SII-SWORD/CoKE huggingface dataset:
Pfam PF01668: SmpB protein (family)
This entry represents SsrA-binding protein (aka small protein B or SmpB), which is a unique RNA-binding protein that is conserved throughout the bacterial kingdom and is an essential component of the SsrA quality-control system. Tight recognition of codon-anticodon pairings by the ribosome ensures the accuracy and fidelity of protein synthesis. In eubacteria, translational surveillance and ribosome rescue are performed by the 'tmRNA-SmpB' system (transfer messenger RNA-small protein B). SmpB binds specifically to the ssrA RNA (tmRNA) and is required for stable association of ssrA with ribosomes. SsrA RNA recognises ribosomes stalled on defective messages and acts to mediate the addition of a short peptide tag to the C terminus of the partially synthesised nascent polypeptide chain. Within a stalled ribosome, SmpB interacts with the three universally conserved bases G530, A1492 and A1493 that form the 30S subunit decoding centre, in which canonical codon-anticodon pairing occurs . The SsrA-tagged protein is then degraded by C-terminal-specific proteases. Formation of an SmpB-SsrA complex appears to be critical in mediating SsrA activity after aminoacylation with alanine but prior to the transpeptidation reaction that couples this alanine to the nascent chain . The SmpB protein has functional and structural similarities with initiation factor 1, and is proposed to be a functional mimic of the pairing between a codon and an anticodon.
Pfam PF19384: Family of unknown function (DUF5959) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001707) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
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 PF19624: Family of unknown function (DUF6129) (family)
This presumed domain is functionally uncharacterised. 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 PF23754: IP5P C-F beta-propeller (repeat)
This entry represents the beta-propeller domain found mainly in plant inositol polyphosphate 5-phosphatases (IP5P), such as Type I IP5P12/IP5PC and IP5P13/IP5PD and Type II IP5P14/IP5PE and IP5P15/IP5PF from Arabidopsis thaliana. IP5Ps have different functions, including the degradation of phosphoinositides in the signalling pathways of various cellular processes such as Ca2+ release, abscisic acid signalling and vesicle trafficking, among others. In the case of IP5P13, the beta propeller domain interacts with the sucrose non-fermenting-1-related kinase (SnRK1.1) in order to achieve a regulatory role linking inositol, sugar and stress signalling.
Pfam PF21036: Erythromycin biosynthesis protein CIII-like, N-terminal domain (domain)
This domain is found at the N-terminal of Erythromycin biosynthesis protein CIII (EryCIII) from Saccharopolyspora erythraea and similar proteins predominantly found in Actinobacteria and Enterobacterales. This protein is organised into two domains, both of them with a Rossmann-like alpha/beta fold. The N-terminal domain contains acceptor binding site.
Pfam PF03051: Peptidase C1-like family (family)
This family is closely related to the Peptidase_C1 family [pfam:PF00112], containing several prokaryotic and eukaryotic aminopeptidases and bleomycin hydrolases.
Pfam PF02896: PEP-utilising enzyme, PEP-binding domain (domain)
This entry represents a TIM barrel domain found at the C terminus of a number of PEP (phosphoenolpyruvate)-utilising proteins. In PPDK  (Pyruvate phosphate dikinase) this C-terminal domain has been shown to be a PEP-binding domain.
Wikipedia: Pyruvate, phosphate dikinase, or PPDK is an enzyme in the family of transferases that catalyzes the chemical reactionATP + pyruvate + phosphate  AMP + phosphoenolpyruvate + diphosphate
Pfam PF12402: NocA-like zinc-finger protein 1 (family)
This domain family is found in eukaryotes, and is typically between 42 and 57 amino acids in length. There is a conserved GAY sequence motif.  There is a single completely conserved residue G that may be functionally important. Nlz1 self-associated via its C terminus, interacted with Nlz2, and bound to histone deacetylases.
Pfam PF24227: Domain of unknown function (DUF7443) (domain)
This entry represents an uncharacterized protein family found in bacteriophages. The function of this family is currently unknown. Members of this family are typically around 90-100 amino acids in length. The family includes proteins from various phage species infecting bacteria such as Salmonella, Klebsiella, and Proteus. Some members of this family contain disordered regions, particularly in their C-terminal portions. Conserved basic and acidic residues are present in many family members, which may be functionally important. This entry represents the globular N-terminal domain of these 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 PF24983: Domain of unknown function (DUF7774) (domain)
This domain is found in uncharacterised worm proteins mainly from clade Rhabditida. It is predicted to adopt a globular structure composed of array of alpha-helices.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09139: Phosphatidate cytidylyltransferase, mitochondrial (family)
Tam41 also known as MMp37 is a mitochondrial phosphatidate cytidylyltransferase (CDP-DAG synthase)([ec:2.7.7.41]) that catalyzes the formation of CDP-diacylglycerol (CDP-DAG) from phosphatidic acid (PA) in the mitochondrial inner membrane. It is required for the biosynthesis of the dimeric phospholipid cardiolipin, which stabilizes supercomplexes of the mitochondrial respiratory chain in the mitochondrial inner membrane. It is suggested that the N-terminal portion of Tam41 may possess the NTase (Nucleotide Transferase) fold, which is consistent with the CDP-DAG synthase function of Tam41. Furthermore, it has been shown that Tam41/MMP37 proteins possess the NTase fold but they have only one active site carboxylate and thus probably are not able to carry out enzymatic reaction. These potentially non-active members of NTase fold superfamily may bind ATP, hydrolysis of which is necessary for the translocation of proteins through the membrane.
Pfam PF11231: Protein of unknown function (DUF3034) (family)
This family of proteins with unknown function appears to be restricted to 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 PF08721: TnsA endonuclease C terminal (domain)
The Tn7 transposase is composed of proteins TnsA and TnsB.  DNA breakage at the 5' end of the transposon is carried out by TnsA, and breakage and joining at the 3' end is carried out by TnsB. The C terminal domain of TnsA binds DNA.
Pfam PF10112: 5-bromo-4-chloroindolyl phosphate hydrolysis protein (family)
Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Pfam PF02053: Gene 66 (IR5) protein (family)
The IR5 open reading frame (ORF) of the Equid herpesvirus 1 (EHV-1) genome maps within the inverted repeat segments. Sequence analyses of the gene region revealed an ORF of 236 amino acids that showed a high degree of similarity to ORF64 of Human herpesvirus 3 (HHV-3) and ORF3 of Equid herpesvirus 4 (EHV-4), both of which map within the inverted repeats, and to the US10 ORF of Human herpesvirus 1 (HHV-1), which maps within the unique short segment. The IR5 ORF houses a sequence of 13 residues (CAYWCCLGHAFAC) that matches perfectly the consensus zinc finger motif (C-X2-4-C-X2-15-C/H-X2-4-C/H) . Putative cis-acting elements flanking the IR5 ORF include a TATA box, a CAAT box, and a polyadenylation signal. Coupled with various experimental data, the IR5 gene of EHV-1 thus exhibits characteristics representative of a late gene of the gamma-1 class. The DNA sequence covering ~70% of the short unique region (Us) and part of the short inverted repeat of the Meleagrid herpesvirus 1 (MeHV-1) GA strain has been determined. Sequence analysis showed the presence of nine potential ORFs in the Us region, four of which were found to be similar to US10 (minor virion protein) .
Pfam PF01440: Geminivirus AL2 protein (family)
Geminiviruses are small, ssDNA-containing plant viruses. Geminiviruses contain three ORFs (designated AL1, AL2, and AL3) that overlap and are specified by multiple polycistronic mRNAs. The AL2 gene product transactivates expression of TGMV coat protein gene, and BR1 movement protein.
Pfam PF00087: Snake toxin and toxin-like protein (domain)
This family predominantly includes venomous neurotoxins and cytotoxins from snakes, but also structurally similar (non-snake) toxin-like proteins (TOLIPs) such as Lymphocyte antigen 6D and  Ly6/PLAUR domain-containing protein. Snake toxins are short  proteins with a compact, disulphide-rich structure. TOLIPs have  similar structural features (abundance of spaced cysteine residues,  a high frequency of charge residues, a signal peptide for secretion  and a compact structure) but, are not associated with a venom  gland or poisonous function. They are endogenous animal proteins  that are not restricted to poisonous animals.
Wikipedia: Snake venom is a highly toxic saliva containing zootoxins that facilitates in the immobilization and digestion of prey. This also provides defense against threats. Snake venom is usually injected by unique fangs during a bite, though some species are also able to spit venom.
Pfam PF22169: AP205 coat protein (domain)
AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence that is not similar to any other known single-stranded RNA phage protein. The AP205 coat protein forms a dimer which adopts the conserved Leviviridae coat protein core fold with exception of the N-terminal region. This coat protein has a similar structure that is circularly permuted compared to the other coat proteins.
Pfam PF00051: Kringle domain (domain)
Kringle domains have been found in plasminogen, hepatocyte growth factors, prothrombin, and apolipoprotein A. Structure is disulfide-rich, nearly all-beta.
Wikipedia: Kringle domains are autonomous protein domains that fold into large loops stabilized by 3 disulfide linkages. These are important in protein–protein interactions with blood coagulation factors. Their name refers to the Kringle, a Scandinavian pastry which they somewhat resemble.
Pfam PF04098: Rad52/22 family double-strand break repair protein (family)
The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to Rad52. These proteins contain two helix-hairpin-helix motifs.
Pfam PF07442: Ponericin (family)
This family contains a number of ponericin peptides (approximately 30 residues long) from the venom of the predatory ant Pachycondyla goeldii. These peptides exhibit antibacterial and insecticidal properties, and may adopt an amphipathic alpha-helical structure in polar environments such as cell membranes.
Pfam PF05590: Xylella fastidiosa protein of unknown function (DUF769) (family)
This family consists of several uncharacterised hypothetical proteins of unknown function from Xylella fastidiosa, the organism that causes Pierce's disease in plants.
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 PF04211: Tetrahydromethanopterin S-methyltransferase, subunit C (family)
The N5-methyltetrahydromethanopterin: coenzyme M ([ec:2.1.1.86]) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump.
Pfam PF14975: Domain of unknown function (DUF4512) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 74 and 104 amino acids in length. There are two completely conserved residues (C and P) 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 PF22752: Inactive DUF488-N3 subclade (domain)
This entry represents a subclade of DUF488 domains lacking the catalytic residues common to the rhodanese-phosphatase superfamily. The C-terminal core strand is degenerate in this subclade.
Pfam PF00105: Double treble clef zinc finger, C4 type (domain)
In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.
Wikipedia: In the field of molecular biology, nuclear receptors are a class of proteins responsible for sensing steroids, thyroid hormones, vitamins, and certain other molecules. These intracellular receptors work with other proteins to regulate the expression of specific genes, thereby controlling the development, homeostasis, and metabolism of the organism.
Pfam PF19576: Acyltransferase (domain)
This family of proteins are likely to function as acyltransferases.  Proteins in this family are found in Bacteria.
Pfam PF08942: Domain of unknown function (DUF1919) (domain)
This domain has no known function. It is found in various hypothetical and putative bacterial proteins. The structure of this domain is known (PDB:2g6t).
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 PF20642: TAF1C, helical bundle domain (domain)
This is the helical bundle domain (also referred to as the headlock domain) of TATA box-binding protein-associated factor RNA polymerase I subunit C (TAF1C) from animals, the orthologue of yeast Rrn6. TAF1C is a component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription.
Pfam PF07385: D-lyxose isomerase (domain)
Members of this family of sugar isomerases belong to the cupin superfamily and consist of group I and II of D-lyxose isomerases. The enzyme from Cohnella laevoribosii has been shown to be specific for D-lyxose, L-ribose, and D-mannose. E. coli sugar isomerase (EcSI) shows a preference for D-lyxose and D-mannose and its active site is highly similar to YdaE from the sigma B regulon of Bacillus subtilis.
Pfam PF18461: Atypical caspase recruitment domain (domain)
The N-terminal effector domain found in NLRC5. It adopts a six alpha-helix bundle with a general death fold. Structure and sequence analysis of the NLRC5-N indicate that it possesses a fold similar to the one of the death-fold domains; however, it displays significant differences in the number of core alpha-helices and their relative orientation. Hence, it is suggested that NLRC5 belongs to the caspase recruitment domain (CARD) subfamily as an atypical CARD.
Wikipedia: Caspase recruitment domains, or caspase activation and recruitment domains (CARDs), are interaction motifs found in a wide array of proteins, typically those involved in processes relating to inflammation and apoptosis. These domains mediate the formation of larger protein complexes via direct interactions between individual CARDs. CARDs are found on a strikingly wide range of proteins, including helicases, kinases, mitochondrial proteins, caspases, and other cytoplasmic factors.
Pfam PF09802: Preprotein translocase subunit Sec66 (family)
Members of this family of proteins are a component of the heterotetrameric Sec62/63 complex composed of SEC62, SEC63, SEC66 and SEC72. The Sec62/63 complex associates with the Sec61 complex to form the Sec complex. Sec 66 is involved in SRP-independent post-translational translocation across the endoplasmic reticulum and functions together with the Sec61 complex and KAR2 in a channel-forming translocon complex. Furthermore, Sec66 is also required for growth at elevated temperatures.
Pfam PF01172: Shwachman-Bodian-Diamond syndrome (SBDS) N-terminal domain (domain)
This entry represents the N-terminal domain of proteins that are highly conserved in species ranging from archaea to vertebrates and plants, including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterised by bone marrow failure and leukemia predisposition. Members of this entry play a role in RNA metabolism. In yeast these proteins have been shown to be critical for the release and recycling of the nucleolar shuttling factor Tif6 from pre-60S ribosomes, a key step in 60S maturation and translational activation of ribosomes. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition.
Wikipedia: Ribosome maturation protein SBDS is a protein that in humans is encoded by the SBDS gene. An alternative transcript has been described, but its biological nature has not been determined. This gene has a closely linked pseudogene that is distally located. This gene encodes a member of a highly conserved protein family that exists in all archaea and eukaryotes.
Pfam PF09121: Tower (domain)
Members of this family adopt a secondary structure consisting of a pair of long, antiparallel alpha-helices (the stem) that support a three-helix bundle (3HB) at their end. The 3HB contains a helix-turn-helix motif and is similar to the DNA binding domains of the bacterial site-specific recombinases, and of eukaryotic Myb and homeodomain transcription factors. The Tower domain has an important role in the tumour suppressor function of BRCA2, and is essential for appropriate binding of BRCA2 to DNA.
Wikipedia: BRCA2 and BRCA2 are human genes and their protein products, respectively. The official symbol and the official name are maintained by the HUGO Gene Nomenclature Committee. One alternative symbol, FANCD1, recognizes its association with the FANC protein complex. Orthologs, styled Brca2 and Brca2, are common in other vertebrate species. BRCA2 is a human tumor suppressor gene, found in all humans; its protein, also called by the synonym breast cancer type 2 susceptibility protein, is responsible for repairing DNA.
Pfam PF18933: PsbP-like protein (domain)
This family is related to the PsbP family.
Pfam PF11555: EGFR receptor inhibitor Mig-6 (family)
When the kinase domain of EGFR binds to segment one of Mitogen induced gene 6 (Mig-6), EGFR becomes inactive due to the conformation it adopts which is Src/CDK like. The binding of the two proteins prevents EGFR acting as a cyclin-like activator for other kinase domains.The structure of Mig-6(1) consists of alpha helices-G and -H with a polar surface and hydrophobic residues for interactions with EGFR. A critical step for the activation of EGFR is the formation of an asymmetric dimer involving the kinase domains of the protein. Since Mig-6 binds to the kinase domain it blocks this process and EGFR becomes inactive.
Pfam PF05867: Protein of unknown function (DUF851) (family)
Proteins in this family have no known function and only seem to occur in Chromadorea.
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 PF13892: DNA-binding domain (domain)
DBINO is a DNA-binding domain found on global transcription activator SNF2L1 proteins and chromatin re-modelling proteins.
Pfam PF12935: Vesicle coat trafficking protein Sec16 N-terminus (domain)
Sec16 is a multi-domain vesicle coat protein. The overall function of Sec16 is in mediating the movement of protein-cargo between the organelles of the secretory pathway. Over-expression of truncated mutants of only the N-terminus are lethal, and this portion does not appear to be essential for function so may act as a stabilising region.
Pfam PF13342: C-terminal repeat of topoisomerase (domain)
This short domain is found in multiple copies at the C-terminus of some topoisomerase enzymes.