SII-SWORD/CoKE huggingface dataset:
Pfam PF21399: Telomerase reverse transcriptase, C-terminal extension (domain)
This domain is found at the C-terminal end of Telomerase reverse transcriptase (TERT), a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes. This entry represents the C-terminal extension (also known as the thumb  domain), which forms an all helical bundle. There are three conserved motifs in this domain involved in nucleic acid binding. In humans, single mutations localised within this portion of telomerase are associated with several bone marrow failure syndromes.
Pfam PF06518: Protein of unknown function (DUF1104) (family)
This family consists of several hypothetical proteins of unknown function which appear to be found largely in Helicobacter pylori. The structure of HP0721 protein consists of a bundle of four alpha-helices connected by loops and stabilised by hydrophobic interactions. It has been suggested that this protein might represent a novel H. pylori.
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 PF00899: ThiF family (domain)
This domain is found in ubiquitin activating E1 family and members of the bacterial ThiF/MoeB/HesA family. It is repeated in Ubiquitin-activating enzyme E1.
Pfam PF07167: Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus (family)
This family represents the N-terminal region of the bacterial poly-beta-hydroxybutyrate polymerase (PhaC). Polyhydroxyalkanoic acids (PHAs) are carbon and energy reserve polymers produced in some bacteria when carbon sources are plentiful and another nutrient, such as nitrogen, phosphate, oxygen, or sulfur, becomes limiting. PHAs composed of monomeric units ranging from 3 to 14 carbons exist in nature. When the carbon source is exhausted, PHA is utilised by the bacterium. PhaC links D-(-)-3-hydroxybutyrl-CoA to an existing PHA molecule by the formation of an ester bond.  This family appears to be a partial segment of an alpha/beta hydrolase domain.
Pfam PF15253: SCL-interrupting locus protein N-terminus (family)
SIL (also called STIL/TAL1 interrupting locus) is an immediate-early gene that is essential for embryonic development and is implicated in T-cell leukemia-associated translocations . Sil protein is necessary for proper mitotic spindle organisation in zebrafish and human cells and localizes to the mitotic spindle poles only during metaphase . Mouse Sil was suggested to play a role as a positive regulator of the sonic hedgehog pathway, acting downstream of PTCH1 . In human, cell cycle-dependent phosphorylation of Sil is required for its interaction with Pin1, a regulator of mitosis .

Primary microcephaly (MCPH) is an autosomal-recessive congenital disorder characterised by smaller-than-normal brain size and mental retardation. Three different homozygous mutations in SIL were identified in patients from three of the five families linked to the MCPH7 locus; all are predicted to truncate the Sil protein .
Wikipedia: SCL-interrupting locus protein is a protein that in humans is encoded by the STIL gene. STIL is present in many different cell types and is essential for centriole biogenesis. This gene encodes a cytoplasmic protein implicated in regulation of the mitotic spindle checkpoint, a regulatory pathway that monitors chromosome segregation during cell division to ensure the proper distribution of chromosomes to daughter cells. The protein is phosphorylated in mitosis and in response to activation of the spindle checkpoint, and disappears when cells transition to G1 phase. It interacts with a mitotic regulator, and its expression is required to efficiently activate the spindle checkpoint.
Pfam PF25047: TEP-1 second beta-propeller (repeat)
This entry represents the second of three presumed beta-propeller domains found at the C-terminal of Telomerase protein component 1 (TEP1), a component of the telomerase ribonucleoprotein complex that is essential for the replication of chromosome termini. It is also a component of the ribonucleoprotein vaults particle, a multi-subunit structure involved in nucleo-cytoplasmic transport.
Pfam PF16585: Lipocalin-like domain (domain)
The lipocalin fold is dominated by eight Î²-strands which together form a cup-shaped antiparallel Î²-barrel that encloses an internal ligand-binding site . This entry represents domains with a fold that is related to the to the lipocalin fold.
Wikipedia: The lipocalins are a family of proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids, and most lipocalins are also able to bind to complexed iron as well as heme. They share limited regions of sequence homology and a common tertiary structure architecture. This is an eight stranded antiparallel beta barrel with a repeated + 1 topology enclosing an internal ligand binding site.
Pfam PF08976: EF-hand domain (domain)
This domain is found predominantly in DJ binding proteins.
Pfam PF02236: Viral DNA-binding protein, all alpha domain (domain)
This family represents a domain of the viral DNA- binding protein, a multi functional protein involved in DNA  replication and transcription control.
Pfam PF14103: Domain of unknown function (DUF4276) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 190 and 224 amino acids in length. There is a single completely conserved residue E 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 PF04820: Tryptophan halogenase (family)
Tryptophan halogenase catalyses the chlorination of tryptophan to form 7-chlorotryptophan.  This is the first step in the biosynthesis of pyrrolnitrin, an antibiotic with broad-spectrum anti-fungal activity. Tryptophan halogenase is NADH-dependent.
Pfam PF18026: Endo/exonuclease (EXOG) C-terminal domain (domain)
This is the C-terminal domain found in EndoG-like mitochondrial endo/exonuclease (EXOG) proteins in higher eukaryotes. Evolutionary conserved mitochondrial nucleases are involved in programmed cell death and normal cell proliferation in lower and higher eukaryotes. It has been proposed that during metazoan evolution duplication of an ancestral nuclease gene could have generated the paralogous EndoG- and EXOG-protein subfamilies in higher eukaryotes, thereby maintaining the full endo/exonuclease activity found in mitochondria of lower eukaryotes. Family members include the human EXOG, a dimeric mitochondrial enzyme that displays 5'-3' exonuclease activity and further differs from EndoG in substrate specificity. This C-terminal domain is predicted to fold into a coiled-coil structure. Deletion of the domain led to a pronounced reduction in EXOG activity, revealing that the presence and most likely the proper positioning of this domain in EXOG proteins is crucial for its enzymatic activity.
Pfam PF02273: Acyl transferase (domain)
This bacterial family of Acyl transferases (or myristoyl-acp-specific thioesterases) catalyse the first step in the bioluminescent fatty acid reductase system.
Pfam PF12622: mRNA biogenesis factor (domain)
The full-length Wbp11 proteins carry several copies of a PPGPPP motif throughout their length. This motif is thought to be necessary for folding of the molecule as it helps to bind the WW domain, Wbp11, [pfam:PF09429]. This domain together with Wbp11 may function as components of an mRNA factory in the nucleus.
Pfam PF13875: Domain of unknown function (DUF4202) (family)
This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 187 and 205 amino acids in length. There are two conserved sequence motifs: LED and KMS. The function of these proteins is unknown, although many are incorrectly annotated as glutamyl tRNA synthetases.
Pfam PF18530: Swi6 N-terminal domain (domain)
This is a putative DNA binding domain, it comprises four alpha helices and five beta strands arranged in a mixed alpha/beta fold.
Pfam PF00886: Ribosomal protein S16 (family)
Ribosomal protein S16 (also known as bS16) is one of the proteins from the small ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups:


 * Eubacterial S16.
 * Algal and plant chloroplast S16.
 * Cyanelle S16.
 * Neurospora crassa mitochondrial S24 (cyt-21).


S16 proteins have about 100 amino-acid residues. There are two paralogues in Arabidopsis thaliana, RPS16-1 (chloroplastic) and RPS16-2 (targeted to the chloroplast and the mitochondrion) .
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 PF12760: Transposase zinc-ribbon domain (domain)
This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It is likely a zinc-binding beta ribbon domain that could bind the DNA.
Pfam PF03085: Rhoptry-associated protein 1 (RAP-1) (family)
Members of this family are found in Babesia species. Though not in this Pfam family, rhoptry-associated proteins are also found in Plasmodium falciparum. Indeed, animal infection with Babesia may produce a pattern similar to human malaria. Rhoptry organelles form part of the apical complex in apicomplexan parasites. Rhoptry-associated proteins are antigenic, and generate partially protective immune responses in infected mammals. Thus RAPs are among the targeted vaccine antigens for babesial (and malarial) parasites. However, RAP-1 proteins are encoded by by a multigene family; thus RAP-1 proteins are polymorphic, with  B and T cell epitopes that are conserved among strains, but not across species. Antibodies to Babesia RAP-1 may also be helpful in the  serological detection of Babesia infections.
Pfam PF14444: S1-like (domain)
S1-like RNA binding domain found in DBC1
Pfam PF10898: Protein of unknown function (DUF2716) (family)
This bacterial family of proteins has 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 PF04414: D-aminoacyl-tRNA deacylase (family)
Several aminoacyl-tRNA synthetases have the ability to transfer the D-isomer of their amino acid onto their cognate tRNA. D-aminoacyl-tRNA deacylases hydrolyse the ester bond between the polynucleotide and the D-amino acid, thereby preventing the accumulation of such mis-acylated and metabolically inactive tRNA molecules.
Pfam PF07835: Bacterial aa3 type cytochrome c oxidase subunit IV (domain)
Bacterial cytochrome c oxidase is found bound to the  to the cell membrane, where it is involved in the  generation of the transmembrane proton electrochemical gradient. It is composed of four subunits. Subunit IV consists of one transmembrane helix that does not interact  directly with the other subunits, but maintains its position by indirect contacts via phospholipid molecules found in the structure. The function of subunit IV is as yet unknown.
Wikipedia: The enzyme cytochrome c oxidase or Complex IV is a large transmembrane protein complex found in bacteria, archaea, and the mitochondria of eukaryotes.
Pfam PF16974: High-affinity nitrate transporter accessory, Ig-like domain (domain)
NAR2 is a family of plant proteins with a C-terminal transmembrane region that is an essential accessory for high-affinity nitrate uptake. This family works together with NRT2, a 12xTM family of proteins that is part of family MFS_1, [pfam:PF07690]. NAR2 is also involved in the repression of lateral root initiation in response to high ratios of sucrose to nitrogen in the medium. Therefore the two component-system of NAR2 and NRT2 itself is likely to be involved in the signalling pathway that integrates nutritional cues for the regulation of lateral root architecture.  The functional unit of the high-affinity nitrate influx complex is likely to be a tetramer, in Arabidopsis, made up of two subunits each of NRT2.1 and NAR2.1. This entry corresponds to an immunoglobulin-like domain.
Pfam PF04910: Transcriptional repressor TCF25 (repeat)
Members of this family are transcriptional repressors. They may act by increasing histone deacetylase activity at promoter regions.
Pfam PF05896: NqrA N-terminal barrel-sandwich hybrid domain (domain)
This domain is found N-terminal in several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NqrA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration. This domain has significant similarity to known barrel-sandwich hybrid domains.
Pfam PF13032: RNaseH domain of pPIWI_RE (domain)
RNaseH domain of the pPIWI_RE PIWI/Argonaute module. pPIWI_RE is found in a conserved three-gene island that also contains a DinG-type helicase and an REase nuclease. This three gene island is predicted to form a conflict system which targets R-loop formation of invasive plasmids during plasmid replication.
Pfam PF23836: Family of unknown function (DUF7206) (family)
This entry represents a family of uncharacterised phage proteins including from bacteriophage T6.
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 PF08086: Ergtoxin family (domain)
This family consists of ergtoxin peptides which are toxins secreted by the scorpions.     The ergtoxins are capable of blocking the function of K+ channels. More than 100 ergtoxins have been found from scorpion venoms and they have been classified into three subfamilies according to their primary structures.
Pfam PF09201: SRX, signal recognition particle receptor alpha subunit (domain)
Members of this family, which are predominantly found in eukaryotic signal recognition particle receptor alpha, consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta). Structurally the alpha subunit is SNARE-like.
Wikipedia: Signal recognition particle (SRP) receptor, also called the docking protein, is a dimer composed of 2 different subunits that are associated exclusively with the rough ER in mammalian cells. Its main function is to identify the SRP units. SRP is a molecule that helps the ribosome-mRNA-polypeptide complexes to settle down on the membrane of the endoplasmic reticulum.
Pfam PF03870: RNA polymerase Rpb8 (family)
Rpb8 is a subunit common to the three yeast RNA polymerases, pol I, II and III.  Rpb8 interacts with the largest subunit Rpb1, and with Rpb3 and Rpb11, two smaller subunits.
Pfam PF06026: Ribose 5-phosphate isomerase A (phosphoriboisomerase A) (family)
This family consists of several ribose 5-phosphate isomerase A or phosphoriboisomerase A ([ec:5.3.1.6]) from bacteria, eukaryotes and archaea.
Pfam PF24870: Domain of unknown function (DUF7735) (domain)
This domain is found in uncharacterised proteins mainly from fungi. It is predicted to form a globular structure consisting of alpha-helices. It contains a set of conserved cysteine residues which are predicted to form disulfide bridges.
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 PF13416: Bacterial extracellular solute-binding protein (family)
This family includes bacterial extracellular solute-binding proteins.
Pfam PF04982: HPP, transmembrane region (domain)
This entry represents the C-terminal transmembrane region of At3g47980 from Arabidopsis thaliana ([swissprot:Q84MC3]), which is involved in nitrite transport and similar integral transmembrane proteins. The most conserved region of the alignment is a motif HPP. It is predicted to show five helices.
Pfam PF20653: Conserved Oligomeric Golgi complex subunit 6, C-terminal (repeat)
COG6 is a component of the peripheral membrane COG complex that is involved in intra-Golgi protein trafficking. COG is located at the cis-Golgi, regulates tethering of retrograde intra-Golgi vesicles and consists of one octamer comprising two tetramers (COG1-4 and COG5-8). COG subunits belong to the Complex Associated with Tethering Containing Helical Rods (CATCHRs) family which also includes subunits from the evolutionary related GARP (Golgi-Associated Retrograde Protein), exocyst and Dsl1 complexes. CATCHRs proteins share a structural fold consisting of alpha-helical bundles in tandem at the C-terminal and a coiled-coil region at the N-terminal. This entry represents the alpha-helical bundle found at the C-terminal of COG6.
Pfam PF04119: Heat shock protein 9/12 (family)
These heat shock proteins (Hsp9 and Hsp12) are strongly expressed, an increase of 100 fold, upon entry into stationary phase in yeast.
Pfam PF22870: Protein YibX (family)
This protein family includes Protein YibX from Escherichia coli, the product of a small open reading frame (smORF) that is encoded antisense to the waaL gene.
Pfam PF15952: Enhancer of split M4 family (family)
This family of proteins includes enhancer of split M4, enhancer of split M2 and enhancer of split MAlpha. These proteins are part of the Notch signaling pathway.
Pfam PF12043: Domain of unknown function (DUF3527) (family)
This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain has a conserved CDCGGWD sequence motif.
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 PF16756: Partner and localizer of BRCA2 WD40 domain (repeat)
This domain is found at the C-terminus of partner and localizer of BRCA2 (PALB2). It is a seven-bladed WD40-type beta-propeller. It binds to the N-terminus of BRCA2.
Pfam PF01405: Photosystem II reaction centre T protein (family)
The exact function of this protein is unknown. It probably consists of a single transmembrane spanning helix. The [swissprot:P37256] protein, appears to be (i) a novel photosystem II subunit and (ii) required for maintaining optimal photosystem II activity under adverse growth conditions.
Pfam PF03444: Winged helix-turn-helix transcription repressor, HrcA DNA-binding (domain)
This domain is always found with a pair of CBS domains [pfam:PF00571].
Pfam PF04710: Pellino, FHA domain (domain)
Pellino proteins are E3 ubiquitin ligases that play important roles in immunity, being involved in Toll-like signalling pathways, and associate with the kinase domain of the Pelle Ser/Thr kinase. Mammalian Pellinos have been shown to mediate polyubiquitination of interleukin-1 receptor-associated kinase (IRAK). They consist of a forkhead-associated (FHA) domain at the  N-terminal and a RING domain at the C-terminal. This entry represents the FHA domain, which is sufficient to interact with the ubiquitination substrates, such as IRAK1. This domain contains an unusual 'wing-like'appendage.
Pfam PF11330: C-Terminal of 30K viral movement proteins (family)
This entry represents the C-terminal region found in viral movement proteins (MP) of the 30K type. This region has been suggested to be conserved in secondary structure in Ophioviruses Mps. It contains two parts, (i) a long segment with the potential to form an alpha-helix (alphaB), rich in charged residues, and (ii) a region highly variable in sequence downstream of alphaB. The C-terminal region corresponds to a protease domain which contains a strictly conserved DTG tripeptide also found in related aspartic retroviral proteases. This protease is required for autocleavage of the Movement Protein of ophioviruses in an N-terminal part that supports movement of viral particles through the plant, and this C-terminal part which retains protease activity. Mutations in the aspartate residue in the core domain [pfam:PF17644] had an impact on cell to cell movement.
Pfam PF12773: Double zinc ribbon (family)
This family consists of a pair of zinc ribbon domains.
Pfam PF10076: Bacteriophage Mu-like, Gp48 (family)
Members of this family of proteins comprise various hypothetical and putative bacteriophage tail proteins, including Gp48 from Bacteriophage Mu and other Mu-like prophages such as FluMu.