SII-SWORD/CoKE huggingface dataset:
Pfam PF14396: Cystic fibrosis TM conductance regulator (CFTR), regulator domain (domain)
Cystic fibrosis transmembrane conductance regulator (CFTR) that belongs to the ATP-binding cassette (ABC) transporter superfamily. It is a member of the ABC-C subfamily, which also contains the SUR receptors and the multidrug- resistance associated proteins (MRP) . The CFTR protein encodes a chloride ion channel, which is controlled by phosphorylation. It has a major role in electrolyte and fluid secretion. CFTR is important in the determination of fluid flow, ion concentration and transepithelial salt transport. Dysfunction of the CFTR channel causes the life-threatening disease, cystic fibrosis, in which trans-epithelial ion transport is disrupted .

This entry represents the CFTR regulator domain .
Wikipedia: Cystic fibrosis transmembrane conductance regulator (CFTR) is a membrane protein and anion channel in vertebrates that is encoded by the CFTR gene.
Pfam PF20062: Family of unknown function (DUF6461) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 198 and 278 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 PF23580: XIAP-associated factor 1-like, N-terminal zinc finger (domain)
This zinc finger domain is found at the N-terminal end of human XIAP-associated factor 1 (XAF1), which seems to function as a negative regulator of members of the IAP (inhibitor of apoptosis protein) family.
Pfam PF14421: LmjF365940 subfamily CDD/CDA-like deaminase (family)
A distinct branch of the CDD/CDA-like deaminases prototyped by Leishmania LmjF36.5940. Members of this family are widely distributed across several microbial eukaryotes such as kinetoplastids,  chlorophyte algae, stramenopiles and the alveolate Perkinsus. Domain  architectures suggest that these proteins might possess mRNA editing  or DNA mutagenizing activity.
Pfam PF22141: Thiaminase-1 domain (domain)
This domain is found in Thiaminase-1 from Paenibacillus thiaminolyticus and similar bacterial sequences. This enzyme degrades thiamine by replacing its thiazole moiety with a wide range of nucleophiles. This entry represents one if its two alpha/beta-type domains.
Pfam PF05527: Domain of unknown function (DUF758) (family)
Family of eukaryotic proteins with unknown function, which are induced by tumour necrosis factor.
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 PF16684: Telomere resolvase ResT/TelK catalytic domain (domain)
Telomere resolvase (protelomerase) catalyses the conversion of linear double-stranded DNA into hairpin telomeres. This entry represents the catalytic domain of ResT and TelK.
Pfam PF13150: Conjugative transposon protein TraL (family)
This family contains conjugal transfer protein TraL.
Pfam PF17538: DNA Binding Domain (C-terminal) Leafy/Floricaula (domain)
This family consists of various plant development proteins which are homologues of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY is a plant-specific transcription factor (TF) essential for flower development. It is one of the few master regulators of flower development, as it integrates environmental and endogenous signals to orchestrate the whole floral network. Transcription factors such as LFY, recognize short DNA motifs primarily through their DNA-binding domain. Upon binding to short stretches of DNA called cis-elements or TF binding sites (TFBS), they regulate gene expression. This entry represents the DNA binding domain found in C-terminal of LFY proteins in plants. Structure-function studies have demonstrated that LFY binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD, a unique helix-turn-helix fold that by itself dimerizes on DNA.
Pfam PF05594: Haemagglutinin repeat (repeat)
This highly divergent repeat occurs in number of proteins implicated in cell aggregation. The Pfam alignment probably contains three such repeats (personal obs: C Yeats). These are likely to have a beta-helical structure.
Pfam PF10954: Protein of unknown function (DUF2755) (family)
Some members in this family of proteins are annotated as YaiY however no function is known. The family appears to be restricted to Enterobacteriaceae.
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 PF19457: Family of unknown function (DUF5994) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000202) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family contains a  protein found in the azicemicin B biosynthetic gene cluster from Kibdelosporangium sp. MJ126-NF4. The function of this protein 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 PF02883: Adaptin C-terminal domain (domain)
Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud  site.  This ig-fold domain is found in alpha, beta and gamma adaptins.
Pfam PF00798: Arenavirus glycoprotein (family)
Arenaviridae are single stranded RNA viruses. The arenaviridae S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein .
Tacaribe virus (TACV) is an arenavirus that is genetically and antigenically closely related to Junin arenavirus (JUNV), the aetiological agent of Argentine haemorrhagic fever (AHF). It is well established that TACV protects experimental animals fully against an otherwise lethal challenge with JUNV. It has been established that it is the heterologous glycoprotein that protects against JUNV challenge. A recombinant vaccinia virus that expresses JUNV glycoprotein precursor (VV-GJun) protected seventy-two percent of the animals inoculated with two doses of VV-GJun against the lethal JUNV challenge .
Pfam PF00244: 14-3-3 protein (repeat)
This entry represents the structural domain found in 14-3-3 proteins.
The 14-3-3 proteins are a large family of approximately 30kDa acidic proteins which exist primarily as homo- and heterodimers within all eukaryotic cells . These are structurally similar phospho-binding proteins that regulate multiple signaling pathways . There is a high degree of sequence identity and conservation between all the 14-3-3 isotypes, particularly in the regions which form the dimer interface or line the central ligand binding channel of the dimeric molecule. Each 14-3-3 protein sequence can be roughly divided into three sections: a divergent amino terminus, the conserved core region and a divergent carboxyl terminus. The conserved middle core region of the 14-3-3s encodes an amphipathic groove that forms the main functional domain, a cradle for interacting with client proteins. The monomer consists of nine helices organised in an antiparallel manner, forming an L-shaped structure. The interior of the L-structure is composed of four helices: H3 and H5, which contain many charged and polar amino acids, and H7 and H9, which contain hydrophobic amino acids. These four helices form the concave amphipathic groove that interacts with target peptides.

The 14-3-3 proteins mainly bind proteins containing phosphothreonine or phosphoserine motifs, however exceptions to this rule do exist. Extensive investigation of the 14-3-3 binding site of the mammalian serine/threonine kinase Raf-1 has produced a consensus sequence for 14-3-3-binding, RSxpSxP (in the single-letter amino-acid code, where x denotes any amino acid and p indicates that the next residue is phosphorylated). The 14-3-3 proteins appear to effect intracellular signalling in one of three ways - by direct regulation of the catalytic activity of the bound protein, by regulating interactions between the bound protein and other molecules in the cell by sequestration or modification or by controlling the subcellular localisation of the bound ligand. Proteins appear to initially bind to a single dominant site and then subsequently to many, much weaker secondary interaction sites. The 14-3-3 dimer is capable of changing the conformation of its bound ligand whilst itself undergoing minimal structural alteration.
Wikipedia: 14-3-3 proteins are a family of conserved regulatory molecules that are expressed in all eukaryotic cells. 14-3-3 proteins have the ability to bind a multitude of functionally diverse signaling proteins, including kinases, phosphatases, and transmembrane receptors. More than 200 signaling proteins have been reported as 14-3-3 ligands.
Pfam PF00578: AhpC/TSA family (domain)
This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA).
Wikipedia: Peroxiredoxins are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels and thereby mediate signal transduction in mammalian cells. The family members in humans are PRDX1, PRDX2, PRDX3, PRDX4, PRDX5, and PRDX6. The physiological importance of peroxiredoxins is indicated by their relative abundance. Their function is the reduction of peroxides, specifically hydrogen peroxide, alkyl hydroperoxides, and peroxynitrite.
Pfam PF19308: CRISPR Cas6 N-terminal domain (domain)
In Type I and III CRISPR/Cas systems, the Cas6 family of endoribonucleases generates functional CRISPR-derived RNAs by site-specific cleavage of repeat sequences in precursor transcripts. The structure of Cas6 showed it adopts a tandem ferredoxin/RRM fold. This entry represents the N-terminal domain.
Pfam PF16785: Small metal-binding protein (domain)
This histidine-rich protein binds metal ions.
Pfam PF00722: Glycosyl hydrolases family 16 (domain)
The glycosyl hydrolases family 16 (GH16)  contains functionally heterogeneous members, including lichenase (3.2.1.73); xyloglucan xyloglucosyltransferase (2.4.1.207); agarase (3.2.1.81); kappa-carrageenase (3.2.1.83); endo-beta-1,3-glucanase (3.2.1.39); endo-beta-1,3-1,4-glucanase (3.2.1.6); endo-beta-galactosidase (3.2.1.103). These enzymes share a common ancestor and have diverged significantly in their primary sequence.

The GH16 catalytic domain has a classical sandwich-like Î²-jelly roll fold, formed by two main, closely packed and curved antiparallel Î²-sheets, creating a deep channel harboring the catalytic machinery. Even though the GH16 domains have now diverged significantly in their primary sequences, they all feature a common catalytic motif, E-[ILV]-D-[IVAF]-[VILMF](0,1)-E. The two glutamic acid residues in the conserved motif are the nucleophile and the general base involved in catalysis, whereas the aspartic acid residue is important in maintaining the relative position of these catalytic amino acids .

Two closely clustered conserved glutamates have been shown  to be involved in the catalytic activity of Bacillus licheniformis lichenase. This domain contains these residues.
Wikipedia: In molecular biology, Glycoside hydrolase family 16 is a family of glycoside hydrolases.
Pfam PF18338: Lower baseplate protein N-terminal domain (repeat)
This domain is found in the N-terminal region of the receptor-binding protein of bacteriophage TP901-1, which infects Lactococcus lactis. The receptor-binding protein of phage TP901-1 is termed the lower baseplate protein (BppL) and is trimeric in nature. The N-terminal domain of BppL plugs into the upper baseplate protein (BppU).
Pfam PF16566: Cell-cycle alteration and expression-elevated protein in tumour (domain)
CREPT (Cell-cycle alteration and expression-elevated protein in tumour) is a family of eukaryotic transcriptional regulators that ptromote the binding of RNA-polymerase to the CYCLIN D1, CCDN1, promoter and other genes involved in the cell-cycle. It promotes the formation of a chromatin loop in the CYCLIN D1 gene, and is preferentially expressed in a range of different human tumours.
Pfam PF24794: Duc1 FFAT-like motif (conserved_site)
This entry represents the FFAT-like motif found in proteins such as Duc1 that interact with VAP (VAMP-associated protein) family members like Scs2 and Scs22. The motif is characterized by two adjacent aromatic residues (typically FF, but YF in Duc1) downstream of an acidic tract. It also contains conserved alanine and glutamate residues at the second and fourth positions after the aromatic pair, respectively. This motif mediates interactions with the Major Sperm Protein (MSP) domains of VAP proteins, playing a crucial role in tethering proteins to ER-PM contact sites.  In Duc1, the core of this motif is Y374 and F375, which are essential for the protein's interaction with Scs2 and Scs22, and consequently for its proper localization and function in maintaining plasma membrane lipid composition and cytokinetic ring anchoring.
Pfam PF17766: Fibronectin type-III domain (domain)
This FN3 like domain is found at the C-terminus of cucumisin proteins.
Pfam PF02614: Glucuronate isomerase (domain)
This is a family of Glucuronate isomerases also known as D-glucuronate  isomerase, uronic isomerase, uronate isomerase, or uronic acid isomerase, [ec:5.3.1.12].  This enzyme catalyses the reactions: D-glucuronate   D-fructuronate and D-galacturonate  D-tagaturonate.  It is not however  clear where the experimental evidence for this functional assignment came from and thus this family has no literature reference.
Pfam PF09754: PAC2 family (family)
This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes.  Proteins in this family are typically between 247 and 307 amino acids in length. These proteins function as a chaperone for the 26S proteasome. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits.
Pfam PF24871: Piezo TM1-24 (domain)
Piezo is a family of proteins that form mechanosensitive non-specific cation channels whose conductance is higher for Li+, intermediate for Na+ and lowest for Li+. Divalent ions except for Mn2+ permeate the channel but more slowly than monovalent ions and can reduce K+ currents. These channels have a homotrimeric three-blade propeller-shaped structure that use a cap-motion and plug-and-latch mechanism to gate their ion-conducting pathways. Each protomer consists of 38 TM helices that form unusual non-planar blades, and an extracellular cap-like structure ([pfam:PF12166]). This entry represents the N-terminal TM segment (TM1-24) which are peripheral part of the blade and exhibit a greater degree of flexibility of these helices relative to TM25-TM36, as apparently, they do not have intracellular supporting structures.
Pfam PF06222: Phage tail assembly chaperone (family)
Tail assembly chaperones (TACs) are required for the morphogenesis of all long-tailed phages. Gp13, a TAC from bacteriophage HK97, is required for tail tube assembly and is thought to be a TAC. The gp13 monomer comprises a single domain consisting of a small three-stranded twisted Î²-sheet connected to a helical bundle. Gp13 adopts a spiral quaternary structure, similar to other TACs . This family includes gp13 and putative TACs from other Siphovirus.
Pfam PF09324: Mon2/Sec7/BIG1-like, HDS (domain)
This entry represents a HDS (homology downstream of Sec7) domain found towards the C-terminal of guanine nucleotide exchange factors involved Golgi transport, such as budding yeast protein Sec7, protein Mon2 and BIG1-like proteins. Sec7 is involved in the secretory pathway as a protein binding scaffold for the COPII-COPI protein switch for maturation of the VTC intermediate compartments for Golgi compartment biogenesis. Sec7 has four HDS1-4 domains, which act to integrate the signals from several small GTPases, including Arf1 itself, to switch Sec7 from a strongly autoinhibited to a strongly auto activated form.
Pfam PF18479: PIN like domain (domain)
This is a eukaryotic/eumetazoan PIN like domain found in the C-terminal region of bilateral ZNF451 proteins such as isoform 1 of human ZNF451.  ZNF451 was shown to interact with p300 by the PIN-like domain and to negatively regulate TGF-beta signalling in a p300-dependent and sumoylation-independent manner. This domain is suggested to posses a potential active nuclease due to the presence of at least four conserved Asp residues in the predicted active site. Furthermore, it contains several conserved Cys and His residues, which may suggest stabilization of the domain structure with an embedded short zinc-binding loop.
Pfam PF13326: Photosystem II Pbs27 (family)
This family of proteins contains Pbs27, a highly conserved component of photosystem II.  Pbs27 is comprised of four helices arranged in a right handed up-down-up-down fold, with a less ordered region located at the N-terminus.
Pfam PF18101: Pan3 Pseudokinase domain (domain)
This is a pseudokinase (PK) domain found in PAB-dependent poly(A)-specific ribonuclease subunit pan3.  PAN3 proteins contain three prominent regions: an unstructured N-terminal region (N-term), a central PK domain, and a highly conserved C-terminal domain (C-term). The PAN3 PK domain has retained its ATP binding capacity, and this function is required for mRNA degradation in vivo.  Analysis of Pan3 amino acids sequences show that, despite of retaining the general structural characteristics of protein kinases, the PK domain has substitutions in all the conserved motifs that are critical for kinase activity, such as in the catalytic VAIK and HRD motifs and in the Mg2+ binding DFG motif. However, the PAN3 PK domain has been shown to bind ATP. Furthermore, similar to other kinases, the ATP-binding site is located in the cleft between the N- and C-lobes of the kinase fold, however, the ATP-binding pocket is wider than that of typical kinases.
Pfam PF11435: RNA binding protein She2p (family)
She2p is a RNA binding protein which binds to RNA via a helical hairpin. The protein is required for the actin dependent transport of ASH1 mRNA in yeast, a form of mRNP translocation. ASH1 mRNP requires recognition of zip code elements by the RNA binding protein She2p. She2p contains a globular domain consisting of a bundle of five alpha-helices.
Pfam PF22067: Cep192 domain 3 (domain)
Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation. Most of the metazoan Cep192 homologs consist of eight ASH/PapD-like domains. These are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion. This entry represents the third domain found in the metazoan Cep192 homologs.
Pfam PF20637: Autophagy protein ATG5, alpha-helical bundle region (domain)
Autophagy protein ATG5 is involved in autophagic vesicle formation. It is conjugated with ATG12, acting as an E3-like ubiquitin enzyme required for lipidation of ATG8 family proteins and their association to the vesicle membranes. ATG5 comprises two ubiquitin-like domains (UblA and UblB) that flank a helix-rich domain. This domain represents the alpha-helical bundle region (HBR) of AT5 which consists of three alpha helices. This region contains the Lys residue required for conjugation with ATG12.
Pfam PF24022: Family of unknown function (DUF7334) (family)
This entry represents a small family of uncharacterised phage proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09741: Uncharacterized conserved protein (DUF2045) (family)
This entry is the conserved 250 residues of proteins of approximately 450 amino acids. It contains several highly conserved motifs including a CVxLxxxD motif.The function 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 PF20019: vWA-MoxR associated protein middle region 20 (family)
Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities.
Pfam PF02406: MmoB/DmpM family (domain)
This family consists of monooxygenase components such as MmoB methane monooxygenase ([ec:1.14.13.25]) regulatory protein B. When MmoB is present at low concentration it converts methane monooxygenase from an oxidase to a hydroxylase and stabilises intermediates required for the activation of dioxygen. Also found in this family is DmpM or Phenol hydroxylase ([ec:1.14.13.7]) protein component P2, this protein lacks redox co-factors and is required for optimal turnover of Phenol hydroxylase.
Pfam PF01680: SOR/SNZ family (domain)
Members of this family are enzymes involved in a new pathway of pyridoxine/pyridoxal 5-phosphate biosynthesis. This family was formerly known as UPF0019.
Pfam PF21785: 5-fold beta-flower protein (domain)
This family of proteins have a repetitive structure composed of pairs of beta strands. In this family the proteins usually have five copies of the beta hairpin repeat.