SII-SWORD/CoKE huggingface dataset:
Pfam PF01394: Clathrin propeller repeat (repeat)
Clathrin is the scaffold protein of the basket-like coat that surrounds coated vesicles.  The soluble assembly unit, a triskelion, contains three heavy chains and three light chains in an extended three-legged structure.  Each leg contains one heavy and one light chain.  The N-terminus of the heavy chain is known as the globular domain, and is composed of seven repeats which form a beta propeller.
Wikipedia: Clathrin is a protein that plays a role in the formation of coated vesicles. Clathrin was first isolated by Barbara Pearse in 1976. It forms a triskelion shape composed of three clathrin heavy chains and three light chains. When the triskelia interact they form a polyhedral lattice that surrounds the vesicle. The protein's name refers to this lattice structure, deriving from Latin clathri meaning lattice. Barbara Pearse named the protein clathrin at the suggestion of Graeme Mitchison, selecting it from three possible options. Coat-proteins, like clathrin, are used to build small vesicles in order to transport molecules within cells. The endocytosis and exocytosis of vesicles allows cells to communicate, to transfer nutrients, to import signaling receptors, to mediate an immune response after sampling the extracellular world, and to clean up the cell debris left by tissue inflammation. The endocytic pathway can be hijacked by viruses and other pathogens in order to gain entry to the cell during infection.
Pfam PF13646: HEAT repeats (repeat)
This family includes multiple HEAT repeats.
Wikipedia: A HEAT repeat is a protein tandem repeat structural motif composed of two alpha helices linked by a short loop. HEAT repeats can form alpha solenoids, a type of solenoid protein domain found in a number of cytoplasmic proteins. The name "HEAT" is an acronym for four proteins in which this repeat structure is found: Huntingtin, elongation factor 3 (EF3), protein phosphatase 2A (PP2A), and the yeast kinase TOR1. HEAT repeats form extended superhelical structures which are often involved in intracellular transport; they are structurally related to armadillo repeats. The nuclear transport protein importin beta contains 19 HEAT repeats.
Pfam PF23898: Crassvirus major capsid protein (family)
This entry represents the major capsid protein found in viruses from the Crassvirales order. The major capsid protein self-assembles to form an icosahedral capsid. In the bacteriophage crAss001, the capsid has a T=9 symmetry and is about 77 nm in diameter. The major capsid protein displays an HK97-like fold with an insertion domain that protrudes at the capsid surface.
Pfam PF01380: SIS domain (domain)
SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.  Presumably the SIS domains bind to the end-product of the pathway.
Pfam PF09956: Phage cement protein (family)
This entry represents a large family of phage proteins. These proteins form a trimeric arrangement which stabilises the phage capsid. The proteins have what is known as a beta-tulip fold.
Pfam PF17400: Family of unknown function (DUF5406) (family)
This is a family of unknown function found in Bacteria.
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 PF18055: 26S proteasome regulatory subunit RPN6 N-terminal domain (repeat)
This is the N-terminal domain found in RPN6 proteins (26S proteasome regulatory subunit).  The 26S proteasome holocomplex consists of a 28-subunit barrel-shaped core particle (CP) in the center capped at the top and bottom by 19-subunit regulatory particles (RPs). The CP forms the catalytic chamber and the RP is formed from two subcomplexes known as the lid and the base. The lid comprises nine Rpn subunits in yeast (Rpn3/5/6/7/8/9/11/12/15) and the base comprises three Rpn subunits (Rpn1/2/13) and six ATPases (Rpt1-6). Phosphorylation of Rpn6 enhances proteasome ATPase activity and promotes the formation of doubly capped (30S) proteasome, hence accelerating the degradation of short-lived proteins.
Pfam PF17773: UPF0176 acylphosphatase like domain (domain)
This domain is found at the N-terminus of UPF0176 family proteins. It adopts a fold similar to the [pfam:PF00708] family.
Pfam PF10644: Misato Segment II tubulin-like domain (domain)
The misato protein contains three distinct, conserved domains, segments I, II and III. Segments I and III are common to Tubulins [pfam:PF00091], but segment II aligns with myosin heavy chain sequences from D. melanogaster (PIR C35815), rabbit (SP P04460), and human (PIR S12458). Segment II of misato is a major contributor to its greater length compared with the various tubulins. The most significant sequence similarities to this 54-amino acid region are from a motif found in the heavy chains of myosins from different organisms. A comparison of segment II with the vertebrate myosin heavy chains reveals that it is homologous to a myosin peptide in the hinge region linking the S2 and LMM domains. Segment II also contains heptad repeats which are characteristic of the myosin tail alpha-helical coiled-coils. This myosin-like homology may be due only to the fact that both myosin and Misato carry coiled-coils, which appear similar but are not necessarily homologous (Wood V, personal communication).
Wikipedia: The Misato segment II myosin-like domain is an evolutionary conserved protein domain. The misato protein contains three distinct, conserved domains, segments I, II and III and is involved in the regulation of mitochondrial distribution and morphology.
Pfam PF06472: ABC transporter transmembrane region 2 (family)
This domain covers the transmembrane of a small family of ABC transporters and shares sequence similarity with [pfam:PF00664]. Mutations in this domain in [swissprot:P28288] are believed responsible for Zellweger Syndrome-2; mutations in [swissprot:P33897] are responsible for recessive X-linked adrenoleukodystrophy. A Saccharomyces cerevisiae homolog is involved in the import of long-chain fatty acids.
Wikipedia: ABC transporter transmembrane domain is the main transmembrane structural unit of ATP-binding cassette transporter proteins, consisting of six alpha helixes that traverse the plasma membrane. Many members of the ABC transporter family have two such regions.
Pfam PF21057: Hikeshi-like, C-terminal domain (domain)
This domain is found at the C-terminal end of Protein Hikeshi from humans and its orthologues OPI10 from other eukaryotes. Hikeshi is an specific nuclear import carrier for HSP70 proteins following heat-shock stress, which is required to protect cells from heat- shock damages. The intrinsically flexible C-terminal domain is responsible for the asymmetric dimeric conformation adopted by the protein, which seems to be an important regulator of Hsp70 binding. It shows three alpha-helices and a short beta-strand in a coiled-coil-like configuration.
Wikipedia: HIKESHI is a protein important in lung and multicellular organismal development that, in humans, is encoded by the HIKESHI gene. HIKESHI is found on chromosome 11 in humans and chromosome 7 in mice. Similar sequences (orthologs) are found in most animal and fungal species. The mouse homolog, lethal gene on chromosome 7 Rinchik 6 protein is encoded by the l7Rn6 gene.
Pfam PF17088: Uncharacterised protein family (family)
Ycf90 is an algal protein located in chloroplasts. Its function is unknown.
Pfam PF14692: Domain of unknown function (DUF4462) (family)
This domain family is found in eukaryotes, and is approximately 30 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 PF01588: Putative tRNA binding domain (domain)
This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding  protein (G4p1 or p42, ARC1), human tyrosyl-tRNA synthetase, and endothelial-monocyte activating polypeptide II.  G4p1 binds specifically to tRNA form a complex with methionyl-tRNA  synthetases. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme. This domain may perform a common function in tRNA aminoacylation.
Pfam PF00448: SRP54-type protein, GTPase domain (domain)
This family includes relatives of the G-domain of the SRP54 family of proteins.
Pfam PF16662: FLYWCH-type zinc finger-containing protein 1 (disordered)
FLYWCH_u is a region of natively unstructured but conserved sequence that lies between the FLYWCH zinc-finger domains on FLYWCH-type zinc finger-containing protein 1 proteins in higher eukaryotes. The function is not known but the N- and C-termini are likely to be part of the zinc-finger domains specific, to the eukaryotes.
Pfam PF00789: UBX domain (domain)
This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module.
Pfam PF20114: Domain of unknown function (DUF6504) (domain)
This entry represents a domain of unknown function found at the C-terminal of functionally uncharacterised bacterial proteins. In some short sequences, it covers the full 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 PF22673: Methyl-accepting chemotaxis protein-like, first PDC sensor domain (domain)
This entry represents the first PDC (PhoQ/DcuS/CitA) sensor domain found in methyl-accepting chemotaxis proteins (MCPs) such as TLQP and MCPA/B.
Pfam PF18104: Jumonji domain-containing protein 2A Tudor domain (domain)
This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD).
Wikipedia: In molecular biology, a Tudor domain is a conserved protein structural domain originally identified in the Tudor protein encoded in Drosophila. The Tudor gene was found in a Drosophila screen for maternal factors that regulate embryonic development or fertility. Mutations here are lethal for offspring, inspiring the name Tudor, as a reference to the Tudor King Henry VIII and the several miscarriages experienced by his wives.
Pfam PF16813: CRISPR-associated protein Csn2 subfamily St (domain)
Cas_St_Csn2 is a family of Csn2 CRISPR-associated (Cas) proteins found in Firmicutes, largely Streptococcus and Enterococcus. CRISPR-associated (Cas) proteins are the main executioners of the process whereby prokaryotes acquire immunity against foreign genetic material.  Cas allow short segments of this DNA, called spacer, to become incorporated into chromosomal loci as clustered regularly interspaced short palindromic repeats or CRISPRs; the resulting encoded RNAs are then processed into small fragments that guide the silencing of the invading genetic elements. Thus Cas are involved in the acquisition of new spacers. This family of St_Csn2 is longer than the canonical Csn2, [pfam:PF09711] through the addition of a large C-terminal domain. The central domain present in both families appears to be a channel that selectively interacts with dsDNA.
Pfam PF18046: FKBP26_C-terminal (domain)
This is the C-terminal domain (CTD) of Methanocaldococcus jannaschii peptidyl-prolyl cis/trans isomerase FKBP26. FKBP26 mediates protein folding. CTD has an alpha/beta-sandwich structure composed of three alpha-helices and a three-stranded, mixed-orientation beta-sheet. The CTD domain is responsible for dimerization of FKBP26 by through inter-subunit antiparallel pairing of the third beta-strands of the two CTDs. The CTD dimer forms a continuous, six-stranded mixed beta-sheet. A CTD-like structure is also found in the phylogenetically conserved NifU proteins (HIRIP5 in mouse and humans).
Pfam PF14089: KinB-signalling pathway activation in sporulation (family)
This family of small proteins is found in the membrane and is necessary for kinase KinB signalling during sporulation. There is a conserved GFF sequence motif. The initiation of sporulation in Bacillus subtilis is dependent on the phosphorylation of the Spo0A transcription factor mediated by the phospho-relay and by two major kinases, KinA and KinB.
Pfam PF18226: LasR-specific antiactivator QslA (domain)
This domain is found in QslA from Pseudomonas aeruginosa. QslA is an antiactivator which binds to the transcription factor LasR, disrupting its dimerization and preventing LasR from binding to target DNA. QslA forms a dimer that interacts with the ligand-binding domain in LasR.
Pfam PF07297: Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2) (family)
This family consists of several eukaryotic dolichol phosphate-mannose biosynthesis regulatory (DPM2) proteins. Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM). DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localisation and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase. Biosynthesis of DPM in mammalian cells is regulated by DPM2.
Pfam PF04262: Glutamate-cysteine ligase (family)
Family of bacterial f glutamate-cysteine ligases ([ec:6.3.2.2]) that carry out the first step of the glutathione biosynthesis pathway.
Pfam PF16481: Domain of unknown function (DUF5058) (family)
This family consists of uncharacterized proteins around 250 residues in length and is mainly found in various Firmicutes species. 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 PF21902: PTM1-like, N-terminal domain (domain)
This entry represents the N-terminal domain of fungal proteins, such as PTM1 from S.cerevisiae and its closely homologues from S.pombe. They have been identified as orthologues of TMEM87A/B from human.  Structure predictions suggest that these proteins has the same domain architecture as GOST (GOLD seven-transmembrane helix) proteins consisting of a GOLD domain atop of a membrane-spanning seven-transmembrane helix domain this domain. This domain represents the GOLD domain. Members of this entry localise to the Golgi and early endosomes; the function is unknown.
Pfam PF21459: SWI/SNF Subunit INI1, DNA binding domain (domain)
SWI/SNF complexes use the energy of ATP hydrolysis to remodel chromatin. In mammals they play a central role in regulating gene expression during differentiation and proliferation. The INI1/hSNF5/SMARCB1 subunit contains and N-terminal winged helix DNA binding domain.
Pfam PF09757: Arb2-like domain (domain)
This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) (also known as histone deacetylase clr3) ([ec:3.5.1.98]) from S. pombe, its orthologue from S. cerevisiae HDA1, and similar sequences. This domain has been defined by sequence homology to the Arb2 protein from S. pombe (not included in this entry). Structure analysis reveals that the Arb2 domain has clear homology to alpha/beta-hydrolases but that it is lacking the catalytic triad of these enzymes. Functional studies show that the this domain is necessary for centromeric heterochromatin silencing suggesting a model where the Arb2-like domain, through residues N562 and Y563, acts as an anchor that connects the HDAC activity of Clr3 to the SHREC complex. SHREC (Snf2/Hdac Repressive) complex in fission yeast drives transcriptional gene silencing in heterochromatin. Studies in HDA1 described that two Arb2-like domains form a compact homo-dimer via the arm elements, and assemble as an inverse 'V' shape and that the domain possesses histone binding ability.
Pfam PF12424: Plasma membrane calcium transporter ATPase C terminal (family)
This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with [pfam:PF00689], [pfam:PF00122], [pfam:PF00702], [pfam:PF00690]. There is a conserved QTQ sequence motif. This family is the C terminal of a calcium transporting ATPase located in the plasma membrane.
Pfam PF13498: Domain of unknown function (DUF4122) (family)
Based on Bacteroides thetaiotaomicron gene BT_2607, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture.
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 PF12195: Beta barrel domain of bacteriophage endosialidase (repeat)
This domain family is found in bacteria and viruses, and is approximately 80 amino acids in length.This domain is the beta barrel domain of bacteriophage endosialidase which represents the one of the two sialic acid binding sites of the enzyme. The domain is nested in the beta propeller domain of the endosialidase enzyme. The endosialidase protein complexes to form homotrimeric molecules.
Pfam PF21155: VpsT-like, receiver domain (domain)
This domain is found at the N-terminal end of the transcriptional regulator VC_A0952 from Vibrio cholerae (VpsT), in CsgD from Salmonella typhimurium and other proteins predominantly found in proteobacteria. VpsT inversely regulates biofilm formation and motility. Like CsgD, it is organised into two domains: an N-terminal regulatory receiver domain (REC, this entry) and a C-terminal helix-turn-helix domain ([pfam:PF00196]). This domain shows five alpha- helices and five beta-strands, with the beta-strands stabilising as a parallel beta-sheet surrounded by the alpha-helices.
Pfam PF11755: Protein of unknown function (DUF3311) (family)
This is a family of short bacterial proteins of unknown 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 PF03956: Lysine exporter LysO (family)
Members of this family contain a conserved core of four predicted transmembrane segments.  Some members have an additional pair of N-terminal transmembrane helices. This family includes lysine exporter LysO (YbjE) from E. coli.
Pfam PF05546: She9 / Mdm33 family (family)
Members of this family are mitochondrial inner membrane proteins with a role in inner mitochondrial membrane organisation and biogenesis.
Pfam PF02181: Formin Homology 2 Domain (family)
Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of the cell cortex including motility, adhesion, and cytokinesis . Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains . The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain is required for the self-association of formin proteins through the ability of FH2 domains to directly bind each other , and may also act to inhibit actin polymerisation . The FH3 domain (IPR010472) is less well conserved and may be important for determining intracellular localisation of formin family proteins. In addition, some formins can contain a GTPase-binding domain (GBD) (IPR010473) required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD).
This entry represents the FH2 domain, which was shown by X-ray crystallography to have an elongated, crescent shape containing three helical subdomains .
Wikipedia: Formins (formin homology proteins) are a group of proteins that are involved in the polymerization of actin and associate with the fast-growing end (barbed end) of actin filaments. Most formins are Rho-GTPase effector proteins. Formins regulate the actin and microtubule cytoskeleton 
 and are involved in various cellular functions such as cell polarity, cytokinesis, cell migration and SRF transcriptional activity. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus.
Pfam PF01448: ELM2 domain (family)
The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain [pfam:PF00249]. ELM2 is also found associated with an ARID DNA binding domain [pfam:PF01388] in [swissprot:O82364]. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.
Pfam PF12600: Protein of unknown function (DUF3769) (family)
This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 560 and 931 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.