SII-SWORD/CoKE huggingface dataset:
Pfam PF15806: TRAPP14 N-terminal (domain)
This entry includes Trafficking protein particle complex subunit 14 (TRAPP14), a specific subunit of the TRAPP (transport protein particle) II complex, a conserved vesicle tethering complex that functions in late Golgi trafficking as a membrane tether. This entry represents the N-terminal region consisting of two domains which adopt a Ig-like fold, where distant amino acids in the sequence contribute to different beta-sheets in the structure.
Pfam PF05140: ResB-like family (family)
This family includes both ResB and cytochrome c biogenesis proteins.  Mutations in ResB indicate that they are essential for growth.  ResB is predicted to be a transmembrane protein.
Pfam PF17082: Spindle Pole Component 29 (family)
Spc29 is a component of the Spc-110 subcomplex and is required for the SPB (Spindle pole body) duplication. Spc29 acts as a linker between the central plaque component Spc42 to the inner plaque component Spc110.
Pfam PF08025: Spider antimicrobial peptide (family)
This family includes antimicrobial peptides isolated from the crude venom of the wolf spider Oxyopes kitabensis. These peptides, known as oxyopinins, are the largest linear cationic amphipathic peptides chemically characterised and exhibit disrupting activities towards biological membranes.
Pfam PF16687: beta-propeller of ELYS nucleoporin (repeat)
ELYS-bb is the N-terminal seven-bladed beta-propeller domain of ELYS nucleoporins in higher eukaryotes. It is required for anchorage of the nucleoporin to the nuclear envelope during cell-division.
Pfam PF04446: tRNAHis guanylyltransferase (domain)
The Thg1 protein from Saccharomyces cerevisiae is responsible for adding a GMP residue to the 5' end of tRNA His. The catalytic domain Thg1 contains a RRM (ferredoxin) fold palm domain, just like the viral RNA-dependent RNA polymerases, reverse transcriptases, family A and B DNA polymerases, adenylyl cyclases,  diguanylate cyclases (GGDEF domain) and the predicted polymerase of the CRISPR system. Thg1 possesses an active site with three  acidic residues that chelate Mg++ cations. Thg1 catalyzes  polymerization similar to the 5'-3' polymerases.
Pfam PF04062: ARP2/3 complex ARPC3 (21 kDa) subunit (family)
The seven component ARP2/3 actin-organising complex is involved in actin assembly and function.
Wikipedia: Actin-related protein 2/3 complex subunit 3 is a protein that in humans is encoded by the ARPC3 gene.
Pfam PF13180: PDZ domain (domain)
PDZ domains (also known as Discs-large homologous regions (DHR) or GLGF)) are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates . PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences . In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated.
Wikipedia: The PDZ domain is a common structural domain of 80-90 amino-acids found in the signaling proteins of bacteria, yeast, plants, viruses and animals. Proteins containing PDZ domains play a key role in anchoring receptor proteins in the membrane to cytoskeletal components. Proteins with these domains help hold together and organize signaling complexes at cellular membranes. These domains play a key role in the formation and function of signal transduction complexes. PDZ domains also play a highly significant role in the anchoring of cell surface receptors to the actin cytoskeleton via mediators like NHERF and ezrin.
Pfam PF12229: Putative peptidoglycan binding domain (domain)
This domain is found associated with the L,D-transpeptidase domain [pfam:PF03734].  The structure of this domain has been solved and shows a mixed alpha-beta fold composed of nine beta strands and four alpha helices. This domain is usually found to be duplicated. Therefore, it seems likely that this domain acts to bind the two unlinked peptidoglycan chains and bring them into close association so they can be cross linked by the transpeptidase domain (Bateman A pers. observation).
Pfam PF11139: Sap, sulfolipid-1-addressing protein (family)
SAP is a transmembrane transport protein with six predicted transmembrane helices, with a hydrophilic domain between helices 3 and 4. This hyrodphobic region is highly variable among identified Gap-like (GPL, peptidoglycolipid, addressing protein) proteins and may be involved in substrate recognition. SAP also belongs to the LysE protein superfamily ([pfam:PF01810]), whose members have been implicated in small molecule transport in bacteria. Other Gap proteins export metabolites across the cell membrane so it is possible that Sap specifically may be involved in transport of sulfolipid-1 across the membrane.
Pfam PF08120: Tamulustoxin family (family)
This family consists of the tamulustoxins which are  found in the venom of the Indian red scorpion (Mesobuthus  tamulus). Tamulustoxin shares no similarity with other  scorpion venom toxins, although the positions of its six  cysteine residues suggest that it shares the same  structural scaffold. Tamulustoxin acts as a potassium channel  blocker.
Pfam PF17334: Minor curli fiber component A (family)
Curli are extracellular functional amyloids that are assembled by enteric bacteria during biofilm formation and host colonization. The csg (curli specific gene) operon encodes major structural and accessory proteins that are required for curli production. The csgBAC operon encodes the major and minor curli fiber components, CsgA and CsgB, respectively. CsgA is secreted to the extracellular milieu as an unfolded protein and forms amyloid polymers upon interacting with the CsgB nucleator. CsgA is comprised of five imperfect repeating units with highly conserved glutamine and asparagine residues that are important for amyloid formation. Each repeating unit is predicted to form a strand-loop-strand motif. In vitro, CsgC inhibits CsgA amyloid formation at substoichiometric concentrations and maintains CsgA in a non-beta-sheet rich conformation, making CsgC an efficient and selective amyloid inhibitor.
Pfam PF09806: Cyclin-dependent kinase 2-associated protein (family)
Members of this family of proteins are cell-growth suppressors, associating with and influencing the biological activities of important cell cycle regulators in the S phase including monomeric non-phosphorylated cyclin-dependent kinase 2 (CDK2) and DNA polymerase alpha/primase. An association between mutations in the gene coding for this protein and oral cancer has been described.
Pfam PF00953: Glycosyl transferase family 4 (family)
This entry represents a family of UDP-GlcNAc/MurNAc: polyisoprenol-P GlcNAc/MurNAc-1-P transferases. Members of the family include eukaryotic N-acetylglucosamine-1-phosphate transferases, which catalyse the conversion of UDP-N-acteyl-D-glucosamine and dolichyl phosphate to UMP and N-acetyl-D-glucosaminyl-diphosphodolichol in the glycosylation pathway; and bacterial phospho-N-acetylmuramoyl-pentapeptide-transferases, which catalyse the first step of the lipid cycle reactions in the biosynthesis of cell wall peptidoglycan.
Pfam PF20672: Spumavirus Gag polyprotein, conserved central domain (domain)
This is the conserved central domain of the Gag polyprotein from Foamyviruses (FVs) or Spuma-retroviruses. Gag is the major structural protein required for genome packaging virion assembly, trafficking and egress. This domain has an all alpha-helical fold and contains the highly conserved PGQA and YxxLGL sequences.
Pfam PF24821: Domain of unknown function (DUF7711) (domain)
This entry represents a small family of uncharacterised Actinomycete proteins. These proteins may form homodimers (AlphaFold3 A6WE73 ipTM = 0.79). The dimerisation is mediated by a C-terminal alpha helical subdomain.
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 PF00710: Asparaginase, N-terminal (domain)
This is the N-terminal domain of this enzyme.
Wikipedia: Asparaginase is an enzyme that is used as a medication and in food manufacturing. As a medication, L-asparaginase is used to treat acute lymphoblastic leukemia (ALL) and lymphoblastic lymphoma (LBL). It is given by injection into a vein, or muscle. A pegylated version is also available. In food manufacturing it is used to decrease acrylamide.
Pfam PF08277: PAN-like domain (domain)
PAN domains have significant functional versatility fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions . These domains contain a hair-pin loop like structure, similar to knottins, but the pattern of disulphide bonds differs.
The PAN-3 or CW is a domain associated with a number of Caenorhabditis elegans hypothetical proteins.
Pfam PF08173: Membrane bound YbgT-like protein (family)
This family contains a set of membrane proteins, typically 33 amino acids long.  The family has no known function, but the protein is found  in the operon CydAB in E. coli. Members have a consensus motif (MWYFXW)  which is rich in aromatic residues. The protein forms a single membrane-spanning helix.  This family seems to be restricted to Proteobacteria.
Pfam PF11899: Protein of unknown function (DUF3419) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 398 to 802 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 PF11820: Protein of unknown function (DUF3339) (family)
This family of proteins are functionally uncharacterised. This family is found in eukaryotes. Proteins in this family are about 70 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 PF02377: Dishevelled specific domain (family)
This domain is specific to the signalling protein dishevelled. The domain is found adjacent to the PDZ domain [pfam:PF00595], often in conjunction with DEP ([pfam:PF00610]) and DIX ([pfam:PF00778]). Much of it is disordered and yet conserved.
Wikipedia: Dishevelled (Dsh) is a family of proteins involved in canonical and non-canonical Wnt signalling pathways. Dsh is a cytoplasmic phosphoprotein that acts directly downstream of frizzled receptors. It takes its name from its initial discovery in flies, where a mutation in the dishevelled gene was observed to cause improper orientation of body and wing hairs. There are vertebrate homologs in zebrafish, Xenopus (Xdsh), mice and humans. Dsh relays complex Wnt signals in tissues and cells, in normal and abnormal contexts. It is thought to interact with the SPATS1 protein when regulating the Wnt Signalling pathway.
Pfam PF07589: PEP-CTERM motif (conserved_site)
This motif has been identified in a wide range of bacteria at their C-terminus.  It has been suggested that this is a protein sorting signal. Based on phylogenetic profiling it has been suggested that the EpsH family of proteins mediate this function.
Pfam PF18098: 26S proteasome regulatory subunit RPN5 C-terminal domain (domain)
This is the C-terminal domain of the 26S proteasome regulatory subunit RPN5 proteins.This helical domain can be found adjacent to [pfam:PF01399]. The 26S proteasome is the major ATP-dependent protease in eukaryotes. Three subcomplexes form this degradation machine: the lid, the base, and the core. The helices found at the C terminus of each lid subunit form a helical bundle that directs the ordered self-assembly of the lid subcomplex. This domain which comprises the tail of RPN5 along with the tail of Rpn9, are important for Rpn12 binding to the lid.
Pfam PF15502: M-phase-specific PLK1-interacting protein (family)
This entry includes animal M-phase-specific PLK1-interacting protein (also known as TTDN1) and plant protein SICKLE.
Wikipedia: M-phase-specific PLK1-interacting protein is a protein that in humans is encoded by the MPLKIP gene. Patients with an inherited defect in both alleles of the gene suffer from trichothiodystrophy (TTD), a disease hallmarked by brittle hair and nails and usually by developmental difficulties as well. One patient carries a homozygous deletion of the whole gene area, which indicates that the gene is not essential for embryonic development. TTD can be diagnosed by the presence of tigertail-striped patterns in hair visible under polarised light microscopy, or biochemically by a reduced Cys content of the hairs. Only a minority of the TTD cases carry a MPLKIP defect: more frequently, the gene ERCC2 is mutated, which encodes a subunit of the protein complex TFIIH that is required for general transcription and for nucleotide excision repair of DNA damage.
Pfam PF01496: V-type ATPase 116kDa subunit family (family)
This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i.  The V-type ATPases family are proton pumps that acidify intracellular compartments  in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices  it has a hydrophilic amino terminal and a hydrophobic carboxy  terminal. It has roles in proton transport and assembly of the V-type ATPase complex.  This subunit is encoded by two homologous gene in yeast VPH1 and STV1.
Wikipedia: Vacuolar-type ATPase (V-ATPase) is a highly conserved evolutionarily ancient enzyme with remarkably diverse functions in eukaryotic organisms. V-ATPases acidify a wide array of intracellular organelles and pumps protons across the plasma membranes of numerous cell types. V-ATPases couple the energy of ATP hydrolysis to proton transport across intracellular and plasma membranes of eukaryotic cells. It is generally seen as the polar opposite of ATP synthase because ATP synthase is a proton channel that uses the energy from a proton gradient to produce ATP. V-ATPase however, is a proton pump that uses the energy from ATP hydrolysis to produce a proton gradient.
Pfam PF15991: G-protein pathway suppressor (family)
This family of proteins inhibits G-protein- and mitogen-activated protein kinase-mediated signal transduction.
Pfam PF18224: ToxB N-terminal domain (domain)
This is the N-terminal domain of ToxB found in Pyrenophora tritici-repentis. This domain is crucial for toxin activity. There are only two amino acid differences between ToxB and toxb, an inactive homolog of ToxB. These two differences are a Val at position 3 in ToxB compared to a Thr in toxb, and an Ala at position 12 in ToxB compared to a Val in toxb. AvrPiz-t, a secreted avirulence protein produced by the rice blast fungus, is a structural homolog to ToxB.
Pfam PF17356: Phage-like element PBSX protein XtrA (family)
This is a family of unknown function found in Bacilli.
Pfam PF07289: Bardet-Biedl syndrome 5 protein (family)
BBS5 is part of the BBSome complex that may function as a  coat complex required for sorting of specific membrane  proteins to the primary cilia. Mutations in the BBS5 gene  cause Bardet-Biedl syndrome 5.
Pfam PF08082: PRO8NT (NUC069), PrP8 N-terminal domain (domain)
The PRO8NT domain is found at the N-terminus of pre-mRNA splicing factors of PRO8 family. The NLS or nuclear localisation signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly variable proline-rich region.
Pfam PF25014: NET2A-like domain (domain)
This domain is found in Protein NETWORKED 2A from Arabidopsis thaliana (NET2A) and similar plant proteins. NET2A associates with F-actin at the plasma membrane in growing pollen tubes. This domain is predicted to adopt an all-alpha configuration.
Pfam PF12996: DUF based on E. rectale Gene description (DUF3880) (family)
Based on Eubacterium rectale gene EUBREC_3218.  As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), It appears to be upregulated in the presence of  Bacteroides thetaiotaomicron vs when isolated in culture.
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 PF23795: YKFC SH3b2 domain (domain)
This entry represents the second of two N-terminal bacterial SH3 (SH3b2) domains found in bacterial dipeptidyl-peptidases VI such as Gamma-D-glutamyl-L-lysine dipeptidyl-peptidase (YKFC). YKFC consist of three domains, the N-terminal SH3b1 (Pfam: PF18348), SH3b2 and a C-terminal NlpC/P60 (Pfam: PF00877). The active site is located at the SH3b1-NlpC/P60 interface, whereas the SH3b2 domain is distal to this.
Pfam PF13785: Domain of unknown function (DUF4178) (family)
This is a domain of unknown function, mainly found in 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 PF05745: Chlamydia 15 kDa cysteine-rich outer membrane protein (CRPA) (family)
This family consists of several Chlamydia 15 kDa cysteine-rich outer membrane proteins which are associated with differentiation of reticulate bodies (RBs) into elementary bodies (EBs).
Pfam PF23800: Family of unknown function (DUF7176) (family)
This family consists of short bacterial phage proteins, typically around 90 amino acids in length, that contain two transmembrane helices.  The family is found in phages that infect Enterobacteria.
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 PF00505: HMG (high mobility group) box (domain)
High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms, and can be broadly divided into two groups, based on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif, while the latter can contain multiple HMG-box motifs.

HMG-box domains can be found in single or multiple copies in the following protein classes: HMG1 and HMG2 non-histone components of chromatin; SRY (sex determining region Y protein) involved in differential gonadogenesis; the SOX family of transcription factors ; sequence-specific LEF1 (lymphoid enhancer binding factor 1) and TCF-1 (T-cell factor 1) involved in regulation of organogenesis and thymocyte differentiation ; structure-specific recognition protein SSRP involved in transcription and replication; MTF1 mitochondrial transcription factor; nucleolar transcription factors UBF 1/2 (upstream binding factor) involved in transcription by RNA polymerase I; Abf2 yeast ARS-binding factor ; yeast transcription factors lxr1, Rox1, Nhp6b and Spp41; mating type proteins (MAT) involved in the sexual reproduction of fungi ; and the YABBY plant-specific transcription factors.
Wikipedia: In molecular biology, the HMG-box is a protein domain which is involved in DNA binding. The domain is composed of approximately 75 amino acid residues that collectively mediate the DNA-binding of chromatin-associated high-mobility group proteins. HMG-boxes are present in many transcription factors and chromatin-remodeling complexes, where they can mediate non-sequence or sequence-specific DNA binding.
Pfam PF13226: Domain of unknown function (DUF4034) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 280 amino acids in length. There is a conserved PRW sequence motif.
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.