SII-SWORD/CoKE huggingface dataset:
Pfam PF12124: Betacoronavirus SUD-C domain (domain)
This domain is found in betacoronavirus non-structural protein NSP3,  and is about 65 amino acids in length. It was originally thought to  exist only in SARS-coronaviruses, and so was termed the SARS-unique  domain (SUD), however this has since been shown to be incorrect. The NSP3 is the product of ORF1a, proteolytically released from the pp1a/1ab polyprotein. The SUD domain has three globular domains, SUD-N (N-terminal), SUD-M (middle region of SUD), and SUD-C (C-terminal). SUD-C adopts a fold consisting of seven beta-strands arranged in an anti-parallel beta-sheet, and two alpha-helices which are packed against the same side of the beta-sheet. It adopts a frataxin-like fold with structural similarities to DNA-binding domains. It has been shown that SUD-C binds to single-stranded RNA and recognises purine bases more strongly than pyrimidine bases, but these interactions are stabilised in the presence of SUD-M. The function of this domain is not clear but studies of structural homologues of SUD-C suggest that it could be related to metal, adenylate and nucleic acid binding.
Pfam PF15432: Accessory Sec secretory system ASP3 (family)
Sec-ASP3 is family of bacterial proteins involved in the Sec secretory system. The family forms part of the accessory SecA2/SecY2 system specifically required to export GspB, a serine-rich repeat cell-wall glycoprotein adhesin encoded upstream in the same operon.
Pfam PF05750: Rubella capsid protein (family)
Rubella virus is an enveloped positive-strand RNA virus of the family Togaviridae. Virions are composed of three structural proteins: a capsid and two membrane-spanning glycoproteins, E2 and E1. During virus assembly,  the capsid interacts with genomic RNA to form nucleocapsids. It has been discovered that capsid phosphorylation serves to negatively regulate binding of viral genomic RNA. This may delay the initiation of nucleocapsid assembly until sufficient amounts of virus glycoproteins accumulate at the budding site and/or prevent non-specific binding to cellular RNA when levels of genomic RNA are low. It follows that at a late stage in replication, the capsid may undergo dephosphorylation before nucleocapsid assembly occurs.
Pfam PF20502: DNA-dependent protein kinase catalytic subunit, CC1/2 (repeat)
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is involved in DNA nonhomologous end joining (NHEJ) which is recruited by Ku70/80 heterodimer to DNA ends and required for double-strand break (DSB) repair. It folds into three well-defined large structural units, consisting of a N-terminal region, the Circular Cradle (consisting of five supersecondary alpha-helical structures CC1 to CC5), and the C-terminal Head (comprising FAT, FRB, kinase, and FATC). The N-terminal and CCs regions resemble HEAT repeats, and thus, they are also referred to as N-HEAT and M-HEAT ('middle'), respectively. The CCs form a curved elliptical ring that serves as a scaffold to maintain the integrity of the whole complex. This entry represents CC1 and CC2, which contain the Highly conserved region I (HCR-I).
Pfam PF00694: Aconitase C-terminal domain (domain)
Members of this family usually also match to [pfam:PF00330]. This domain undergoes conformational change in the enzyme mechanism.
Pfam PF21287: Complement factor I, KAZAL domain (domain)
Complement factor I (CFAI) is a trypsin-like serine protease that plays an essential role in regulating the immune response by controlling all complement pathways. It cleaves three peptide bonds in the alpha-chain of C3b and two in the alpha-chain of C4b which inactivate these proteins. It consists of an N-terminal FI and membrane attack domain (FIMAC or Factor I-like modules FIM), a scavenger receptor cysteine-rich (SRCR) domain ([pfam:PF00530]), LDLRA1 and LDLRA2 ([pfam:PF00057]) and a C-terminal catalytic serine protease domain ([pfam:PF00089]). FIMs are also present in complement proteins C6 and C7, and participate in protein-protein interactions that critical to the progress of a complement-mediated immune response. In CFAI, the FIMAC domain is important for the ability of FI to degrade C4b and C3b. It consists of a small N-terminal FOLN subdomain ([pfam:PF21286]) and a larger C-terminal KAZAL domain. This entry represents the KAZAL domain of CFAI FIMAC domain.
Pfam PF24026: Family of unknown function (DUF7337) (family)
This entry represents a small family of uncharacterised phage 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 PF24193: Domain of unknown function (DUF7418) (domain)
This entry represents a small uncharacterised family of phage proteins.  It adopts a novel triangular beta prism 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 PF23245: PARP14, second RRM domain (domain)
This domain is found in human Protein mono-ADP- ribosyltransferase PARP14 and related proteins. PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins. In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation. The domain represented by this entry is an RRM domain found second in the human PARP14.
Pfam PF00189: Ribosomal protein S3, C-terminal domain (domain)
This family contains a central domain [pfam:PF00013], hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain.      Some are much longer.
Pfam PF10083: Uncharacterized protein conserved in bacteria (DUF2321) (family)
Members of this family of hypothetical bacterial proteins have 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 PF03358: NADPH-dependent FMN reductase (domain)
This domain in found in several flavoproteins such as FMN-dependent NADPH-azoreductase, which catalyses the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines , and NAD(P)H:quinone oxidoreductase, which reduces quinones to the hydroquinone state to prevent interaction of the semiquinone with O2 and production of superoxide . In Arabidopsis NADPH:quinone oxidoreductase is involved in detoxification pathways . NAD(P)H:quinone oxidoreductase prefers NADH over NADPH, while FMN-dependent NADPH-azoreductase requires NADPH, but not NADH, as an electron donor for its activity.
Pfam PF05178: KRI1-like family (family)
The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus.
Pfam PF09706: CRISPR-associated protein (Cas_CXXC_CXXC) (domain)
CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes a conserved region of about 65 amino acids from an otherwise highly divergent protein found in a minority of CRISPR-associated protein regions. This region features two motifs of CXXC.
Pfam PF02295: Adenosine deaminase z-alpha domain (domain)
This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric  hindrance.
Wikipedia: In molecular biology, the protein domain Adenosine deaminase z-alpha domain  refers to an evolutionary conserved protein domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA-editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.
Pfam PF21255: DNMT3, ADD PHD zinc finger (domain)
DNMT3s are de novo DNA methyltransferases responsible for the establishment of DNA methylation patterns in mammalian genomes. The ATRX-DNMT3-DNMT3L (ADD) domain contains two parts, a C2-C2-like zinc finger ([pfam:PF17980]) and a PHD-like zinc finger, represented in this entry. In this domain, the conserved His residue observed in classical PHD zinc fingers is replaced by a cysteine.
Pfam PF00411: Ribosomal protein S11 (family)
Small ribosomal subunit protein uS11, previously known as Ribosomal protein S11 , plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit.
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 PF08205: CD80-like C2-set immunoglobulin domain (domain)
These domains belong to the immunoglobulin superfamily.
Wikipedia: The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three or four constant domains. Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set, C1-set, C2-set and I-set. Structural studies have shown that these domains share a common core Greek-key beta-sandwich structure, with the types differing in the number of strands in the beta-sheets as well as in their sequence patterns.
Pfam PF01649: Ribosomal protein S20 (family)
Bacterial ribosomal protein S20 interacts with 16S rRNA.
Pfam PF07692: Low iron-inducible periplasmic protein (family)
In Chlamydomonas reinhardtii, the gene encoding [swissprot:Q9LD42] is induced by iron deficiency.  In green algae, this protein is periplasmic. The two paralogues FEA1 and FEA2 are the major proteins secreted by iron-deficient Chlamydomonas reinhardtii, and both are up-regulated in response to iron deficiency. FEA1 but not FEA2 is up-regulated by high CO2 concentration. Both FEA1 and FEA2 are secreted into the periplasmic space and genetic evidence confirms that their association with the cell is required for growth in low iron.
Pfam PF02232: Alpha trans-inducing protein (Alpha-TIF) (family)
Alpha-TIF, a virion protein (VP16), is involved in transcriptional activation of viral immediate early (IE) promoters (alpha genes). Specificity of [swissprot:P23990] for IE genes is conferred by the  400 residue N-terminal, the 80 residue C-terminal is responsible for transcriptional activation.
Wikipedia: Vmw65, also known as VP16 or α-TIF is a trans-acting protein that forms a complex with the host transcription factors Oct-1 and HCF to induce immediate early gene transcription in the herpes simplex viruses.
Pfam PF09599: Salmonella-Shigella invasin protein C (IpaC_SipC) (family)
This entry represents a family of proteins associated with bacterial type III secretion systems, which are injection machines for virulence factors into host cell cytoplasm. Characterized members of this protein family are known to be secreted and are described as invasins, including IpaC from Shigella flexneri and SipC from Salmonella typhimurium. Members may be referred to as invasins, pathogenicity island effectors, and cell invasion proteins.
Pfam PF08780: Nucleotidyltransferase substrate binding protein like (domain)
Nucleotidyltransferases (EC 2.7.7) comprise a large enzyme family with diverse roles in polynucleotide synthesis and modification. This domain is structurally related to kanamycin nucleotidyltransferase (KNTase) and forms a complex with HI0073, a sequence homolog of the nucleotide-binding domain of this nucleotidyltransferase superfamily.
Pfam PF16111: Domain of unknown function (DUF4829) (family)
This family consists of several uncharacterized proteins around 150 residues in length and is mainly found in various Clostridium species. The function of this family is unknown.
Pfam PF22160: Maltose-forming alpha-amylase-like, C-terminal domain (domain)
This domain is found in the maltose-forming alpha-amylase from the hyperthermophilic archaeon Pyrococcus sp. ST04 (PSMA). This enzyme is able to hydrolyse both alpha-1,4-glucosidic and alpha-1,6-glucosidic bonds. PSMA protein consists of two domains: an N-terminal domain with a typical glycoside hydrolase 57 family (beta]/alpha)7-barrel fold and a C-terminal domain composed of alpha-helical bundles. This entry represents the C-terminal domain.
Pfam PF09584: Phage shock protein PspD (Phageshock_PspD) (family)
Members of this family are phage shock protein PspD, found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown.
Pfam PF22307: Envelope glycoprotein GP2-like, HR1-HR2 (domain)
This entry spans heptad repeats 1 and 2 of the glycoprotein (GP) from Ebola and Marburg viruses. Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). This domain may have been acquired via horizontal transfer from retroviruses.
Pfam PF01702: Queuine tRNA-ribosyltransferase (domain)
This is a family of queuine tRNA-ribosyltransferases [ec:2.4.2.29], also known as tRNA-guanine transglycosylase and guanine insertion enzyme. Queuine tRNA-ribosyltransferase modifies tRNAs for asparagine,  aspartic acid, histidine and tyrosine with queuine.  It catalyses the exchange of guanine-34 at the wobble position with 7-aminomethyl-7-deazaguanine, and the addition of a cyclopentenediol  moiety to 7-aminomethyl-7-deazaguanine-34 tRNA; giving a hypermodified base queuine in the wobble position. The aligned region contains a zinc binding motif C-x-C-x2-C-x29-H,  and important tRNA and 7-aminomethyl-7deazaguanine binding residues.
Pfam PF04358: DsrC like protein (family)
Family member [swissprot:P45573] has been observed to co-purify with Desulfovibrio vulgaris dissimilatory sulfite reductase, and many  members of this family are annotated as the third (gamma) subunit of  dissimilatory sulphite reductase. However, this protein appears to be only loosely associated to the  sulfite reductase, which suggests that DsrC may not be an integral part of the dissimilatory sulphite reductase.  Members of this family are found in organisms such as E. coli and H. influenzae which do not contain  dissimilatory sulphite reductases but can synthesise assimilatory sirohaem  sulphite and nitrite reductases.  It is speculated that DsrC may be  involved in the assembly, folding or stabilisation of sirohaem proteins. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds.
Pfam PF14682: Sporulation initiation phospho-transferase B, C-terminal (domain)
Sporulation initiation phospho-transferase B or SpoOB is part of a phospho-relay that initiates sporulation in Bacillus subtilis. Spo0B is a two-domain protein consisting of an N-terminal alpha-helical hairpin domain and a C-terminal alpha/beta domain, represented by this family. Two subunits of Spo0B dimerise by a parallel association of helical hairpins to form a novel four-helix bundle from which the active histidine - involved in the auto-phosphorylation - protrudes. In the phospho-relay, the signal-receptor histidine kinases are dephosphorylated by a common response regulator, Spo0F. Spo0B then takes phosphorylated Spo0F as substrate hereby mediating the transfer of a phosphoryl group to Spo0A, the ultimate transcription factor.
Pfam PF08604: Nucleoporin Nup153-like (family)
This family contains both the nucleoporin Nup153 from human and Nup154 from fission yeast.  These have been demonstrated to be functionally equivalent.
Pfam PF05550: Pestivirus Npro endopeptidase C53 (domain)
Unique to pestiviruses, the N-terminal protein encoded by the bovine viral diarrhoea virus genome is a cysteine protease (Npro) responsible for  a self-cleavage that releases the N terminus of the core protein.  This unique protease is dispensable for viral replication, and its  coding region can be replaced by a ubiquitin gene directly fused in frame to the core.
Pfam PF07695: 7TM diverse intracellular signalling (domain)
This entry represents the transmembrane region of the 7TM-DISM (7TM Receptors with Diverse Intracellular Signalling Modules).
Pfam PF22729: NACHT C-terminal Helical domain 3 (domain)
Helical domain found at the C-terminus of bacterial NACHT conflict systems.
Pfam PF08514: STAG domain (repeat)
STAG domain proteins are subunits of cohesin complex - a protein complex required for sister chromatid cohesion in eukaryotes. The STAG domain is present in Schizosaccharomyces pombe mitotic cohesin Psc3, and the meiosis specific cohesin Rec11. Many organisms express a meiosis-specific STAG protein, for example, mice and humans have a meiosis specific variant called STAG3, although budding yeast does not have a meiosis specific version.
Pfam PF00617: RasGEF domain (family)
Guanine nucleotide exchange factor for Ras-like small GTPases.
Wikipedia: RasGEF domain  is domain found in the CDC25 family of guanine nucleotide exchange factors for Ras-like small GTPases.
Pfam PF15552: Domain of unknown function (DUF4657) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 305 and 370 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 PF01441: Lipoprotein (family)
Members of this family are lipoproteins that are probably involved in evasion of the host immune system by pathogens.
Pfam PF08108: Halocidin family (family)
This family consists of the halocidin family of antimicrobial peptides. Halocidins are isolated from the haemocytes of the tunicate, Halocynthia aurantium. They are dimeric in structures which are found via a disulfide linkage between cysteines of two different- sized monomers. Halocidins have been shown to have strong antimicrobial activities against a wide variety of pathogenic bacteria and could be ideal candidates as peptide antibiotics against multidrug-resistant bacteria.
Pfam PF09230: DNA fragmentation factor 40 kDa (domain)
Members of this family of eukaryotic apoptotic proteins induce DNA fragmentation and chromatin condensation during apoptosis.
Wikipedia: Caspase-activated DNase (CAD) or DNA fragmentation factor subunit beta is a protein that in humans is encoded by the DFFB gene. It breaks up the DNA during apoptosis and promotes cell differentiation. It is usually an inactive monomer inhibited by ICAD. This is cleaved before dimerization.
Pfam PF09707: CRISPR-associated protein (Cas_Cas2CT1978) (family)
This entry represents a minor branch of the Cas2 family of CRISPR-associated protein which are found in IPR003799. Cas proteins are found adjacent to a characteristic short, palindromic repeat cluster termed CRISPR, a probable mobile DNA element.
Pfam PF10955: Anti-sigma-F factor Fin (family)
Fin (formerly known as YabK) is a small protein required for efficient switching from sigma(F)- to sigma(G)-directed gene expression during sporulation in Bacillus subtilis. Fin has been proposed to be an anti-sigma(F) factor which, by disabling sigma(F), promotes the switch to late developmental gene expression in the forespore.
Pfam PF02755: RPEL repeat (disordered)
The RPEL repeat is named after four conserved amino acids it contains. The RPEL motif binds to actin.
Pfam PF17568: Family of unknown function (DUF5474) (family)
This is a family of unknown function found in Saccharomycetales.
Pfam PF12861: Anaphase-promoting complex subunit 11 RING-H2 finger (domain)
Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome. The APC subunits are cullin family proteins with ubiquitin ligase activity. Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability.