SII-SWORD/CoKE huggingface dataset:
Pfam PF05234: UAF complex subunit Rrn10 (family)
The protein Rrn10 has been identified as a component of the Upstream Activating Factor (UAF), an RNA polymerase I (pol I) specific transcription stimulatory factor
Pfam PF11127: Inner membrane protein YgaP-like, transmembrane domain (domain)
This domain is found in proteins from bacteria and archaea, including Inner membrane protein YgaP from Escherichia coli, a membrane protein with a rhodanese domain (Pfam: PF00581) that may have sulfurtransferase activity. YgaP adopts a dimeric assembly. This entry represents the transmembrane domain. It consist of two slightly tilted alpha-helices. Structure prediction suggests that this region may homodimerise to form a 4 helical bundle.
Pfam PF21033: Regulator of microtubule dynamics protein 1-3 (repeat)
This is the C-terminal domain of Regulator of microtubule dynamics proteins 1-3 (RMD1-3) which consists of alpha-helical repeats. These are microtubule-binding proteins. RMD3 is involved in cellular calcium homeostasis regulation, and it may participate in differentiation and apoptosis of keratinocytes. RMD1 from C. elegans functions in chromosome segregation.
Pfam PF24503: Domain of unknown function (DUF7590) (domain)
This domain is found in uncharacterised proteins mainly from Fungi. It has a detectable similarity to known galactose-binding domains, in particular to the C-terminal domain of Bacillus sp. alkaline serine protease, and is predicted to adopt similar 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 PF23906: Family of unknown function (DUF7248) (family)
This entry represents a small family of uncharacterised phage proteins that have a single transmembrane helix followed by a conserved C-terminal sequence. The family includes proteins from phage T4 and 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 PF09276: Pertussis toxin S5 subunit (domain)
Members of this family of Bordetella pertussis toxins adopt a structure consisting of an OB fold, with a closed or partly opened beta-barrel in a Greek-key topology.
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 PF11061: Cytochrome b6f, subunit Tsr0524-like (family)
This family of proteins is predominantly found in cyanobacteria and red algae, including Tsr0524 from Thermosynechococcus vestitus. Tsr0524 (also known as PetP) is a component of the cyanobacterial cytochrome b6f that may play an essential role in the regulation of photosynthetic electron transport. It shows an SH3 domain fold with five antiparallel beta-sheets.
Pfam PF12241: Trans-2-enoyl-CoA reductase catalytic region (family)
This family of trans-2-enoyl-CoA reductases, [ec:1.3.1.44], carries the the catalytic sites of the enzyme, characterised by the conserved sequence motifs: YNThhhFxK, and YShAPxR. In Euglena where the enzyme has been characterised it catalyses the reduction of enoyl-CoA to acyl-CoA in an unusual fatty acid pathway in mitochondria. the whole path performs a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation.
Pfam PF03972: MmgE/PrpD N-terminal domain (domain)
This entry represents the N-terminal domain of 2-methylcitrate dehydratase [ec:4.2.1.79] (PrpD) that is required for propionate catabolism. It catalyses the third step of the 2-methylcitric acid cycle. This enzyme consists of two domains: a large domain with an all-helical fold and a smaller domain that folds into an alpha/beta domain. Cis-aconitic acid decarboxylase (CAD) shares high identity with proteins of the MmgE/PrpD family. Citrate/2-methylcitrate dehydratase from Bacillus subtilis is involved in the tricarboxylic acid (TCA) and methylcitric acid cycles as it has both 2-methylcitrate dehydratase and citrate dehydratase activities. This entry represents the N-terminal domain of 2-methylcitrate dehydratase PrpD, which has an all-helical fold.
Pfam PF22422: Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain (repeat)
This entry represents the glycoside hydrolase domain found at the C-terminal of Mannosylglycerate hydrolase MGH1 and similar sequences.
Pfam PF19528: Family of unknown function (DUF6056) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 448 and 528 amino acids in length. There is a conserved NYL 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 PF16676: Transactivation domain of FOXO protein family (domain)
TAD is a promiscuous binding domain that mediates the association of the transcription factor FOXO with the coactivator CBP/p300. Both this domain and the FOXO-KIX_bd family [pfam:PF16675] bind simultaneously the KIX domain of CBP/p300. Coactivator CBP/p300 is recruited by FOXO3 though binding to these two regions.  The promiscuity of the TAD is further evidenced by that the finding that they also bind the TAZ1 and TAZ2 domains of CBP/p300.
Pfam PF09531: Nucleoporin protein Ndc1-Nup (family)
Ndc1 is a nucleoporin protein that is a component of the Nuclear Pore Complex, and, in fungi, also of the Spindle Pole Body. It consists of six transmembrane segments, three lumenal loops, both concentrated at the N-terminus and cytoplasmic domains largely at the C-terminus, all of which are well conserved.
Pfam PF18059: Csd3 N-terminal (domain)
Csd3 (also known as HdpA) is a bi-functional enzyme with delta,delta-endopeptidase activity and delta,delta-carboxypeptidase activity. The N-terminal domain is also known as domain 1 and is composed of an alpha/beta fold consisting of a five-stranded antiparallel beta-sheet and three short alpha-helices. Domain 1 blocks the active-site cleft of the LytM domain, with the protruding helix alpha-3 contributing to the Zn2+ coordination sphere. The fold of domain 1 is very remotely related to monellin/cystatin superfamily proteins, some of which act as inhibitors of cysteine peptidases.
Pfam PF09792: Ubiquitin 3 binding protein But2 C-terminal domain (domain)
This family is of proteins conserved in yeasts. It binds to Uba3 and is involved in the NEDD8 signalling pathway. This family represents a presumed C-terminal domain.
Pfam PF11563: Protoglobin (domain)
This family includes protoglobin from Methanosarcina acetivorans C2A. It is also found near the N-terminus of the Haem-based aerotactic transducer HemAT in Bacillus subtilis ([swissprot:O07621]). It is part of the haemoglobin superfamily. Protoglobin has specific loops and an amino-terminal extension which leads to the burying of the haem within the matrix of the protein. Protoglobin-specific apolar tunnels allow the access of O2, CO and NO to the haem distal site. In HemAT it acts as an oxygen sensor domain. It can also recognise cyanide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF15380: Domain of unknown function (DUF4607) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 207 and 359 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 PF11862: Domain of unknown function (DUF3382) (family)
This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 100 amino acids in length. This domain is found associated with [pfam:PF02653].
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 PF03427: Carbohydrate binding domain (family 19) (domain)
This entry represents CBM19 which consists of 60-70 residues with chitin-binding function.
A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins.

CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose . However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology.

Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see .
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF10034: Q-cell neuroblast polarisation (family)
Dyp-19, formerly known as DUF2211, is a transmembrane domain family that is required to orient the neuroblast cells, QR and QL accurately on the anterior-posterior axis: QL and QR are born in the same anterior-posterior position, but polarise and migrate left-right asymmetrically, QL migrating towards the posterior and QR migrating towards the anterior. It is also required, with unc-40, to express mab-5 correctly in the Q cell descendants. The Dpy-19 protein derives from the C. elegans DUMPY mutant, [swissprot:P34413].
Pfam PF14314: Virus-capping methyltransferase, MT domain (domain)
This is the methyltransferase region of the Mononegavirales single-stranded RNA viral RNA polymerase enzymes (L proteins). This region is involved in the mRNA-capping of the virion particles.
Pfam PF08226: Domain of unknown function (DUF1720) (domain)
This domain is found in different combinations with cortical patch components EF hand, SH3 and ENTH and is therefore likely to be involved in cytoskeletal processes.  This family contains many hypothetical 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 PF23279: Fungal tetratrico peptide repeats (repeat)
These predicted tetratrico peptide repeats (TPR) are found in a group of fungal proteins. This domain is often found associated with [pfam:PF23276].
Pfam PF02251: Proteasome activator PA28, N-terminal (domain)
Proteasome activator 28 (PA28), also known as 11s regulator of REG, binds to the 20S proteasome and simulates peptidase activity in an ATP-independent manner. This entry represents a single alpha-helix N-terminal domain found in PA28 subunits, including PA28alpha/beta/gamma (also known as Proteasome activator complex subunit 1-3).
Pfam PF00471: Ribosomal protein L33 (family)
Ribosomal protein bL33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, bL33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups:


 * Eubacterial bL33.
 * Algal and plant chloroplast bL33c.
 * Cyanelle bL33.
 * Animal bL33m.
 * Fungal bL33m (also known as MRPL39).


bL33 is a small protein of 49 to 66 amino-acid residues.
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 PF02655: ATP-grasp domain (family)
No functional information or experimental verification of function is known in this family. This family appears to be an ATP-grasp domain (Pers. obs. A Bateman).
Pfam PF10283: PBZ domain (domain)
This domain is a zinc-finger motif that in humans is part of the APLF, aprataxin- and PNK-like forkhead association domain-containing protein. The ZnF is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues and is configured CX5CX6HX5H. Many of the proteins containing the APLF-like ZnF are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism.
Pfam PF16754: Bacterial toxin homologue of phage lysozyme, C-term (domain)
This the C-terminal activator domain of pesticin, a hydrolase enzyme secreted by Yersinia pestis and other Gammaproteobacteria to kill related bacteria occupying the same ecological niche. It is referred to as a bacteriocin and it leads to the hydrolysis of peptidoglycan. Its immunity protein is Pim. Pesticin carries an elongated N-terminal translocation domain, an intermediate receptor binding domain, and a C-terminal activity domain with structural analogy to lysozyme homologues. The full-length protein is toxic to bacteria when taken up to the target site via the outer or the inner membrane. The receptor domain is necessary for the close contact with the outer membrane; the N-terminal is a type of translocational, TonB box; the C-terminal domain is the death-delivering domain.
Pfam PF15646: Restriction endonuclease fold toxin 2 (family)
A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 7 or PrsW-peptidase dependent secretion system.
Pfam PF00307: Calponin homology (CH) domain (domain)
The CH domain is found in both cytoskeletal proteins and signal transduction proteins.  The CH domain is involved in actin binding in some members of the family.  However in calponins there is evidence that the CH domain is not involved in its actin binding activity.  Most member proteins have from two to four copies of the CH domain, however some proteins such as calponin and [swissprot:P15498] have only a single copy.
Wikipedia: Calponin homology domain (or CH domain) is a family of actin binding domains found in both cytoskeletal proteins and signal transduction proteins. The domain is about 100 amino acids in length and is composed of four alpha helices. It comprises the following groups of actin-binding domains:Actinin-type (including spectrin, fimbrin, ABP-280)
Calponin-type
Pfam PF00981: Rotavirus RNA-binding Protein 53 (NS53) (family)
This protein is also known as NSP1. NS53 is encoded by gene 5. It is made in low levels in the infected cells and is a component of early replication.  The protein is known to accumulate on the cytoskeleton of the infected cell.  NS53 is an RNA binding protein that contains a characteristic cysteine rich region.
Wikipedia: In virology, a nonstructural protein is a protein encoded by a virus but that is not part of the viral particle. They typically include the various enzymes and transcription factors the virus uses to replicate itself, such as a viral protease, an RNA replicase or other template-directed polymerases, and some means to control the host.
Pfam PF08991: Mature-T-Cell Proliferation I type (domain)
Members of this family adopt a coiled coil structure, with two antiparallel alpha-helices that are tightly strapped together by two disulfide bridges at each end. The protein sequence shows a cysteine motif, required for the stabilisation of the coiled-coil-like structure. Additional inter-helix hydrophobic contacts impart stability to this scaffold. The precise function of this eukaryotic domain is, as yet, unknown. MTCP1 is found in mitochondria.  Mature-T-Cell Proliferation) is the first gene unequivocally identified in the group of uncommon leukemias with a mature phenotype.
Pfam PF24840: SigF NTF2-like domain (domain)
This domain is found in the SrfA-induced gene F protein (SigF) from Dictyostelium discoideum and related eukaryotic proteins. SigF was identified amongst genes whose expression is dependent on the MADS box transcription factor SrfA and are induced late in development. This domain has a detectable similarity to NTF2 domains and it is predicted to adopt similar structure.
Pfam PF06375: AP-3 complex subunit delta-1 (family)
AP-3 complex subunit delta-1 (AP3D1) is part of the AP-3 complex, an adaptor-related complex which is not clathrin- associated. The complex is associated with the Golgi region  as well as more peripheral structures. AP3D1 is required for efficient transport of VSV-G (vesicular stomatitis virus glycoprotein) from the trans-Golgi network to the cell  surface.
Pfam PF18670: V-type ATPase subunit I, N-terminal domain (domain)
Vacuolar H+-ATPase (V-ATPase) is a ubiquitous multi-subunit proton pump that acidifies a wide variety of intracellular compartments, which in turn affects many biological processes, including membrane trafficking, protein degradation and coupled transport of small molecules and pH homeostasis. Subunit 'a' of V0 (the functional domain responsible for proton transport) sector is highly conserved across eukaryotic species and exists in multiple isoforms. It is the largest subunit of V-ATPases and partitioned almost equally into an N-terminal cytosolic domain and a C-terminal integral membrane. Structure analysis of the N-terminal cytosolic domain from the Meiothermus ruber subunit 'I' homolog of subunit a shows that it is composed of a curved long central alpha-helix bundle capped on both ends by two lobes with similar alpha/beta architecture.
Wikipedia: Vacuolar-type ATPase (V-ATPase) is a highly conserved evolutionarily ancient enzyme with remarkably diverse functions in eukaryotic organisms. V-ATPases acidify a wide array of intracellular organelles and pumps protons across the plasma membranes of numerous cell types. V-ATPases couple the energy of ATP hydrolysis to proton transport across intracellular and plasma membranes of eukaryotic cells. It is generally seen as the polar opposite of ATP synthase because ATP synthase is a proton channel that uses the energy from a proton gradient to produce ATP. V-ATPase however, is a proton pump that uses the energy from ATP hydrolysis to produce a proton gradient.
Pfam PF07396: Phosphate-selective porin O and P (family)
This family represents a conserved region approximately 400 residues long within the bacterial phosphate-selective porins O and P. These are anion-specific porins, the binding site of which has a higher affinity for phosphate than chloride ions. Porin O has a higher affinity for polyphosphates, while porin P has a higher affinity for orthophosphate. In P. aeruginosa, porin O was found to be expressed only under phosphate-starvation conditions during the stationary growth phase.
Wikipedia: Phosphate-selective porins are a family of outer bacterial membrane proteins. These are anion-specific porins, the binding site of which has a higher affinity for phosphate than chloride ions. Porin O has a higher affinity for polyphosphates, while porin P has a higher affinity for orthophosphate. In Pseudomonas aeruginosa, porin O was found to be expressed only under phosphate-starvation conditions during the stationary growth phase.