SII-SWORD/CoKE huggingface dataset:
Pfam PF08700: Vps51/EXO84/COG1 N-terminal (repeat)
This entry represents a conserved domain found in a number of components of multisubunit tethering complexes. Complexes associated with tethering containing helical rods (CATCHR) include exocyst, COG, GARP, and DSL1 complexes, which share a common origin reflected in their structure and organisation similarities. CATCHR share a fold consisting of helical bundles arranged in tandem towards the C-terminal and they usually have a coiled-coil (CC) region at the N-terminal. Each complex has a specialised function at a particular location in the secretory pathway, including vesicle recycling. This domain is found at the N-terminal of Vps51 (also known as Vps67), a subunit of GARP and interacts with the SNARE Tlg1, Exo84/Exo8 from the exocyst and COG1 subunit of the eight-unit Conserved Oligomeric Golgi (COG) complex.
Pfam PF16903: Major capsid protein N-terminus (domain)
This is the N-terminal domain of the major capsid protein in several dsDNA viruses.
Pfam PF17278: Family of unknown function (DUF5343) (family)
This is a family of unknown function which is found in Bacteria and Archaea.
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 PF24461: Family of unknown function (DUF7576) (family)
This entry represents a small family of uncharacterised archaeal proteins. They contain two pairs of conserved cysteine residues and are predicted to adopt a fold typical for Treble-clef zinc fingers.
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 PF09851: Short C-terminal domain (domain)
The Short C-terminal (SHOCT) domain is widespread in bacteria but is missing from the most commonly studied model organisms, despite being present in closely related species. It's predominantly C-terminal location, co-occurrence with numerous other domains and short size is reminiscent of the Gram-positive anchor motif, however it is present in a much wider range of species. It may be involved in oligomerisation and nucleic acid binding .
Pfam PF18582: Hydrazine synthase alpha subunit middle domain (domain)
The crystal structure of hydrazine synthase multiprotein complex isolated from the anammox organism Kuenenia stuttgartiensis implies a two-step mechanism for hydrazine synthesis: a three-electron reduction of nitric oxide to hydroxylamine at the active site of the gamma-subunit and its subsequent condensation with ammonia, yielding hydrazine in the active centre of the alpha-subunit. The alpha-subunit consists of three domains: an N-terminal domain which includes a six-bladed beta-propeller, a middle domain binding a pentacoordinated c-type haem (haem alphaI) and a C-terminal domain which harbours a bis-histidine-coordinated c-type haem (haem alphaII). This entry represents the middle domain of subunit alpha of hydrazine synthase (HZS).
Pfam PF09301: Domain of unknown function (DUF1970) (domain)
Members of this family consist of various uncharacterised viral hypothetical 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 PF11671: Complementary sex determiner protein (family)
This family of proteins represents the complementary sex determiner in the honeybee. In the honeybee, the mechanism of sex determination depends on the csd gene which produces an SR-type protein. Males are homozygous while females are homozygous for the csd gene. Heterozygosity generates an active protein which initiates female development.
Pfam PF22487: Complement regulator-acquiring surface protein 2 (family)
This protein family includes Complement regulator-acquiring surface protein 2 from Borreliella burgdorferi (CRASP-2, also known as CspZ), the causative agent of Lyme disease. CRASP-2 can bind both the major alternative pathway complement regulator factor H (CFH) and factor H-like protein 1 (CFHL-1), contributing to the resistance of the bacteria to the host's immune response. This protain consists of a single domain almost entirely formed by alpha-helices.
Pfam PF10501: Ribosomal subunit 39S (domain)
The 39S ribosomal protein appears to be a subunit of one of the larger mitochondrial 66S or 70S units. Under conditions of ethanol-stress in rats the larger subunit is largely dissociated into its smaller components. In E. coli, in the absence of the enzyme pseudouridine synthase (RluD) synthase, there is an accumulation of 50S and 30S subunits and the appearance of abnormal particles (62S and 39S), with concomitant loss of 70S ribosomes.
Pfam PF07416: Crinivirus P26 protein (family)
This family consists of several Crinivirus P26 proteins which seem to be found exclusively in the Lettuce infectious yellows virus. The function of this family is unknown.
Pfam PF21171: 2',5'-phosphodiesterase 12-like, N-terminal domain (domain)
This domain is found in 2',5'-phosphodiesterase 12 from humans (PDE12) and similar animal proteins. Pde12 cleaves 2',5'- phosphodiester bond linking adenosines of oligoadenylates. It plays a role as a negative regulator of the 2-5A system that is one of the major pathways for antiviral and antitumour functions induced by interferons (IFNs). PDE12 is organised into two clear domains: an N-terminal domain (this entry) and a C-terminal domain ([pfam:PF03372]). This domain is primarily composed of extended loop regions around a core composed of a six beta-strand meander that forms a two-layer beta-sandwich, showing an immunoglobulin-like fold.
Pfam PF13839: GDSL/SGNH-like Acyl-Esterase family found in Pmr5 and Cas1p (family)
The PC-Esterase family is comprised of Cas1p, the Homo sapiens C7orf58, Arabidopsis thaliana PMR5 and a group of plant freezing resistance/cold acclimatization proteins typified by Arabidopsis thaliana ESKIMO1, animal FAM55D proteins, and animal FAM113 proteins. The PC-Esterase family has features that are both similar and different from the canonical GDSL/SGNH superfamily. The members of this family are predicted to have Acyl esterase activity and predicted to modify cell-surface biopolymers such as glycans and glycoproteins. The Cas1p protein has a Cas1_AcylT domain, in addition, with the opposing acyltransferase activity. The C7orf58 family has a ATP-Grasp domain fused to the PC-Esterase and is the first identified secreted tubulin-tyrosine ligase like enzyme in eukaryotes. The plant family with PMR5, ESK1, TBL3 etc have a N-terminal C rich potential sugar binding domain followed by PC-Esterase domain.
Pfam PF18626: Glutaminase (domain)
Protein glutaminase (PG, EC 3.5.1.44) can deamidate glutamine residues in proteins to glutamate residues. This entry represents the mature PG enzyme which bears partial homology to factor XIII-like Transglutaminase (TG), especially its Cys-His-Asp catalytic triad. A similar triad (Cys-His-Asn) is also shared by some cysteine proteases such as papain and actinidin. The mature PG is a monomer enzyme consisting of 185 amino acid residues.
Pfam PF16070: TMEM132 fourth domain (domain)
This is the forth 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], the one represented here, 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 PF02476: US2 family (family)
This is a family of unique short (US) region proteins from the herpesvirus strain. The US2 family have no known function.
Pfam PF11309: Protein of unknown function (DUF3112) (family)
This eukaryotic family of 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 PF01795: MraW methylase family (family)
Members of this family are probably SAM dependent methyltransferases based on [swissprot:P18595]. This family appears to be related to [pfam:PF01596].
Pfam PF20168: Sister chromatid cohesion protein PDS5 protein (repeat)
This entry represents the Sister chromatid cohesion protein PDS5. The large PDS5 molecule is exclusively alpha helical, composed of a large number of HEAT-like repeats and helical extensions/additions that deviate from the HEAT repeat pattern.
Pfam PF01906: Putative heavy-metal-binding (family)
From comparative structural analysis, this family is likely to be a heavy-metal binding domain. The domain oligomerises as a pentamer. The domain is about 100 amino acids long and is found in prokaryotes.
Pfam PF05108: Type VII secretion system ESX-1, transport TM domain B (family)
EccB is a family of largely Gram-positive bacterial transmembrane componenets of the type VII secretion system characterised in Mycobacterium tuberculosis, systems ESX1-5. Translocation of virulent peptides through the membranes is thought to be mediated via a complex that includes EccB, EccC, EccD, EccE, and MycP. EccB, EccC, EccD, and EccE form a stable complex in the mycobacterial cell envelope.
Pfam PF09885: Uncharacterized protein conserved in archaea (DUF2112) (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 PF06084: Cytomegalovirus TRL10 protein (family)
This family consists of several Cytomegalovirus TRL10 proteins. TRL10 represents a structural component of the virus particle and like the other HCMV envelope glycoproteins, is present in a disulfide-linked complex.
Pfam PF18760: ADP-Ribosyltransferase in polyvalent proteins (family)
A family of ADP-Ribosyltransferases found in polyvalent proteins of phages and conjugative elements. These are in turn related to the Tox-ART-HYD2 group of ADP-Ribosyltransferases that are seen in polymorphic toxin systems and in toxin-antitoxin systems. These are predicted to modify host proteins.
Pfam PF12780: P-loop containing dynein motor region D4 (domain)
The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF15193: FAM24 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 87 and 101 amino acids in length. There are two conserved sequence motifs: FDLRT and CLY. The function of this family is unknown.
Pfam PF15508: beta subunit of N-acylethanolamine-hydrolyzing acid amidase (family)
NAAA-beta is a family of vertebral sequences that form the beta subunit of vertebral N-acylethanolamine-hydrolyzing acid amidase, a member of the choloylglycine hydrolase acid ceramidase family. The alpha subunit is represented by family CBAH, [pfam:PF02275].
Wikipedia: The ASAH1 gene encodes in humans the acid ceramidase enzyme.
Pfam PF11196: Protein of unknown function DUF2834 (family)
The function of DUF2834 is not clear.
Pfam PF24898: Cyclic-di-AMP phosphodiesterase GdpP-like, GGDEF domain (domain)
This domain is found in Cyclic-di-AMP phosphodiesterase GdpP from Bacillus subtilis. This domain binds and hydrolises ATP. It is predicted to adopt an alpha-beta configuration.
Pfam PF11411: DNA ligase IV (family)
DNA ligase IV along with Xrcc4 functions in DNA non-homologous end joining. This process is required to mend double-strand breaks. Upon ligase binding to an Xrcc4 dimer, the helical tails unwind leading to a flat interaction surface.
Pfam PF22221: Lipoprotein BF3042 OB domain (domain)
This OB fold domain is found in the prokaryotic lipoprotein BF3042.
Pfam PF13575: Domain of unknown function (DUF4135) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 380 amino acids in length. The family is found in association with [pfam:PF05147]. This domain may be involved in synthesis of a lantibiotic compound.
Pfam PF16127: Domain of unknown function (DUF4839) (family)
This family consists of uncharacterized proteins around 300 residues in length and is mainly found in various Clostridium species. The function of this family is unknown.
Pfam PF10634: Fe2+ transport protein (family)
This is a bacterial family of periplasmic proteins that are thought to function in high-affinity Fe2+ transport.
Pfam PF04701: Pox virus D2 protein (family)
This entry represents the Pox virus D2 proteins, also known as OPG114. D2 is a late protein which is part of a large complex required for early virion morphogenesis. This complex participates in the formation of virosomes and the incorporation of virosomal contents into nascent immature virions .
Pfam PF00900: Ribosomal family S4e (family)
A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of them consists of the small ribosomal subunit protein eS4 from archaea and eukaryotes. Small ribosomal subunit protein eS4A from yeast is also known as S7/YS6; archaeal members are also known as S4e; and mammalian and plant cytoplasmic proteins were previously known as S4 . Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids.

This entry represents the central region of these proteins.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF02175: Serpentine type 7TM GPCR chemoreceptor Srb (family)
Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srb is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Pfam PF08374: Protocadherin (family)
The structure of protocadherins is similar to that of classic cadherins ([pfam:PF00028]), but particularly on the cytoplasmic domains they also have some unique features.  They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites.  Their expression seems to be developmentally regulated.
Wikipedia: Protocadherins (Pcdhs) are the largest mammalian subgroup of the cadherin superfamily of homophilic cell-adhesion proteins. They were discovered by Shintaro Suzuki's group, when they used PCR to find new members of the cadherin family. The PCR fragments that corresponded to protocadherins were found in vertebrate and invertebrate species. This prevalence in a wide range of species suggested that the fragments were part of an ancient cadherin and were thus termed "Protocadherins" as the "first cadherins". Of the approximately 70 Pcdh genes identified in mammalian genomes, over 50 are located in tightly linked gene clusters on the same chromosome. Until recently, it was assumed that this kind of organization can only be found in vertebrates, but Octopus bimaculoides has 168 genes of which nearly three-quarters are found in tandem clusters with the two largest clusters compromising 31 and 17 genes, respectively.
Pfam PF17185: NlpE C-terminal OB domain (domain)
This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. In Escherichia coli and Salmonella typhi, NlpE is also known to confer copper tolerance in copper-sensitive strains of Escherichia coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes. This domain is found at the C-terminus of the NlpE protein.
Pfam PF06089: L-asparaginase II (family)
This family consists of several bacterial L-asparaginase II proteins.  L-asparaginase ([ec:3.5.1.1]) catalyses the hydrolysis of L-asparagine to L-aspartate and ammonium. Rhizobium etli possesses two asparaginases: asparaginase I, which is thermostable and constitutive, and asparaginase II, which is thermolabile, induced by asparagine and repressed by the carbon source.
Pfam PF18832: Large polyvalent protein-associated domain 18 (domain)
This is a mostly all beta domain which contains conserved acidic residues. It is mainly found in polyvalent proteins of conjugative elements.
Pfam PF16324: Domain of unknown function (DUF4960) (family)
This family consists of uncharacterised proteins around 460 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown.
Pfam PF04240: Carotenoid biosynthesis protein (family)
The representative member of this family is CruF, a C50 carotenoid 2',3'-hydratase involved in the synthesis of the C50 carotenoid bacterioruberin in the halophilic archaeon Haloarcula japonica.
Pfam PF00497: Bacterial extracellular solute-binding proteins, family 3 (domain)
This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognises Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate.
Pfam PF11929: Domain of unknown function (DUF3447) (repeat)
This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 80 amino acids in length.  This domain is found associated with [pfam:PF00023]. This domain has a conserved SHN sequence motif. It seems likely that this region represents divergent Ankyrin repeats.
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 PF15153: Cytokine-like protein 1 (family)
The function of this family of proteins, CYTL1, has not, as yet, been determined. However it is thought to be a secretory protein expressed in CD34+ haemopoietic cells. This family of proteins is found in eukaryotes. Proteins in this family are typically between 134 and 145 amino acids in length. There are two conserved sequence motifs: PPTCYSR and DDC.
Pfam PF24246: SH3b_T domain (domain)
This domain is found twice towards the C-terminal end of the staphylococcal phage protein [swissprot:I6T7G5] and similar peptidoglycan-degrading enzymes mainly from bacteriophages. This domain, usually found associated with [pfam:PF01510] and [pfam:PF05257], is involved in the binding of ligands at the bacterial surface.