SII-SWORD/CoKE huggingface dataset:
Pfam PF00223: Photosystem I psaA/psaB protein (family)
Photosystem I (PSI)  is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. PSI is found in the chloroplast of plants and cyanobacteria. The electron transfer components of the reaction centre of PSI are a primary electron donor P-700 (chlorophyll dimer) and five electron acceptors: A0 (chlorophyll), A1 (a phylloquinone) and three 4Fe-4S iron-sulphur centres: Fx, Fa, and Fb.

PsaA and psaB, two closely related proteins, are involved in the binding of P700, A0, A1, and Fx. psaA and psaB are both integral membrane proteins of 730 to 750 amino acids that seem to contain 11 transmembrane segments. The Fx 4Fe-4S iron-sulphur centre is bound by four cysteines; two of these cysteines are provided by the psaA protein and the two others by psaB. The two cysteines in both proteins are proximal and located in a loop between the ninth and tenth transmembrane segments. A leucine zipper motif seems to be present  downstream of the cysteines and could contribute to dimerisation of psaA/psaB.
Wikipedia: Photosynthetic reaction centre proteins are main protein components of photosynthetic reaction centres (RCs) of bacteria and plants. They are transmembrane proteins embedded in the chloroplast thylakoid or bacterial cell membrane.
Pfam PF18211: Csm1 subunit domain B (domain)
This domain is found in the Csm1 subunit of the Csm complex found in Thermococcus onnurineus. Csm is a type III-A CRISPR-Cas system, which is an RNA-guided immune defense mechanism that detects and destroys foreign DNA or RNA. This domain is known as domain A and is positioned side by side with domain C. Both domain A and domain C adopt the BABBA topology. Domain A interacts primarily with domain B.
Pfam PF00436: Single-strand binding protein family (domain)
This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA.
Wikipedia: Single-strand DNA-binding protein (SSB) is a protein found in Escherichia coli bacteria, that binds to single-stranded regions of deoxyribonucleic acid (DNA). Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination, and repair. As well as stabilizing this single-stranded DNA, SSB proteins bind to and modulate the function of numerous proteins involved in all of these processes.
Pfam PF07383: Protein of unknown function (DUF1496) (family)
This family consists of several bacterial proteins of around 90 residues in length. Members of this family seem to be found exclusively in the Orders Vibrionales and Enterobacteriales. The function of this family is unknown.
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 PF06629: MltA-interacting protein MipA (family)
This family consists of several bacterial MltA-interacting protein (MipA) like sequences. As well as interacting with the membrane-bound lytic transglycosylase MltA, MipA is known to bind to PBP1B, a bifunctional murein transglycosylase/transpeptidase. MipA is considered to be a structural protein mediating the assembly of MltA to PBP1B into a complex.
Pfam PF17774: Putative RNA-binding domain in YlmH (domain)
This domain adopts an RRM like fold and is found in the B. subtilis YlmH cell division protein.
Pfam PF19943: Family of unknown function (DUF6405) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000434) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in  particular the SW-163C biosynthetic gene cluster from Streptomyces  sp. SNA15896.
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 PF23630: Tumor Necrosis Factor Receptor Superfamily Member 11B death domain (domain)
This entry represents the death domains found in TNFRSF11B family proteins.  The TNFRSF11B family proteins function as decoy receptors for TNFSF11/RANKL, neutralizing its role in osteoclastogenesis by inhibiting osteoclast activation and promoting apoptosis, which is crucial for bone homeostasis. The balance between TNFSF11 and TNFRSF11B is essential for this process. Additionally, these proteins may prevent arterial calcification and act as decoy receptors for TNFSF10/TRAIL, offering protection against apoptosis and modulating osteoclastogenesis inhibition.
Wikipedia: The death domain (DD) is a protein interaction module composed of a bundle of six alpha-helices. DD is a subclass of protein motif known as the death fold and is related in sequence and structure to the death effector domain (DED) and the caspase recruitment domain (CARD), which work in similar pathways and show similar interaction properties. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats, caspase-like folds, kinase domains, leucine zippers, leucine-rich repeats (LRR), TIR domains, and ZU5 domains.
Pfam PF07561: Domain of Unknown Function (DUF1540) (family)
This family has four conserved cysteines, which is suggestive of a metal binding function.
Pfam PF04345: Chorismate lyase (domain)
Chorismate lyase catalyses the first step in ubiquinone synthesis, i.e. the removal of pyruvate from chorismate, to yield 4-hydroxybenzoate.
Wikipedia: The enzyme chorismate lyase catalyzes the first step in ubiquinone biosynthesis, the removal of pyruvate from chorismate, to yield 4-hydroxybenzoate in Escherichia coli and other Gram-negative bacteria. It belongs to the family of lyases, specifically the oxo-acid-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is chorismate pyruvate-lyase (4-hydroxybenzoate-forming). Other names in common use include CL, CPL, and UbiC.
Pfam PF24248: Domain of unknown function (DUF7451) (domain)
This entry represents a presumed domain found in a group of uncharacterised sequences from bacteria. According to structure predictions, this domain may adopt and all-beta configuration with beta-strands of different lengths. This domain is usually associated with DUF7450 ([pfam:PF24247]).
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 PF17911: Ski2 N-terminal region (domain)
This region is the N-terminal extended region found in the Ski2 protein. The Ski complex is a conserved multiprotein assembly required for the cytoplasmic functions of the exosome, including RNA turnover, surveillance, and interference. Ski2, Ski3, and Ski8 assemble in a tetramer with 1:1:2 stoichiometry.
Pfam PF20166: ATG4, F-type LIR motif (conserved_site)
LC3 Interacting Regions (LIRs), also known as ATG8-interacting motifs (AIMs), are short-linear motifs (SLiMs) of autophagy receptors and adaptor proteins that facilitates the selective recruitment of autophagy substrates to the autophagosome. ATG8 proteins are highly conserved in eukaryotes and play a key role in selective autophagy as they recognise and bind different autophagy receptors and adaptors containing a specific class of SLiMs. LIRs are characterised by degenerated sequences with a four-residue core central sequence involved in ATG8-binding, with the W/Y/FxxL/I/V pattern. Based on the aromatic amino acid in position 1 they can be classified into W-type, Y-type and F-type. This entry is the F-type LIR motif from ATG4, which contains the seqeunce FEI/VL. There are acidic residues at the N-terminal of this motif (Asp and Glu), which may contribute to stabilize the binding or may provide specificity toward a certain class of ATG8 proteins.
Pfam PF08245: Mur ligase middle domain (domain)
The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:


 * (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc).
 * (2) addition of a short polypeptide chain to the UDPMurNAc.
 * (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.


Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8) , MurD (6.3.2.9) , MurE (6.3.2.13)  and MurF (6.3.2.10) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid . All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that binds the incoming amino acid . Residues found in the three domains (the Asp50, Lys130 (GKT motif), and Glu174 residues, MurC numbering) are involved in the catalytic process . The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .
This entry represents the central domain from all four stage 2 Mur enzymes: UDP-N-acetylmuramate-L-alanine ligase (MurC), UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD), UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (MurE), and UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF). This entry also includes folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) .
Pfam PF15246: Nck-associated protein 5, Peripheral clock protein (disordered)
NCKAP5 is short for Nck-associated protein 5, which is also known as the Peripheral clock protein. NCKAP5 is a protein family, which interacts with the SH3-containing region of the adaptor protein Nck. Nck is a protein that interacts with receptor tyrosine kinases and guanine nucleotide exchange factor Sos. The role of Nck can be thought of as similar to Grb2. The role of NCKAP5 is to assist Nck with its adaptor protein role.
Pfam PF01398: JAB1/Mov34/MPN/PAD-1 ubiquitin protease (family)
Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain and PAD-1-like domain, JABP1 domain or JAMM domain.  These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signalling and protein turnover pathways in eukaryotes. Versions of the domain in prokaryotic cognates of the ubiquitin-modification pathway are shown to have a similar role, and the archael protein from Haloferax volcanii is found to cleave ubiquitin-like small archaeal modifier proteins (SAMP1/2) from protein conjugates.
Pfam PF10398: Protein of unknown function (DUF2443) (domain)
This is a small family of highly conserved proteins from bacteria, in particular Helicobacter species, The structure is a bundle of alpha helices. The function is not known.
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 PF15083: Colipase-like (family)
This is a family of colipase-like proteins.
Pfam PF06020: Drosophila roughex protein (family)
This family consists of several roughex (RUX) proteins specific to Drosophila species. Roughex can influence the intracellular distribution of cyclin A and is therefore defined as a distinct and specialised cell cycle  inhibitor for cyclin A-dependent kinase activity. Rux is though to regulate the metaphase to anaphase transition during development.
Pfam PF24349: Domain of unknown function (DUF7509) (domain)
This domain is found in a group of uncharacterised proteins from Halobacteria. It has detectable sequence similarity to domains members of the N-(deoxy)ribosyltransferase-like superfamily and it is predicted to adopt similar structure.
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 PF24413: W02B3.4-like, N-terminal domain (domain)
This domain is found at the N-terminal end of the uncharacterised protein W02B3.4 from Caenorhabditis elegans and similar animal proteins. This domain is predicted to adopt an alpha-beta fold.
Pfam PF07670: Nucleoside recognition (domain)
This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins (e.g [swissprot:O00337]). In the FeoB proteins (e.g.  [swissprot:O25396]), which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'.
Pfam PF12521: Protein of unknown function (DUF3724) (family)
This domain family is found in viruses, and is approximately 20 amino acids in length. The family is found in association with [pfam:PF00073]. There is a single completely conserved residue Y 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 PF18954: Family of unknown function (DUF5697) (family)
This entry likely contains an N-terminal Helix-tun-helix motif and is therefore likely to be a transcriptional regulator.
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 PF00403: Heavy-metal-associated domain (domain)
Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures.

These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases .

A conserved domain has been found in a number of these heavy metal transport or detoxification proteins . The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding.

Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel Î²-sheet and two Î±-helices packed in an Î±-Î² sandwich fold . This fold is common to other domains and is classified as "ferredoxin-like".
Wikipedia: In molecular biology, the HMA domain is a conserved protein domain found in a number of heavy metal transport or detoxification proteins.
Pfam PF05589: Protein of unknown function (DUF768) (family)
This family consists of several uncharacterised hypothetical proteins from Rhizobium loti.
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 PF08337: Plexin cytoplasmic RasGAP domain (domain)
This family features the C-terminal regions of various plexins (e.g. [swissprot:P51805]). Plexins are receptors for semaphorins, and plexin signalling is important in path finding and patterning of both neurons and developing blood vessels. The cytoplasmic region, which has been called a SEX domain in some members of this family, is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins. This domain acts as a RasGAP domain.
Wikipedia: A plexin is a protein which acts as a receptor for semaphorin family signaling proteins. It is classically known for its expression on the surface of axon growth cones and involvement in signal transduction to steer axon growth away from the source of semaphorin. Plexin also has implications in development of other body systems by activating GTPase enzymes to induce a number of intracellular biochemical changes leading to a variety of downstream effects.
Pfam PF22355: tRNA-splicing endonuclease subunit NEQ261 N-terminal domain (domain)
This entry represents the N-terminal domain of the tRNA-splicing endonuclease structural (beta) subunit NEQ261 from Nanoarchaeum equitans.
Pfam PF03311: Cornichon protein (family)
This entry represents a group of conserved proteins from fungi, plants to animals. They are transmembrane proteins. Proteins in this entry include budding yeast Erv14/15, Drosophila Cornichon and human CNIH1/2/3/4.
Pfam PF10576: Iron-sulfur binding domain of endonuclease III (domain)
Escherichia coli endonuclease III (EC 4.2.99.18) is a DNA repair enzyme that acts both as a DNA N-glycosylase, removing oxidised pyrimidines from DNA, and as an apurinic/apyrimidinic (AP) endonuclease, introducing a single-strand nick at the site from which the damaged base was removed. Endonuclease III is an iron-sulfur protein that binds a single 4Fe-4S cluster. The 4Fe-4S cluster does not seem to be important for catalytic activity, but is probably involved in the proper positioning of the enzyme along the DNA strand. The 4Fe-4S cluster is bound by four cysteines which are all located in a 17 amino acid region at the C-terminal end of endonuclease III. A similar region is also present in the central section of mutY and in the C-terminus of ORF-10 and of the Micro-coccus UV endonuclease.
Pfam PF22077: CRISPR-associated endonuclease C2c1 Nuc-II domain (domain)
C2c1 is a class 2 type V-B effector protein that was shown to be active for target DNA cleavage in vivo and in vitro. In contrast to Cpf1, this enzyme cleavage activity requires both crRNA and tracrRNA. The structure of C2c1 consists of an alpha-helical recognition (REC) lobe, including Helical-I and Helical-II, and a NUC lobe, including OBD, RuvC, and two Nuc domains. This entry represents the C-terminal second Nuc (Nuc-II) domain. This domain folds into an open five-stranded beta-barrel and an alpha-helix. Nuc-II is essential for cleavage activity.
Pfam PF23777: GEMI5 RBS C-terminal domain (domain)
This entry represents the RNA-binding domains RBS1 and RBS2 found at the C-terminal of Gem-associated protein 5 (GEMI5) from animals. GEMI5 is a component of the survival of motor neurons (SMN) complex, that binds small nuclear RNAs (snRNAs). The SMN complex assembles the heptameric Sm protein core on snRNAs playing a critical role in the biogenesis of small nuclear ribonucleoproteins (snRNPs). GEMI5 is also implicated in translation control, and gene expression reprogramming. GEMI5 from animals share a domain architecture consisting of two N-terminal beta-propellers followed by a TPR domain ([pfam:PF23774]) and a C-terminal RNA-binding domain. The RBS1 domain is involved in the recognition of viral IRES elements and cellular RNAs. This domain is intrinsically unstructured and interacts with RNA through conserved Arg and aromatic residues.
Pfam PF15943: Bacterial toxin YdaS (family)
YdaS is a transcription factor found in the cryptic prophage Rac of E. coli K12 and represents a novel family within the HigA superfamily as it is distantly related to HigA antitoxins. YdaS can act as a toxin whose expression is regulated by RacR and behaves as a monomer in solution. Previously, it was thought to be an antitoxin that neutralises the toxin YdaT.
Pfam PF02178: AT hook motif (conserved_site)
At hooks are DNA binding motifs with a preference for A/T rich regions.
Wikipedia: The AT-hook is a DNA-binding motif present in many proteins, including the high mobility group (HMG) proteins, DNA-binding proteins from plants and hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex.
Pfam PF06473: FGF binding protein 1 (FGF-BP1) (family)
This family consists of several mammalian FGF binding protein 1. Fibroblast growth factors (FGFs) play important roles during fetal and embryonic development. Fibroblast growth factor-binding protein (FGF-BP) 1 is a secreted protein that can bind fibroblast growth factors (FGFs) 1 and 2.
Pfam PF10841: Protein of unknown function (DUF2644) (family)
This family of proteins with unknown function appear to be restricted to Pasteurellaceae.
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.