SII-SWORD/CoKE huggingface dataset:
Pfam PF05982: Na+-dependent bicarbonate transporter superfamily (family)
Family of bacterial proteins that are likely to be part of the Na(+)-dependent bicarbonate transporter (sbt) family. Members carry 10TMS in a 5+5 duplicated structure. The loop between helices 5 and 6 in Synechocystis PCC6803 is likely to be the location for regulatory mechanisms governing the activation of the transporter.
Pfam PF15530: Bacterial toxin 25 (family)
This domain family, predicted to have RNase activity, is found in a group of toxins mainly found in Enterobacterales. It shows a conserved FGPY motif and a histidine residue and is predicted to have a mostly all-beta fold. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 5 secretion system. Some members of this family are annotated as CdiA, a member of a contact-dependent growth inhibition system (CDI) that show diverse functions implicated in bacterial competition, including the dissipation of the proton motive force (PMF) and the degradation of DNA or RNA.
Pfam PF21737: Family of unknown function (DUF6865) (family)
This entry represents a short family of uncharacterised proteins from plants. AlphaFold predictions suggest that the protein contains two non-contacting alpha-helices.
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 PF24415: Irg-7-like, Ig-like domain (domain)
This domain is found in Irg-7 from Caenorhabditis elegans and similar animal sequences. Irg-7 plays a role in innate immunity, probably via the atf-7 pathway, to confer resistance to pathogenic bacteria. This domain is predicted to adopt an immunoglobulin-like fold.
Pfam PF11386: Vitelline envelope receptor for lysin (family)
VERL, the egg vitelline envelope (VE) receptor for lysin, is a giant unbranched glycoprotein comprising 30% of the vitelline envelope. Lysin binds to VERL and creates a hole as VERL molecules lose cohesion and splay apart. These proteins are important in the mediation of fertilisation
Pfam PF16366: Cytoplasmic polyadenylation element-binding protein ZZ domain (domain)
This ZZ-type zinc finger domain binds zinc via two conserved histidines in the C-terminal part of the domain.
Pfam PF07966: A1 Propeptide (conserved_site)
Most eukaryotic endopeptidases (Merops Family A1) are synthesised with signal and propeptides.  The animal pepsin-like endopeptidase propeptides form a distinct family of propeptides, which contain a conserved motif approximately 30 residues long. In pepsinogen A, the first 11 residues of the mature pepsin sequence are displaced by residues of the propeptide.  The propeptide contains two helices that block the active site cleft, in particular the conserved Asp11 residue, in pepsin, hydrogen bonds to a conserved Arg residues in the propeptide. This hydrogen bond stabilises the propeptide conformation and is probably responsible for triggering the conversion of pepsinogen to pepsin under acidic conditions.
Wikipedia: Aspartic proteases are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. In general, they have two highly conserved aspartates in the active site and are optimally active at acidic pH. Nearly all known aspartyl proteases are inhibited by pepstatin.
Pfam PF01640: Peptidase C10 family (domain)
This family represents just the active peptide part of these proteins. Residues 1-120 are not part of the model as they form the pro-peptide, which before cleavage blocks the active site from the substrate.  The catalytic residues of histidine and cysteine are brought close together at the active site by the folding of the active peptide.
Pfam PF03694: Erg28 like protein (family)
This is a family of integral membrane proteins, which may contain four  transmembrane helices.  Members of this family are thought to be involved  in sterol C-4 demethylation. In S. cerevisiae they may tether Erg26p  (sterol dehydrogenase/decarboxylase) and Erg27p (3-ketoreductase) to the endoplasmic reticulum or may facilitate interaction between these proteins.  The family contains a conserved arginine and histidine that may be  functionally important.
Pfam PF08477: Ras of Complex, Roc, domain of DAPkinase (domain)
Roc, or Ras of Complex, proteins are mitochondrial Rho proteins (Miro-1, [swissprot:Q8IXI2], and Miro-2, [swissprot:Q8IXI1]) and atypical Rho GTPases. Full-length proteins have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains ([pfam:PF00036]) that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.
Pfam PF06434: Aconitate hydratase 2 N-terminus (family)
This family represents the N-terminal region of several bacterial Aconitate hydratase 2 proteins and is found in conjunction with [pfam:PF00330].
Pfam PF10686: YspA, cpYpsA-related SLOG family (family)
Family in the SLOG superfamily, related to YspA and cpYpsA families and shows associations with NAD utilization and ADP-ribosylation domains including NUDIX, NADAR and MACRO. Members of this family are predicted to function as sensors of nucleotide, nucleotide-derived ligands, or nucleic acids, which are potentially processed/modified by associating effectors. Also associates in a distinct system with a phosphoribosyltransferase (PRTase) domain.
Pfam PF16696: Zinc finger FYVE domain-containing protein 21 C-terminus (domain)
This is the C-terminal domain of Zinc finger FYVE domain-containing protein 21. It has a PH-like fold and is required for the regulation of focal adhesions and in cell migration.
Pfam PF02937: Cytochrome c oxidase subunit VIc (family)
Cytochrome c oxidase, a 13 sub-unit complex, [ec:1.9.3.1] is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIc.
Pfam PF22581: Ciliary microtubule inner protein 3 (family)
This family represents the homologues of the Ciliary microtubule inner protein 3 (CIMIP3). CIMIP3 is a microtubule inner protein (MIP) part of the doublet microtubules (DMTs) in the sperm axoneme. It binds to protofilament B10 in the sperm DMTs.
Pfam PF17124: ThiJ/PfpI family-like (domain)
This is a family of fungal and bacterial ThiJ/PfpI-like proteins.
Pfam PF08362: YcdC-like protein, C-terminal region (domain)
This family comprises proteins that belong to the TetR family of transcriptional regulators. They bear particular similarity to YcdC ([swissprot:P75899]), a putative HTH-containing protein. This family features the C-terminal region of these sequences, which does not include the helix-turn-helix.
Pfam PF03013: Pyrimidine dimer DNA glycosylase (domain)
Pyrimidine dimer DNA glycosylases excise pyrimidine dimers by hydrolysis of the glycosylic bond of the 5' pyrimidine, followed by the intra-pyrimidine phosphodiester bond. Pyrimidine dimers are the major UV-lesions of DNA.
Pfam PF18311: Exosome complex exonuclease Rrp40 N-terminal domain (domain)
This is the N-terminal domain of Rrp40 of the exosome complex present in Saccharomyces cerevisiae. The RNA exosome complex is responsible for degrading RNA molecules in the 3' to 5' direction. Rrp40 is a 'cap' protein and binds the RNase PH barrel on the opposite side from the S1/KH ring. The N-terminal domain of Rrp44 forms a long beta-hairpin that is wedged in between Rrp41-Rrp42 and approaches the N terminus of the cap protein Rrp4. This domain adopts a beta- sandwich hybrid structure.
Pfam PF07691: PA14 domain (domain)
This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium prespore-cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding.
Pfam PF22238: RIP/P131 family (family)
This family represents the RNAP Inhibitory Protein (RIP) and its paralog, the major capsid protein (MCP) P131. These proteins adopt very similar bundle structures consisting of six alpha-helices.  RIP factor binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. MCP P131 is a building block of the viral capsid.
Pfam PF21289: Enhancer of mRNA-decapping protein 4, C-terminal (repeat)
Enhancer of mRNA-decapping protein 4 (EDC4, also known as Ge-1), is a regulator of mRNA decapping to function in the mRNA P-bodies within the cytoplasm. It has been shown to interact with mTORC1, coenzyme A synthase and MARF1. It is also involved in the regulation of immune system. This is the C-terminal domain which is necessary and sufficient for P-body targeting and in plants, it also mediates DCP1 and DCP2 interaction, as well as self-association. It adopts an helical-repeat fold similar to that of ARM/HEAT repeat proteins.
Pfam PF12826: Helix-hairpin-helix motif (conserved_site)
The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Pfam PF08803: Putative mono-oxygenase ydhR (domain)
ydhR is a homodimeric protein that comprises of a central four-stranded beta sheet and four surrounding alpha helices. It shows structural homology to the ActVA-Orf6 and YgiN proteins which indicates it could be a mono-oxygenase.
Pfam PF11840: Protein of unknown function (DUF3360) (domain)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 489 to 517 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 PF23489: V-type proton ATPase subunit f-like (family)
This protein family represents a group of short protein sequences from eukaryotes, including the small open reading reading frame (smORF) encoded V-type proton ATPase subunit f from Saccharomyces cerevisiae (V-ATPase subunit f) and human Ribonuclease kappa. These proteins play a role in the activity of vacuolar (H+)-ATPase (V-ATPase), which is responsible for acidifying and maintaining the pH of intracellular compartments.
Pfam PF06328: Ig-like C2-type domain (domain)
This domain is a ligand-binding immunoglobulin-like domain. The two cysteine residues form a disulphide bridge.
Pfam PF16990: Carbohydrate binding module (family 35) (domain)
This is a mannan-specific carbohydrate binding domain, previously known as the X4 module. Unlike other carbohydrate binding modules, binding to substrate causes a conformational change.
Pfam PF05816: Toxic anion resistance protein (TelA) (family)
This family consists of several prokaryotic TelA like proteins. TelA and KlA are associated with tellurite resistance and plasmid fertility inhibition.
Pfam PF19614: Family of unknown function (DUF6119) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 523 and 552 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 PF09660: Protein of unknown function (DUF2397) (family)
Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria).
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 PF24153: Maternally expressed gene family (family)
This entry represents Maternally expressed gene (Meg) family which is a multigene family expressed in maize that encodes cysteine-rich proteins. The founding member of the family, Meg1, is required for normal development of the basal endosperm transfer cell layer and is involved in the allocation of maternal nutrients to growing seeds. Expansion of Meg family involves potentially adaptive functional and structural transitions.
Pfam PF24311: THSD1 third Ig-like domain (domain)
This domain is found in the human Thrombospondin type-1 domain-containing protein 1 (THSD1) and related proteins. THSD1 is involved in endothelial cell to extracellular matrix adhesion. THSD1 forms a multimeric protein complex with FAK/talin/ vinculin, wherein THSD1 promotes talin binding to FAK but not to vinculin, a key step in nascent adhesion assembly. The domain represented by this entry is predicted to adopt Ig-like beta-sandwich.
Pfam PF16600: Caskin1 CASK-interaction domain (family)
The Caskin1 protein interacts with the CASK protein via this region.CASK and Caskin1 are synaptic scaffolding proteins. The binding motif on human Caskin1 is EEIWVLRK. A similar motif is found on protein MINT1 and protein TIAM1, both shown to be able to bind to CASK though the motif. MINT1 and TIAM1 are not part of this family. This region is predicted to be natively unstructured.
Pfam PF01247: Ribosomal protein L35Ae (domain)
The ribosomal eL33 eukaryotic and archaebacterial ribosomal proteins, previously known as L35A, can be grouped on the basis of sequence similarities. One of these families consists of:


 * Vertebrate eL33 (old name L35A).
 * Caenorhabditis elegans eL33 (old name L35A (F10E7.7)).
 * Saccharomyces cerevisiae eL33A/eL33B (old name L37A/L37B (Rp47)).
 * Plant eL33 (old name L35A).
 * Pyrococcus woesei eL33 (old name L35A) homologue .


These proteins have 87 to 110 amino-acid residues.
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 PF12655: Domain of unknown function (DUF3787) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in Clostridia. Proteins in this family are approximately 60 amino acids in length. There is a conserved TAAW sequence motif that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF22601: RIM2-alpha zinc finger (domain)
This entry represents the zinc finger domain of Regulating synaptic membrane exocytosis protein 2 (RIM2a) and related proteins. This domain alone is responsible for the interaction with Munc13-1 by engaging with the Munc13-1 C2A domain. Structurally, this domain is similar to FIVE zinc fingers.
Pfam PF20299: Nucleotidyltransferase-Associated Rossmannoid Fold (family)
This family represents an inactive member of the Receiver superfamily of the Rossmonnoid fold, predicted to function as a sensor domain in certain nucleotide-activated effector conflict systems. It is thought to bind nucleotides synthesized by both the SMODS domain and the CRISPR polymerase (Cpol) domain of the Cas10-like proteins, depending on genome context. N-terminal transmembrane segments are observed, suggesting that nucleotide binding initiates a membrane-perforating and cell-suicide response in conflict.
Pfam PF07274: Protein of unknown function (DUF1440) (family)
This family contains a number of bacterial proteins of unknown function approximately 180 residues long. These are possibly integral membrane 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 PF15357: Psoriasis susceptibility 1 candidate 1 (family)
This family is considered a candidate for susceptibility to psoriasis.
Pfam PF00978: RNA dependent RNA polymerase (family)
This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins:     2A protein from bromoviruses     putative RNA dependent RNA polymerase from tobamoviruses     Non structural polyprotein from togaviruses
Pfam PF03964: Chorion family 2 (disordered)
The chorion genes of Drosophila are amplified in  response to developmental signals in the follicle  cells of the ovary.
Pfam PF17017: Aberrant zinc-finger (family)
This is a family of largely microsporidia-specific proteins with an aberrant zinc-finger motif of Cx(4)C2H repeated.
Pfam PF23372: BBS7 C-terminal helix (domain)
This entry represents the C-terminal helices found in Bardet-Biedl syndrome 7 (BBS7) proteins from animals. This protein forms a part of the BBSome complex, which is required for ciliogenesis. BBS7 is the BBSome subunit responsible for the binding to SMO H8.
Pfam PF04937: Protein of unknown function (DUF 659) (family)
Transposase-like protein with 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 PF08884: Flagellin D3 domain (domain)
This domain is found in the central portion bacterial flagellin FliC.  The domain contains a structural motif called a beta-folium fold.  Although no specific function is assigned to this domain its deletion leads to a reduction in filament stability.
Pfam PF20864: Putative testis-expressed protein 13C, zinc finger domain (domain)
This entry represents the RANBP2-type zinc finger domain found at the C-terminal of the Putative testis-expressed protein 13C from human.
Pfam PF20875: SidC, C-terminal domain (domain)
SidC is one of the effectors delivered by Legionella pneumophila into the host cell. Like its paralogue SdcA, SidC anchor on the Legionella-containing vacuole (LCV) to facilitate the recruitment of endoplasmic reticulum (ER) proteins. This protein is organised into four domains that are packed into an arch-like shape: the N- terminal SNL domain ([pfam:PF18219]), the INS domain (which is inserted within the SNL domain), the P4C domain, and a C-terminal domain. This entry represents the latter, which shows an alpha-helical fold. Its function is unknown.
Pfam PF16658: Class II release factor RF3, C-terminal domain (domain)
This entry represents the C-terminal domain (domain III) of peptide chain release factor 3 (RF3), a bacterial class 2 release factor . TRF3 is believed to have a role in dissociating the class 1 release factors from the ribosome following termination.
Pfam PF04763: Protein of unknown function (DUF562) (family)
Family of uncharacterised proteins.