SII-SWORD/CoKE huggingface dataset:
Pfam PF04752: ChaC-like protein (family)
The ChaC family of proteins function as gamma-glutamyl cyclotransferases acting specifically to degrade glutathione but not other gamma-glutamyl peptides. It is is conversed across all phyla and represents a new pathway for glutathione degradation in living cells.
Pfam PF12277: Protein of unknown function (DUF3618) (family)
This domain family is found in bacteria, and is approximately 50 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 PF17807: Variant UBP zinc finger (domain)
This domain is found in ubiquitin C-terminal hydrolase enzymes and is related to the [pfam:PF02148] domain.  However, it has an altered pattern of zinc binding residues.
Pfam PF12293: Putative outer membrane core complex of type IVb secretion (family)
T4BSS_DotH_IcmK is a family of bacterial transporter proteins from Proteobacteria. DotH is an integral outer membrane component and it may form an outer membrane complex along with DotD and DotC functionally equivalent to secretins. DotH is the strongest candidate for the VirB9 counterpart of other T4BSS systems.
Wikipedia: Secretion is the movement of material from one point to another, such as a secreted chemical substance from a cell or gland. In contrast, excretion is the removal of certain substances or waste products from a cell or organism. The classical mechanism of cell secretion is via secretory portals at the plasma membrane called porosomes. Porosomes are permanent cup-shaped lipoprotein structures embedded in the cell membrane, where secretory vesicles transiently dock and fuse to release intra-vesicular contents from the cell.
Pfam PF25068: Tetratricopeptide repeat protein 21 forth ARM domain (repeat)
This entry represents the forth ARM-repeats domain found around the middle of Tetratricopeptide repeat protein 21 (TT21) from human and its homologues. TT21 is an intraflagellar transport (IFT)-associated protein required for spermatogenesis. It is involved in sperm flagellar formation and intraflagellar transport.
Pfam PF23908: Domain of unknown function (DUF7250) (domain)
This entry represents a domain of unknown function found in phage proteins, approximately 100 residues in length. The domain is found in Microbacterium phages.
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 PF14410: HNH/ENDO VII superfamily nuclease with conserved GHE residues (family)
A predicted nuclease of the HNH/EndoVII superfamily of the treble  clef fold which is closely related to the NucA-like family. The  name is derived from the conserved G, H and E residues. It is found in several bacterial polymorphic toxin systems. Some GH-E members preserve the conserved cysteines of the treble-clef  suggesting that they might represent potential evolutionary  intermediates from a classical HNH domain to the derived NucA-like  form.
Pfam PF10414: Sirohaem synthase dimerisation region (domain)
Bacterial sulfur metabolism depends on the iron-containing porphinoid sirohaem. CysG, S-adenosyl-L-methionine (SAM)-dependent bis-methyltransferase, dehydrogenase and ferrochelatase, synthesises sirohaem from uroporphyrinogen III via reactions which encompass two branchpoint intermediates in tetrapyrrole biosynthesis, diverting flux first from protoporphyrin IX biosynthesis and then from cobalamin (vitamin B12) biosynthesis. CysG is a dimer of two structurally similar protomers held together asymmetrically through a number of salt-bridges across complementary residues in the CysG_dimeriser region to produce a series of active sites, accounting for CysG's multifunctionality, catalysing four diverse reactions: two SAM-dependent methylations, NAD+-dependent tetrapyrrole dehydrogenation and metal chelation. The CysG_dimeriser region holding the two protomers together is of 74 residues.
Wikipedia: In molecular biology, sirohaem synthase (CysG) is a multi-functional enzyme with S-adenosyl-L-methionine (SAM)-dependent bismethyltransferase, dehydrogenase and ferrochelatase activities. Bacterial sulphur metabolism depends on the iron-containing porphinoid sirohaem. CysG synthesizes sirohaem from uroporphyrinogen III via reactions which encompass two branchpoint intermediates in tetrapyrrole biosynthesis, diverting flux first from protoporphyrin IX biosynthesis and then from cobalamin biosynthesis. CysG is a dimer. Its dimerisation region is 74 amino acids long, and acts to hold the two structurally similar protomers held together asymmetrically through a number of salt-bridges across complementary residues within the dimerisation region. CysG dimerisation produces a series of active sites, accounting for CysG's multi-functionality, catalysing four diverse reactions:Two SAM-dependent methylations
NAD+-dependent tetrapyrrole dehydrogenation
Metal chelation
Pfam PF18115: DNA repair protein Crb2 Tudor domain (domain)
This is the tudor domain found in DNA repair protein crb2. Structural and functional studies of Crb2 and its mammalian homologue 53BP1 indicate that the conserved tandem-Tudor domain of 53BP1 and Crb2 preferentially interacts with H4K20me2, though it also binds to H4K20me1. Furthermore, despite low amino acid sequence similarity, Crb2 is structurally related to 53BP1 in having two tudor domains and a conserved dimethyllysine-binding pocket, and that, like 53BP1, it directly binds H4-K20me2.
Wikipedia: In molecular biology, a Tudor domain is a conserved protein structural domain originally identified in the Tudor protein encoded in Drosophila. The Tudor gene was found in a Drosophila screen for maternal factors that regulate embryonic development or fertility. Mutations here are lethal for offspring, inspiring the name Tudor, as a reference to the Tudor King Henry VIII and the several miscarriages experienced by his wives.
Pfam PF00515: Tetratricopeptide repeat (repeat)
The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins . It mediates protein-protein interactions and the assembly of multiprotein complexes . The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.

The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel Î±-helices . The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B.
Pfam PF05703: Auxin canalisation (family)
This domain is frequently found at the N-terminus of proteins containing [pfam:PF08458] at the C-terminus. It is a component of the auto-regulatory loop which enables auxin canalisation by recruitment of the PIN1 auxin efflux protein to the cell membrane.
Pfam PF05083: LST-1 protein (family)
B144/LST1 is a gene encoded in the human major histocompatibility complex that produces multiple forms of alternatively spliced mRNA and encodes peptides fewer than 100 amino acids in length. B144/LST1 is strongly expressed in dendritic cells. Transfection of B144/LST1 into a variety of cells induces morphologic changes including the production of long, thin filopodia.
Pfam PF01749: Importin beta binding domain (repeat)
This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates  formation of the importin alpha beta complex; required for classical  NLS import of proteins into the nucleus, through the nuclear pore  complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain.
Wikipedia: Importin is a type of karyopherin that transports protein molecules from the cell's cytoplasm to the nucleus. It does so by binding to specific recognition sequences, called nuclear localization sequences (NLS).
Pfam PF06323: Phage antitermination protein Q (family)
This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 82 gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator.
Pfam PF00021: u-PAR/Ly-6 domain (domain)
This extracellular disulphide bond rich domain is related to [pfam:PF00087].
Wikipedia: The LU domain is an evolutionarily conserved protein domain of the three-finger protein superfamily. This domain is found in the extracellular domains of cell-surface receptors and in either GPI-anchored or secreted globular proteins, for example the Ly-6 family, CD59, and Sgp-2.
Pfam PF02589: LUD domain (domain)
This entry represents a domain found in lactate utilization proteins B (LutB) and C (LutC), as well as several uncharacterised proteins. LutB and LutC are encoded by th conserved LutABC operon in bacteria. They are involved in lactate utilization and is implicated in the oxidative conversion of L-lactate into pyruvate
Pfam PF02839: Carbohydrate-binding module family 5/12 (family)
This short domain is found in many different glycosyl hydrolase enzymes, representing the carbohydrate-binding module family 5/12, including proteins such as chitinase A1, chitinase B, and endoglucanase. The domain has a carbohydrate-binding function and contains six aromatic groups that may be important for binding. These modules have a core structure consisting of a 3-stranded meander beta-sheet.
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF15151: Response gene to complement 32 protein family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 44 and 130 amino acids in length. There is a conserved KLGDT sequence motif.
Wikipedia: Regulator of cell cycle RGCC (RGCC) also known as response gene to complement 32 protein (RGC-32) is a protein that in humans is encoded by the RGCC gene.
Pfam PF10120: Thiamine-phosphate synthase ThiN (domain)
This entry represents thiamine-phosphate synthase ThiN which condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP). Vitamin B1 (thiamine pyrophosphate) is involved in several microbial metabolic functions. Thiamine biosynthesis is accomplished by joining two intermediate molecules that are synthesized separately, HMP-PP and HET-P. In the archaeon Natrialba magadii, ThiE and ThiN, are known to join HMP-PP ( hydroxymethylpyrimidine pyrophosphate) and HET-P (hydroxyethylthiazole phosphate) to generate thiamine phosphate. Whereas ThiE in Natrialba magadii is a mono-functional protein, ThiN exists as a C-terminal domain in a ThiDN fusion protein - examples of all three forms, from various prokaryotes, are found in this entry. Another example is the transcriptional repressor ThiR from Haloferax volcanii (SwissProt:D4GSS2) which contains a ThiN domain but it is catalytically inactive as it lacks the conserved Met residue found in the extended alpha-helix near the active site His in ThiN. Moreover, it was shown that thiamine biosynthesis in archaea is regulated by ThiR and not by a riboswitch.
Pfam PF20740: Outer membrane-associated lipoprotein TP0453 (domain)
This domain is found in TP0453, a lipoprotein associated with the inner leaflet of the outer membrane of Treponema pallidum. This protein consists of an alpha/beta/alpha-fold and includes five stably folded amphipathic helices and may function as a carrier of lipids, glycolipids, and/or derivatives during the biogenesis of the outer membrane.
Pfam PF12912: NLPC_P60 stabilising domain, N term (family)
This domain, at the N-terminus, appears to be the stabilising domain for the structure from [swissprot:Q72DN3], PDB:3m1u, which is a four-domain protein. The next domain is an SH3b1, the third an SH3b2 and the last, the C-terminal region, the catalytic domain of the cysteine-peptidase type, ie family NLPC_P60, [pfam:PF00877] (details derived from TOPSAN).
Pfam PF01775: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A (domain)
This family includes: archaeal 50S ribosomal protein L18Ae, often referred to as L20e or LX; fungal 60S ribosomal protein L20; and higher eukaryote 60S ribosomal protein L18A.
Pfam PF08707: Primase C terminal 2 (PriCT-2) (domain)
This alpha helical domain is found at the C terminal of primases.
Pfam PF11804: Protein of unknown function (DUF3325) (family)
This family of short proteins are functionally uncharacterized. This family is restricted to Alpha-, Beta- and Gamma-proteobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF21900: Family of unknown function (DUF6920) (domain)
This entry represents a set of uncharacterised proteins found in prokaryotes. They share remote similarity to LolA and LolB outer-membrane lipoproteins. Similar to LolA and LolB these proteins are predicted to have a hydrophobic cavity consisting of an unclosed beta-barrel and an alpha-helical lid.
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 PF03791: KNOX2 domain (family)
The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerisation.
Pfam PF01099: Uteroglobin family (domain)
Uteroglobin is a homodimer of two identical 70 amino acid polypeptides linked by two disulphide bridges. The precise role of uteroglobin has still to be  elucidated.
Pfam PF00169: PH domain (domain)
PH stands for pleckstrin homology.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF00969: Class II histocompatibility antigen, beta domain (domain)
This entry represents the N-terminal domain (also called beta-1 domain) of the beta chain of class II MHC glycoproteins from vertebrates.
Major Histocompatibility Complex (MHC) glycoproteins are heterodimeric cell surface receptors that function to present antigen peptide fragments to T cells responsible for cell-mediated immune responses. MHC molecules can be subdivided into two groups on the basis of structure and function: class I molecules present intracellular antigen peptide fragments (~10 amino acids) on the surface of the host cells to cytotoxic T cells; class II molecules present exogenously derived antigenic peptides (~15 amino acids) to helper T cells. MHC class I and II molecules are assembled and loaded with their peptide ligands via different mechanisms. However, both present peptide fragments rather than entire proteins to T cells, and are required to mount an immune response.
Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection) .

MHC class II molecules are comprised of two membrane-spanning chains, alpha and beta, of similar size. Both chains consist of two globular domains (N-and C-terminal), and a transmembrane segment to anchor them to the membrane . A groove in the structure acts as the peptide-binding site.
Pfam PF05434: TMEM9 (family)
This family contains several eukaryotic transmembrane proteins which are homologous to human transmembrane protein 9 [swissprot:Q9P0T7]. The TMEM9 gene encodes a 183 amino-acid protein that contains an N-terminal signal peptide, a single transmembrane region, three potential N-glycosylation sites and three conserved cys-rich domains in the N-terminus, but no known functional domains. The protein is highly conserved between species from Caenorhabditis elegans to man and belongs to a novel family of transmembrane proteins. The exact function of TMEM9 is unknown although it has been found to be widely expressed and localised to the late endosomes and lysosomes. Members of this family contain [pfam:PF03128] repeats in their N-terminal region.
Pfam PF12940: Recombination-activation protein 1 (RAG1), recombinase (family)
This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex.  The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination.  RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS).  Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerises with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerisation and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008.
Wikipedia: The recombination-activating genes (RAGs) encode parts of a protein complex that plays important roles in the rearrangement and recombination of the genes encoding immunoglobulin and T cell receptor molecules. There are two recombination-activating genes RAG1 and RAG2, whose cellular expression is restricted to lymphocytes during their developmental stages. The enzymes encoded by these genes, RAG-1 and RAG-2, are essential to the generation of mature B cells and T cells, two types of lymphocyte that are crucial components of the adaptive immune system.
Pfam PF00570: HRDC domain (domain)
The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.
Pfam PF12679: ABC-2 family transporter protein (domain)
This family is related to the ABC-2 membrane transporter family.
Wikipedia: The ABC transporters, ATP synthase (ATP)-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. ABC transporters belong to translocases.
Pfam PF16977: C-terminal domain of apextrin (family)
ApeC domain was first identified from two apextrin-like proteins (ALP) of the amphioxus Branchiostoma japonicum. Our functional studies show that amphioxus ALP1 and ALP2 are important anti-bacterial effectors, and that the apeC domain of the ALP1/2 mediates the bacterial recognition by binding to bacterial muramyl dipeptide (MDP). Further analysis shows that the apeC domain is present in various proteins from cnidarians, molluscs, arthropods, hemichordates, echinoderms and amphioxus. The apeC domain is also found to form different domain combinations with other domains (in press).
Pfam PF16244: YcdB, YcdC repeated domain (domain)
This entry represents a domain that is generally found in two copies in YcdB and YcdC from B.  subtilis. These proteins are uncharacterised. The C-terminal half of this domain appears to show similarity at the sequence level to the PEPSY domain.
Pfam PF21006: Nitrile hydratase beta subunit, N-terminal (domain)
Nitrile hydratases (NHases) [ec:4.2.1.84] are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit. Beta subunit consists of an N-terminal helical domain, represented in this entry, and a C-terminal SH3-like domain ([pfam:PF02211]). Thiocyanate hydrolase (SCNase) is a member of the NHase family and comprises alpha, beta and gamma subunits, which share amino acid sequence similarities with NHase beta subunit C-terminal, beta subunit N-terminal and NHase alpha subunit, respectively.
Wikipedia: Nitrile hydratases are mononuclear iron or non-corrinoid cobalt enzymes that catalyse the hydration of diverse nitriles to their corresponding amides:R-C≡N + H2O → R-C(O)NH2
Pfam PF12208: Domain of unknown function (DUF3601) (domain)
This domain family is found in bacteria, and is approximately 80 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.