SII-SWORD/CoKE huggingface dataset:
Pfam PF21325: E3 ubiquitin-protein ligase SHPRH, first helical domain (repeat)
This entry represents the first helical domain found towards the C-terminal end of the E3 ubiquitin-protein ligase SHPRH, a protein involved in  DNA repair. Helices in this domain adopt an arrangement similar to TPRs.
Pfam PF15414: Protein of unknown function (DUF4621) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 350 amino acids in length.
Pfam PF00519: Papillomavirus helicase (domain)
This is the C-terminal ATPase/helicase domain of Papillomavirus E1 protein, a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein [pfam:PF00508]. The domain architecture of E1 is similar to that of the SV40 T-antigen.
Pfam PF10418: Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B (domain)
Lactococcus lactis is one of the few organisms with two dihydroorotate dehydrogenases, DHODs, A and B. The B enzyme is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a hetero-tetramer composed of a central homodimer of PyrDB subunits resembling the DHODA structure and two PyrK subunits along with three different cofactors: FMN, FAD, and a [2Fe-2S] cluster. The [2Fe-2S] iron-sulfur cluster binds to this C-terminal domain of the PyrK subunit, which is at the interface between the flavin and NAD binding domains and contains three beta-strands. The four cysteine residues at the N-terminal part of this domain are the ones that bind, in pairs, to the iron-sulfur cluster. The conformation of the whole molecule means that the iron-sulfur cluster is localised in a well-ordered part of this domain close to the FAD binding site. The FAD and and NAD binding domains are FAD_binding_6, [pfam:PF00970] and NAD_binding_1, [pfam:PF00175].
Pfam PF19852: Family of unknown function (DUF6327) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 71 and 82 amino acids in length. There are two conserved sequence motifs: KKY and YQK.
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 PF23310: Plant tetratrico peptide repeats (repeat)
This entry represents the predicted tetratrico peptide repeats (TPR) found in F-box protein At2g35280 from Arabidopsis thaliana and similar plant proteins. This entry is found associated with [pfam:PF01753] in some members of this family.
Pfam PF09490: Probable cobalt transporter subunit (CbtA) (family)
This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems. Evidence for this assignment includes 1) prediction of five transmembrane segments, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localisation with a small protein (CbtB) having a single additional transmembrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site.
Pfam PF06172: Cupin superfamily (DUF985) (domain)
Family of uncharacterised proteins found in bacteria and eukaryotes that belongs to the Cupin superfamily.
Wikipedia: The cupin superfamily is a diverse superfamily of proteins named after its conserved barrel domain. The superfamily includes a wide variety of enzymes as well as non-enzymatic seed storage proteins.
Pfam PF22713: Short NACHT-associated C-Terminal domain, family 6 (domain)
The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors.
Pfam PF16809: NleF caspase inhibitor (domain)
Binds to and inhibits caspase-9, caspase-8 and caspase-4. therefore preventing caspase-induced apoptosis in the host cell.
Pfam PF05509: TraY domain (domain)
This family consists of several enterobacterial TraY proteins. TraY is involved in bacterial conjugation where it is required for efficient nick formation in the F plasmid. These proteins have a ribbon-helix-helix fold and are likely to be DNA-binding proteins.
Pfam PF01042: Endoribonuclease L-PSP (domain)
Endoribonuclease active on single-stranded mRNA.  Inhibits protein synthesis by cleavage of mRNA.  Previously thought to inhibit protein synthesis initiation. This protein may also be involved in the regulation of purine biosynthesis. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella.
Pfam PF02542: YgbB family (family)
The ygbB protein is a putative enzyme of deoxy-xylulose pathway (terpenoid biosynthesis).
Wikipedia: In molecular biology, YgbB is a protein domain. This entry makes reference to a number of proteins from eukaryotes and prokaryotes which share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme thought to aid terpenoid and isoprenoid biosynthesis, a vital chemical in all living organisms. This protein domain is part of an enzyme which catalyses a reaction in a complex pathway.
Pfam PF07955: Protein of unknown function (DUF1687) (family)
This is a putative redox protein which is predicted to have a thioredoxin fold containing a single active cysteine.
Pfam PF11826: Vibrionales, replication initiator protein RctB, central region (domain)
This region is found in the replication initiator protein RctB from Vibrio cholerae ([swissprot:Q9KNG2]) and similar sequences predominantly found in Vibrionales. RctB mediates oriCII-based replication and other regulatory processes. This protein is organised into four domains and adopts a dimeric configuration. This entry represents the two central domains, one consisting of a seven-stranded beta- sheet that forms the interface of the dimer by forming a swapped configuration with the same domain of the other monomer. It seems to be involved in DNA binding.
Pfam PF00396: Granulin (family)
Metazoan granulins  are a family of cysteine-rich peptides of about 6 Kd which may have multiple biological activity. A precursor protein (known as acrogranin) potentially encodes seven different forms of granulin (grnA to grnG) which are probably released by post-translational proteolytic processing. Granulins are evolutionary related to PMP-D1, a peptide extracted from the pars intercerebralis of migratory locusts . A schematic representation of the structure of a granulin is shown below:

       xxxCxxxxxCxxxxxCCxxxxxxxxCCxxxxxxCCxxxxxCCxxxxxCxxxxxxCx

'C': conserved cysteine probably involved in a disulphide bond.

In plants a granulin domain is often associated with the C terminus of cysteine proteases belong to the MEROPS peptidase family C1, subfamily C1A (papain).
Wikipedia: Granulin is a protein that in humans is encoded by the GRN gene. Each granulin protein is cleaved from the precursor progranulin, a 593 amino-acid-long and 68.5 kDa protein. While the function of progranulin and granulin have yet to be determined, both forms of the protein have been implicated in development, inflammation, cell proliferation and protein homeostasis. The 2006 discovery of the GRN mutation in a population of patients with frontotemporal dementia has spurred much research in uncovering the function and involvement in disease of progranulin in the body. While there is a growing body of research on progranulin's role in the body, studies on specific granulin residues are still limited.
Pfam PF15497: snRNA-activating protein complex subunit 19, SNAPc subunit 19 (family)
SNAPc19 is a family of proteins found in eukaryotes. It is one of the five core components of the snRNA-activating protein complex or SNAPc that helps direct the nucleation of RNA polymerases II and III. The core RNA polymerase II snRNA promoters consist of a single essential element, the proximal sequence element (PSE), whereas the core RNA polymerase III snRNA promoters consist of both a PSE and a TATA box. The SNAPc binds to the PSE of both of these. SNAPc recognises the PSE sequence common to all human snRNA genes, irrespective of polymerase specificity. SNAPc is also known as the PSE transcription factor (PTF) or PSE-binding protein (PBP). The human SNAP19 and SNAP45 subunits are dispensable for transcription in vitro and are not as widely conserved as the other three, SNAP190, SNAP43 and SNAP50, suggesting that these vertebrate-specific SNAPc subunits may have adapted specialised regulatory roles for snRNA gene transcription.
Pfam PF06727: Protein of unknown function (DUF1207) (family)
This family consists of a number of hypothetical bacterial proteins of around 410 residues in length which seem to be specific to Chlamydia species. 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 PF23925: ELP1 alpha-solenoid (repeat)
This entry represents the alpha-solenoid domain found within the C-terminal dimerization domain of Elongator complex protein 1 (ELP1), from eukaryotes. Elongator is a conserved protein complex implicated in multiple processes including regulation of transcription, alpha-tubulin acetylation and tRNA modification. Mutations in the ELP1 gene have been shown to cause the neurodegenerative disease familial dysautonomia. The C-terminal dimerization domain consists of 28 alpha-helices organised in three domains: an elongated alpha-solenoid domain (helices 1 to 14); a TPR-like domain, formed by six double-helix repeats (helices 15 to 26); and a three-helix bundle, C-terminal cap (helices 26 to 28). Residues within the alpha-14-helix are highly conserved from yeast to human and act as a kink to maintain the TPR-like domain and alpha-solenoid domain at nearly a 90-degree angle. ELP1 self-association contributes to its stability and is important for Elongator assembly. ELP1 is considered to function both as a scaffold, for Elongator complex ELP2 and ELP3 binding, and as a docking site for various factors that regulate Elongator activity. Also known as IKAP, ELP1 acts as a regulator of IkB kinase complex involved in proinflammatory cytokine signalling.
Pfam PF16451: Betacoronavirus-like spike glycoprotein S1, N-terminal (domain)
This entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like domain (NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Either the S1 NTD or S1 RBD, or occasionally both, are involved in binding to host receptors. S1 NTD is located on the side of the spike trimer and mainly recognises sugar receptors. For many betacoronaviruses (b-CoVs), for example mouse hepatitis virus (MHV), the RBD is located in the NTD. The structure of the MHV S1 NTD showed the same fold as human galectins (galactose-binding lectin), however it does not bind any sugar; instead, it binds to the carcinoembryonic antigen cell-adhesion molecule CEACAM1) through protein-protein interactions. All three CEACAM21a-binding sites in MHV spikes can be fully occupied by CEACAM1a. It has been shown that CEACAM1a binding to the MHV spike weakens the interactions between S1 and S2 and facilitates the proteolysis of the spike protein and dissociation of S1. The homologous bovine CoV (BCov) S1 NTD also possesses a galectin fold but binds to sialic acid-containing moieties on host cell membranes, as does the NTD of three other group A b-Covs, namely human CoV (HCoV) OC43, avian b-CoV, and infectious bronchitis virus (IBV). Despite the S1 NTD of human respiratory b-CoV HKU1 being highly homologous to the NTDs of MHV and bovine CoV, it does not bind to either sugar or human carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) and the RBD is found instead in the S1 RBD domain.
Pfam PF14533: Ubiquitin-specific protease C-terminal (family)
This C-terminal domain on many long ubiquitin-specific proteases has no known function.
Pfam PF10587: Eukaryotic elongation factor 1 beta central acidic region (domain)
Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome . EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.
Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) .
This region is found in the centre of the beta subunits of Elongation factor-1.
Wikipedia: eEF-1 are two eukaryotic elongation factors. It forms two complexes, the EF-Tu homolog EF-1A and the EF-Ts homolog EF-1B, the former's guanide exchange factor. Both are also found in archaea.
Pfam PF21574: CRISPR-associated endonuclease Cas9, C-terminal domain (domain)
This domain is found at the C-terminal end of CRISPR-associated endonuclease Cas9 from Staphylococcus aureus (Cas9). This protein adopts a bilobed architecture consisting of a REC lobe and a NUC lobe connected by an arginine-rich bridge helix and a linker loop. The C-terminal region, known as the PI domain, can be divided into a Topoisomerase-homology (TOPO) domain ([pfam:PF18070]) and a C- terminal domain (this entry). This domain forms a twisted six- stranded anti-parallel beta-sheet.
Pfam PF03946: Ribosomal protein L11, N-terminal domain (domain)
The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain.
Pfam PF15251: Telomere attrition and p53 response 1 protein-like (family)
This entry represents the Telomere attrition and p53 response 1 protein (TAPR1) from eukaryotes, including TAPR1 from human (also known as C16orf72/HAPSTR1), which is a multistress-responsive protein that functions as a negative regulator of TP53/P53 in the cellular response to telomere erosion and probably also DNA damage. It may attenuate p53/TP53 activation through the E3 ubiquitin ligase HUWE1 which also promotes TAPR1's degradation. This family also includes uncharacterised proteins from fungi, such as YJR056C from yeast.
Pfam PF09681: N-terminal phage replisome organiser (Phage_rep_org_N) (family)
This entry represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region is N-terminal to the low-complexity region.
Pfam PF25145: NfeD1b, N-terminal domain (domain)
This domain is found N-terminal in the membrane protein NfeD1b from B. subtilis and related bacterial proteins. The NfeD1b is composed of an N-terminal cytoplasmic ClpP serine protease-like domain (this entry), transmembrane domain, and a C-terminal OB (oligosaccharide / oligonucleotide-binding) fold domain. NfaD1b is a member of the NfeD (nodulation formation efficiency D) family which was divided into two groups : long and short forms. Long-form NfeD homologs contain a putative ClpP serine protease-like domain while short-form homologs have in common the C-terminal OB fold domain ([pfam:PF01957]). Despite global similarity to ClpP serine proteases, this domain lacks the typical for these enzymes Ser, His, Asp catalytic triad and of these, has only Ser residue conserved in equivalent position.
Pfam PF09129: Cholesterol oxidase, substrate-binding (domain)
The substrate-binding domain found in Cholesterol oxidase is composed of an eight-stranded mixed beta-pleated sheet and six alpha-helices. This domain is positioned over the isoalloxazine ring system of the FAD cofactor bound by FAD_binding_4 (PF:PF01565) and forms the roof of the active site cavity, allowing for catalysis of oxidation and isomerisation of cholesterol to cholest-4-en-3-one.
Wikipedia: In enzymology, a cholesterol oxidase (EC 1.1.3.6) is an enzyme that catalyzes the chemical reactioncholesterol + O2  cholest-4-en-3-one + H2O2
Pfam PF12419: SNF2 Helicase protein (family)
This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with [pfam:PF00271], [pfam:PF00176]. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this.
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 PF02366: Dolichyl-phosphate-mannose-protein mannosyltransferase (family)
This is a family of Dolichyl-phosphate-mannose-protein mannosyltransferase proteins [ec:2.4.1.109].  These proteins are responsible for O-linked glycosylation of proteins, they catalyse the reaction:- Dolichyl phosphate D-mannose + protein  dolichyl phosphate + O-D-mannosyl-protein.  Also in this family is [swissprot:Q94891] Drosophila rotated abdomen protein which is a putative mannosyltransferase. This family appears to be distantly related to [pfam:PF02516] (A Bateman pers. obs.). This family also contains sequences from ArnTs (4-amino-4-deoxy-L-arabinose lipid A transferase). They catalyse the addition of 4-amino-4-deoxy-l-arabinose (l-Ara4N) to the lipid A moiety of the lipopolysaccharide. This is a critical modification enabling bacteria (e.g. Escherichia coli and Salmonella typhimurium) to resist killing by antimicrobial peptides such as polymyxins. Members such as [swissprot:O52327] are predicted to have 12 trans-membrane regions. The N-terminal portion of these proteins is hypothesised to have a conserved glycosylation activity which is shared between distantly related oligosaccharyltransferases ArnT and PglB families.
Pfam PF18475: PIN domain (domain)
This is a bacterial PIN-like domain of unknown function.
Pfam PF04209: Homogentisate 1,2-dioxygenase C-terminal (domain)
Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria.  The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is coordinated near the interface between the trimers. This entry represents the C-terminal active site domain.
Pfam PF16365: Ethanolamine utilization protein EutK C-terminus (domain)
This is the C-terminal domain of the ethanolamine utilization protein EutK. It is a helix-turn-helix domain and is predicted to bind to nucleic acids.
Pfam PF11989: Retrograde transport protein Dsl1 C terminal (repeat)
Dsl1 is a peripheral membrane protein required for transport between the Golgi and the endoplasmic reticulum. It is localised to the ER membrane, and in vitro it specifically binds to coatomer, the major component of the protein coat of COPI vesicles. Binding sites for coatomer are found on a disorganised region between the C and N termini of Dsl1. The C terminal domain is involved in binding to the Sec39 subunit of the Dsl1p complex. The N terminal complexes with another subunit of the Dsl1p complex called Tip20 which forms heterodimers by pairing the N termini of each protein. It is a component of DSL1 complex, which, together with the exocyst, conserved oligomeric Golgi (COG) and Golgi-associated retrograde protein (GARP), are part of the complexes associated with tethering containing helical rods (CATCHR) family, sharing an evolutionary origin and structure organisation. This domain has an alpha-helical bundle fold.
Pfam PF10596: U6-snRNA interacting domain of PrP8 (domain)
This domain incorporates the interacting site for the U6-snRNA as part of the U4/U6.U5 tri-snRNPs complex of the spliceosome, and is the prime candidate for the role of cofactor for the spliceosome's RNA core. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor.
Pfam PF03846: Cell division inhibitor SulA (family)
This family includes the cell division inhibitor SulA, which binds to FtsZ and halts cell division. It binds the T7 loop surface of FtsZ, which locates opposite the nucleotide-binding site, and blocks polymer formation.
Pfam PF04696: pinin/SDK/memA/ protein conserved region (family)
Members of this family have very varied localisations within the eukaryotic cell. pinin is known to localise at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque.  SDK2/3 is a dynamically localised nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing.  memA is a tumour marker preferentially expressed in human melanoma cell lines.  A common feature of the members of this family is that they may all participate in regulating protein-protein interactions.