SII-SWORD/CoKE huggingface dataset:
Pfam PF22501: Domain of unknown function (DUF6991) (domain)
This entry represents a C-terminal domain of a functionally unknown conserved protein from Bacillus anthracis (PDB:4fca).
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 PF20579: LapA domain (domain)
This Ig-like domain is found repeated in the LapA adhesin found in pseudomonas species. This domain is likely calcium binding and distantly related to the CalX-beta domain [pfam:PF03160].
Pfam PF10796: Sigma-S stabilisation anti-adaptor protein (family)
This family is conserved in Enterobacteriaceae. It is one of a series of proteins, expressed by these bacteria in response to stress, that help to regulate Sigma-S, the stationary phase sigma factor of Escherichia coli and Salmonella. IraP is essential for Sigma-S stabilisation in some but not all starvation conditions.
Pfam PF07015: VirC1 protein (family)
This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon which enhances T-DNA processing probably does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA.
Pfam PF04758: Ribosomal protein S30 (family)
This entry is for the ribosomal protein eS30.
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 PF11047: Salmonella outer protein D (family)
SopD is a type III virulence effector protein whose structure consists of 38% alpha-helix and 26% beta-strand.
Pfam PF18600: Fungal MCSS domain (domain)
Polycomb repressive complex 2 (PRC2) carries out the methylation of lysine 27 of histone H3, a hallmark of repressive chromatin. Three core subunits make up the catalytic core of PRC2; the SET domain containing EZH2, the zinc-finger containing SUZ12 and the WD40 repeat protein EED. The complex forms a compact arrangement of three lobes. The middle lobe largely comprises two domains that mark the beginning of the carboxy (C)-terminal region of EZH2 (MCSS and SANT2) and the helical, C-terminal, component of the Suz12 Vefs domain. This entry describes the MCSS (also known as SANT2L) domain. There is one zinc binding (Zn1Cys3His1) which is formed solely by MCSS.
Pfam PF18750: Secreted Novel AID/APOBEC-like Deaminase 4 (family)
A family of secreted AID/APOBEC like deaminases found only in sponges that often shows lineage-specific expansions.
Pfam PF04402: Protein of unknown function (DUF541) (family)
Members of this family have so far been found in bacteria and mouse SwissProt or TrEMBL entries.  However possible family members have also been identified in translated rat (Genbank:AW144450) and human (Genbank:AI478629) ESTs. A mouse family member has been named SIMPL (signalling molecule that associates with mouse pelle-like kinase).  SIMPL appears to facilitate and/or regulate complex formation between IRAK/mPLK (IL-1 receptor-associated kinase) and IKK (inhibitor of kappa-B kinase) containing complexes, and thus regulate NF-kappa-B activity. Separate experiments demonstrate that a mouse family member (named LaXp180) binds the Listeria monocytogenes surface protein ActA, which is a virulence factor that induces actin polymerisation. It may also bind stathmin, a protein involved in signal transduction and in the regulation of microtubule dynamics. In bacteria its function is unknown, but it is thought to be located in the periplasm or outer membrane.
Pfam PF06698: Protein of unknown function (DUF1192) (family)
This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. 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 PF17273: Family of unknown function (DUF5338) (family)
This is a family of unknown function which can be found mostly in 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 PF02056: Family 4 glycosyl hydrolase (family)
O-Glycosyl hydrolases (3.2.1.) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Glycoside hydrolase family 4 (GH4) is a protein family that comprises enzymes with several known activities; 6-phospho-beta-glucosidase (3.2.1.86); 6-phospho-alpha-glucosidase (3.2.1.122); alpha-galactosidase (3.2.1.22). These enzymes require both NAD(H) and divalent metal (such asMn2+, Fe2+, Co2+, or Ni2+) for its activity .
Wikipedia: In molecular biology, glycoside hydrolase family 4 is a family of glycoside hydrolases EC 3.2.1., which are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of &gt;100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Pfam PF07923: N1221-like protein (family)
The sequences featured in this family are similar to a hypothetical protein product of ORF N1221 in the CPT1-SPC98 intergenic region of the yeast genome ([swissprot:P53917]). This encodes an acidic polypeptide with several possible transmembrane regions.
Pfam PF06023: CRISPR-associated exonuclease Csa1 (family)
CRISPR (clustered regularly interspaced short palindromic repeats) elements and cas (CRISPR-associated) genes are widespread in Bacteria and Archaea. The CRISPR/Cas system operates as a defense mechanism against mobile genetic elements (i.e., viruses or plasmids). Csa1 is part of the archaeal subtype I-A system. Cas1 has not yet been enzymatically characterised.
Pfam PF09593: Beta-satellite pathogenicity beta C1 protein (domain)
Cotton leaf-curl disease - CLCuD - is of major economic importance in cotton-growing areas of the far-east. The infectious agent appears to be a single-stranded DNA molecule of approx 1350 nucleotides in length, which, when inoculated with the Begomovirus into cotton, induces symptoms typical of CLCuD. This molecule requires the Begomovirus for replication and encapsidation. DNA beta encodes a single protein, betaC1. The intracellular distribution of betaC1 is consistent with the hypothesis that it has a role in transporting the DNA A of Begomovirus from the nuclear site of replication to the plasmodesmatal exit sites of the infected cell. The DNA beta-encoded protein, betaC1, is the determinant of both pathogenicity and suppression of gene silencing.
Pfam PF05128: Domain of unknown function (DUF697) (domain)
Family of bacterial hypothetical proteins that is sometimes associated with GTPase domains.
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 PF10608: Polyubiquitination (PEST) N-terminal domain of MAGUK (domain)
The residues upstream of this domain are the probable palmitoylation sites, particularly two cysteines. The domain has a putative PEST site at the very start that seems to be responsible for poly-ubiquitination. PEST domains are polypeptide sequences enriched in proline (P), glutamic acid (E), serine (S) and threonine (T) that target proteins for rapid destruction. The whole domain, in conjunction with a C-terminal domain of the longer protein, is necessary for dimerisation of the whole protein.
Pfam PF01923: Cobalamin adenosyltransferase (domain)
Cobalamin adenosyltransferase This family contains the gene products of PduO and EutT which are both cobalamin adenosyltransferases. PduO is a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is the conversion of inactive cobalamins to AdoCbl for 1,2-propanediol degradation.The EutT enzyme appears to be an adenosyl transferase, converting CNB12 to AdoB12.
Wikipedia: In molecular biology, cob(I)yrinic acid a,c-diamide adenosyltransferase EC 2.5.1.17 is an enzyme which catalyses the conversion of cobalamin into one of its coenzyme forms, adenosylcobalamin. Adenosylcobalamin is required as a cofactor for the activity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond.
Pfam PF10539: Development and cell death domain (domain)
The DCD domain is found in plant proteins involved in development and cell death. The DCD domain is an approximately 130 amino acid long stretch that contains several mostly invariable motifs. These include a FGLP and a LFL motif at the N-terminus and a PAQV and a PLxE motif towards the C-terminus of the domain. The DCD domain is present in proteins with different architectures. Some of these proteins contain additional recognisable motifs, like the KELCH repeats or the ParB domain.
Pfam PF04761: Lactococcus bacteriophage putative transcription regulator (family)
This family represents a number of putative transcription repressor proteins found in several Lactococcus bacteriophages. Horizontal transfer may account for the presence of similar proteins in Lactococcus.
Pfam PF01118: Semialdehyde dehydrogenase, NAD binding domain (domain)
This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase
Pfam PF12298: Eukaryotic mitochondrial regulator protein (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 168 and 381 amino acids in length. Bot1p localizes to the mitochondria in live cells and cofractionates with purified mitochondrial ribosomes. Bot1p has a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery. Observations also indicate that in fission yeast, alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms.
Pfam PF17792: ThiD2 family (domain)
This domain functions as a ThiD protein and is called the ThiD2 family.  The domain is associated with the ThiE domain in some proteins.
Pfam PF07680: TQO small subunit DoxA (family)
Thiosulphate:quinone oxidoreductase (TQO) is one of the early steps in elemental sulphur oxidation.  A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in [swissprot:Q8AAF0].
Pfam PF02917: Pertussis toxin, subunit 1 (domain)
A large group of bacterial exotoxins are referred to as "A/B toxins", essentially because they are formed from two subunits . The "A" subunit possesses enzyme activity, and is transferred to the host cell following a conformational change in the membrane-bound transport "B" subunit .

Bordetella pertussis is the causative agent of whooping cough, and is a Gram-negative aerobic coccus. Its major virulence factor is the pertussis toxin, an A/B exotoxin that mediates both colonisation and toxaemic stages of the the disease . Recombinant, inactive forms of the 5 subunits that make up the toxin have proven to be good vaccines. The S1 ("A") subunit of pertussis toxin causes the characteristic sound of the "whoop" in whooping cough. It achieves this through ADP-ribosylation of host Gi alpha-units, an adenylate cyclase inhibitor . Uninhibited, this enzyme produces elevated levels of cAMP, leading to increased cell exudate and inflammation in the lungs .

The crystal structure of pertussis toxin has been determined to 2.9A resolution . The catalytic A-subunit (S1) shares structural similarity with other ADP-ribosylating bacterial toxins, although differences in the C-terminal portion explain its unique activation mechanism. Despite its heterogeneous subunit composition, the structure of the cell-binding B-oligomer (S2, S3, two copies of S4, and S5) resembles the symmetrical B-pentamers of the cholera and shiga toxin families, but it interacts differently with the A-subunit and there is virtually no sequence similarity between B-subunits of the different toxins.
Wikipedia: Pertussis toxin (PT) is a protein-based AB5-type exotoxin produced by the bacterium Bordetella pertussis, which causes whooping cough. PT is involved in the colonization of the respiratory tract and the establishment of infection. Research suggests PT may have a therapeutic role in treating a number of common human ailments, including hypertension, viral infection, and autoimmunity.
Pfam PF06894: Bacteriophage lambda tail assembly chaperone, TAC, protein G (domain)
This domain is found Bacteriophage lambda minor tail protein G and related sequences. The construction of phage tails involves a stage of tail-tube formation, and tail-tube polymerisation requires two additional proteins, gpG and gpGT. The open reading frames, ORFs, for gpG and gpGT are overlapping and are related by a programmed translational frameshift. During virion morphogenesis, gpG is expressed in large amounts, and about 3.5%  of the time, a -1 translational frameshift leads to the production of the larger fusion protein, gpGT. The correct ratio of gpG to gpGT, as determined by the frequency of frameshifting, is crucial for tail assembly. Since gpG accumulates to high levels during a lambda infection and yet is not found in mature phage particles it is believed to act as a chaperone.
Pfam PF06167: Glucose-regulated metallo-peptidase M90 (family)
MtfA (earlier known as YeeI) is a transcription factor A that binds Mlc (make large colonies), itself a repressor of glucose and hence a protein important in regulation of the phosphoenolpyruvate:glucose-phosphotransferase (ptsG) system, the major glucose transporter in E.coli. Mlc is a repressor of ptsG, and MtfA is found to bind and inactivate Mlc with high affinity. The membrane-bound protein EIICBGlc encoded by the ptsG gene is the major glucose transporter in Escherichia coli. MtfA is found to be a glucose-regulated peptidase, whose activity is regulated by binding to Mlc available in the cytoplasm, which in turn has been released from EIICBGlc during times when no glucose is taken up. A physiologically relevant target for this peptidase is not yet known.
Pfam PF22006: PilZ domain-like (domain)
This domain is found in [swissprot:Q5ZYK8] from Legionella pneumophila and similar sequences mainly found in gammaproteobacteria. It shows a great structural similarity with [pfam:PF07238].
Pfam PF07574: Nse1 non-SMC component of SMC5-6 complex (family)
S. cerevisiae Nse1 ([swissprot:Q07913]) forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism.  It is conserved in eukaryotes from yeast to human. This domain lies immediately up-stream of the DNA-binding zinc-finger domain, zf-RING-like [pfam:PF08746].
Pfam PF19608: Family of unknown function (DUF6113) (family)
This family of putative integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 136 and 154 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 PF24868: YABBY, N-terminal (domain)
YABBY proteins are a group of plant-specific transcription involved in the specification of abaxial polarity in lateral organs. This entry represents it N-terminal domain, which is found associated with [pfam:PF04690].
Pfam PF05783: Dynein light intermediate chain (DLIC) (family)
This family consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo.
Wikipedia: Dyneins are a family of cytoskeletal motor proteins that move along microtubules in cells. They convert the chemical energy stored in ATP to mechanical work. Dynein transports various cellular cargos, provides forces and displacements important in mitosis, and drives the beat of eukaryotic cilia and flagella. All of these functions rely on dynein's ability to move towards the minus-end of the microtubules, known as retrograde transport; thus, they are called "minus-end directed motors". In contrast, most kinesin motor proteins move toward the microtubules' plus-end, in what is called anterograde transport.
Pfam PF13037: Domain of unknown function (DUF3898) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 90 amino acids in length. There are two conserved sequence motifs: DFG and FEKG.
Pfam PF13332: Hemagglutinin repeat (repeat)
This hemagglutinin repeat is found in hemolysins and filamentous hemagglutinin. Bacterial hemolysins are exotoxins that attack blood cell membranes and cause cell rupture by mechanisms not clearly defined. Filamentous hemagglutinins have a role in host-cell binding and infection.
Pfam PF18207: Leukemia inhibitory factor receptor N-terminal domain (domain)
This domain can be found in leukemia inhibitory factor receptor (LIFR). LIFR is a cell surface receptor that mediates the actions of LIF and other interleukin-6 type cytokines through the formation of signalling complexes with gp130. This is the N-terminal domain, referred to as domain 1, which contains conserved disulfide bonds between Cys-10 to Cys-20 and Cys-37 to Cys-45.
Pfam PF17576: Family of unknown function (DUF5480) (family)
This is a family of unknown function found in Podoviridae.
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 PF21883: Wntless, GOLD domain (domain)
This entry represents the GOLD domain from wntless (WLS) proteins. WLS membrane trafficking and secretion chaperones for lipidated Wnt signaling proteins. They are homologous to GPR180, TMEM145, and TMEM181, which have been described as GOST proteins (for GOLD domain seven-transmembrane helix proteins) together with TMEM87A/B, GPR107, and GPR108, as they share the same domain architecture consisting of a GOLD domain atop of a membrane-spanning seven-transmembrane helix domain.
Pfam PF13447: Seven times multi-haem cytochrome CxxCH (domain)
This domain carries up to seven CxxCH repeated sequence motifs, characteristic of multi-haem cytochromes.
Pfam PF22646: PPP2R1A-like HEAT repeat (repeat)
This entry represents HEAT repeats found in protein phosphatase 2A PR65/A subunit (PPP2R1A).