lysozyme encoded by the Streptococcus pneumoniae bacteriophage Cp-7 ([swissprot:P19385]). It is also found in the cell wall hydrolases of human and life-stock pathogens. CW_7 repeats make up a cell wall binding motif.
Pfam PF21555: Prokaryotic cation-chloride cotransporter, C-terminal domain, 1st (domain)
This domain is found in the C-terminal region of a group of prokaryotic cation-chloride cotransporters (CCCs), including Na-K-Cl cotransporter from Methanosarcina acetivorans ([swissprot:Q8THK8]). These proteins consist of an N-terminal transmembrane transport region ([pfam:PF00324] and [pfam:PF13520]) followed by a cytoplasmic regulatory domain. The C-terminal domain adopts a compact trapezoid-shaped elongated structure with a mixed alpha-beta fold and can be divided in two structurally related subdomains. This entry represents the first subdomain, which shows a central five-stranded parallel beta- sheet and three alpha-helices that pack on either face of the sheet.
Pfam PF16664: Unstructured on SH3 and cysteine-rich domain-containing protein 2 (disordered)
STAC2_u1 is a region of natively unstructured but highly conserved sequence between C1_1 [pfam:PF00130], and an SH3 domain, eg [pfam:PF00018], on SH3 and cysteine-rich domain-containing proteins from higher eukaryotes.  The function is not known.
Pfam PF12566: Protein of unknown function (DUF3748) (repeat)
This domain family is found in bacteria and eukaryotes, and is approximately 120 amino acids in length. It is likely to contain 2 to 3 copies of a PD40-like repeat.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02637: GatB domain (domain)
This domain is found in GatB. It is about 140 amino acid residues long.  This domain is found at the C terminus of GatB [swissprot:O30509] which transamidates Glu-tRNA to Gln-tRNA.
Pfam PF20608: Phage tail tube protein C-terminal domain (domain)
This short all beta domain is found at the C-terminus of some phage tube proteins
Pfam PF19602: Family of unknown function (DUF6107) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 105 and 125 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 PF04614: Pex19 protein family (family)
Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid beta-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts.

PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognised as peroxisome biogenesis diseases. Pex19 is involved in membrane assembly and maintenance and functions as a receptor and chaperone of peroxisomal membrane proteins (PMPs) .
Pfam PF00398: Ribosomal RNA adenine dimethylase (domain)
The bacterial enzyme KsgA catalyses the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism . In contrast, the yeast ortholog, Dim1, is essential. In Saccharomyces cerevisiae (Baker's yeast), and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity . Another orthologue is the eukaryotic transcription factor B (TFB), which has a second function; this enzyme is a nuclear-encoded mitochondrial transcription factor and is essential for mitochondrial gene expression . The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain.
rRNA adenine N-6-methyltransferases Erm methylate a single adenosine base in 23S rRNA. They confer resistance to the MLS-B group of antibiotics . Despite their sequence similarity to KsgA, the two enzyme families have strikingly different levels of regulation that remain to be elucidated.
Pfam PF06830: Root cap (family)
The cells at the periphery of the root cap are continuously sloughed off from the root into the mucilage, and are thought to be programmed to die.This family represents a conserved region approximately 60 residues in length within plant root cap proteins, which may be involved in the process.
Pfam PF17490: L1 transposable element dsRBD-like domain (domain)
This entry represents the double stranded RNA-binding-like domain.
Pfam PF16878: Transcriptional regulator, SIX1, N-terminal SD domain (domain)
SIX1_SD is a family of eukaryotic proteins, and it is found N-terminal to the Homeobox domain. As a transcription factor it lacks intrinsic activation domains and thus needs to bind to the EYA family of co-factors in order to mediate transcriptional activation. It is the SD domain that is necessary for this protein-protein interaction, binding to the C-terminal region of EYA - Eyes absent homologue proteins.
Pfam PF01278: Omptin family (family)
The omptin family is a family of  serine proteases.
Wikipedia: Omptins are a family of bacterial proteases. They are aspartate proteases, which cleave peptides with the use of a water molecule. Found in the outer membrane of gram-negative enterobacteria such as Shigella flexneri, Yersinia pestis, Escherichia coli, and Salmonella enterica. Omptins consist of a widely conserved beta barrel spanning the membrane with 5 extracellular loops. These loops are responsible for the various substrate specificities. These proteases rely upon binding of lipopolysaccharide for activity.
Pfam PF18798: Large polyvalent protein-associated domain 3 (family)
This domain is predicted to adopt an alpha and beta fold. The secondary structure arrangement suggests it to be a member of the BECR fold. The domain is found in polyvalent proteins of both conjugative elements and phages/prophages.
Pfam PF12811: Bax inhibitor 1 like (family)
The Bax-inhibitor-1 region of the receptor molecules is conserved from bacteria to humans.
Pfam PF20491: Ermin (family)
This is a cytoskeletal protein exclusively expressed in oligodendrocytes that plays a role in cytoskeletal rearrangements during the late wrapping and/or compaction phases of myelinogenesis and in maintenance and stability of myelin sheath in the adult. It may also play an important role in late-stage oligodendroglia maturation, myelin/Ranvier node formation during CNS development, and in the maintenance and plasticity of related structures in the mature CNS. Ermin associates with the myosin phosphatase Rho interacting protein protein (Mprip/p116RIP) and inactivates RhoA, a GTPase that controls cytoskeletal rearrangement in differentiating cells, thus contributing to oligodendrocyte morphogenesis. It has a C-terminal actin-binding domain similar to those of members of the ERM family but lacks the conserved N-terminal FERM domain.
Pfam PF21879: C381 turret protein Nucleoplasmin-like/VP domain (domain)
This entry represents the Sulfolobus turreted icosahedral virus (STIV) turret protein third jelly roll domain. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions of the membrane and various protein components involved. The turret protein is apposed on the penton base C-terminal jelly-roll ring and forms a pentamer consisting of three consecutive layers of jelly-rolls, with each jelly-roll exhibiting different orientations. The interior of the C381 pentamer harbors two rather large cavities, which exhibit an overall positive electrostatic potential, suggesting that the turrets may act as STIV receptor-binding proteins carrying out recognition and attachment to the host receptors. The turret protein shares similarity with many carbohydrate-binding modules as well as domains involved in protein-protein interactions.
Pfam PF08141: Small acid-soluble spore protein H family (family)
This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus  subtilis and are expressed only in the forespore compartment  during sporulation of this organism. The sspH genes are  monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role  of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties.
Pfam PF03430: Trans-activating transcriptional regulator (family)
This family of trans-activating transcriptional regulator (TATR), also known as intermediate early protein 1, are common to the  Nucleopolyhedroviruses.
Pfam PF00598: Influenza Matrix protein (M1) (domain)
This protein forms a continuous shell on the inner side of the lipid bilayer, but its function is unclear.
Wikipedia: The M1 protein is a matrix protein of the influenza virus. It forms a coat inside the viral envelope. This is a bifunctional membrane/RNA-binding protein that mediates the encapsidation of nucleoprotein cores into the membrane envelope. It is therefore required that M1 binds both membrane and RNA simultaneously.
Pfam PF24783: FANCA arcN subdomain (repeat)
Fanconi anemia (FA) is a human disorder characterised by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages. The FA complex repairs the interstrand cross-linking (ICL) lesions and coordinates activities of the downstream DNA repair pathway including nucleotide excision repair, translesion synthesis, and homologous recombination. The FA core complex consists of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM, FANCT (UBET2), FAAP100 and FAAP24. This entry represents the N-terminal half of the arc-shaped C-terminal domain of FANCA (arcN) which interacts with the C-terminal half of a second FANCA molecule which interact in a head-to-tail manner to form a pseudo-symmetric dimeric interface. The C-terminal domain of FANCA (arcN and arcC halves) consists of HEAT repeats.