SII-SWORD/CoKE huggingface dataset:
Pfam PF18091: E3 Ubiquitin Ligase RBR C-terminal domain (domain)
This is the C-terminal domain of HOIP present in Homo sapiens. HOIP synthesize the linear ubiquitin chains that help control innate immunity and inflammation. This region has an RBR domain which catalyzes the transfer of ubiquitin onto a substrate.
Pfam PF13174: Tetratricopeptide repeat (repeat)
The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins . It mediates protein-protein interactions and the assembly of multiprotein complexes . The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.

The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel Î±-helices . The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B.
Wikipedia: The tetratricopeptide repeat (TPR) is a structural motif. It consists of a degenerate 34 amino acid tandem repeat identified in a wide variety of proteins. It is found in tandem arrays of 3–16 motifs, which form scaffolds to mediate protein–protein interactions and often the assembly of multiprotein complexes. These alpha-helix pair repeats usually fold together to produce a single, linear solenoid domain called a TPR domain. Proteins with such domains include the anaphase-promoting complex (APC) subunits cdc16, cdc23 and cdc27, the NADPH oxidase subunit p67-phox, hsp90-binding immunophilins, transcription factors, the protein kinase R (PKR), the major receptor for peroxisomal matrix protein import PEX5, protein arginine methyltransferase 9 (PRMT9), and mitochondrial import proteins.
Pfam PF15666: Germinal center-associated lymphoma (family)
HGAL is a family of mammalian sequences typically between 104 and 179 amino acids in length. Members were discovered in a search for proteins precipitating diffuse large B-cell lymphomas. HGAL interacts with the cytoskeleton and aids the activity of interleukin-6 on cell migration. It also modulates the RhoA signalling pathway.
Pfam PF02071: Aromatic-di-Alanine (AdAR) repeat (repeat)
This repeat is found in NSF attachment proteins. Its structure is similar to that found in TPR repeats [pfam:PF00515].
Pfam PF15039: Domain of unknown function (DUF4530) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically around 140 amino acids in length. The human member of this family is C19orf69.
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 PF13731: WxL domain surface cell wall-binding (family)
The WxL motif appears in two or three copies in these bacterial proteins and confers a cell surface localisation function. It seems likely that this region is the cell wall-binding domain of gram-positive bacteria, and may interact with the peptidoglycan.
Pfam PF23851: Domain of unknown function (DUF7214) (domain)
This entry represents a phage protein of unknown function. According to AlphaFold models the domain forms a four stranded beta sheet followed by a single alpha helix. This domain forms a confident dimer according to AlphaFold.
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 PF10779: Haemolysin XhlA (coiled_coil)
XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes. This family has had DUF1267, [pfam:PF06895], merged into it.
Pfam PF13433: Periplasmic binding protein domain (domain)
This domain is found in a variety of bacterial periplasmic binding proteins.
Pfam PF24666: Fungal C2H2 zinc finger (domain)
This is a putative C2H2-type zinc finger domain found in a group of fungal uncharacterised proteins.
Pfam PF21299: ADAM10, cysteine-rich domain (domain)
Disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) is a transmembrane endopeptidase responsible for the proteolytic release of several cell-surface proteins, including the membrane-bound precursor of TNF-alpha, ligands and receptors of the Notch, Eph, and erbB families, thereby activating signaling pathways critical for tumour initiation and maintenance. This entry represents the cysteine-rich domain which mediates non-catalytic interactions with the substrate that are key for effective cleavage. This domain, together with disintegrin domain ([pfam:PF00200]), plays an important modulatory role.
Pfam PF23706: Rv1893-like (family)
This protein family includes a group of short sequences from actinomycetes, including Rv1893 from Mycobacterium tuberculosis ([swissprot:O07739]).
Pfam PF01139: tRNA-splicing ligase RtcB (family)
This family of RNA ligases ([ec:6.5.1.3]) join 2',3'-cyclic phosphate and 5'-OH ends. They catalyse the splicing of tRNA and may also participate in tRNA repair and recovery from stress-induced RNA damage.
Wikipedia: RNA 2',3'-cyclic phosphate and 5'-OH ligase is a protein that in humans is encoded by the RTCB gene. It is found in the stress granule of cells.
Pfam PF16891: Serine-threonine protein phosphatase N-terminal domain (family)
This family is often found at the N-terminus of Metallophos family, in serine-threonine protein phosphatases.
Pfam PF20879: SidM, N-terminal domain (domain)
This domain is found in the type IV virulence effector SidM/DrrA from Legionella pneumophila. This protein has dual GEF and GDF activity specifically toward Rab1, a key regulator for endoplasmic reticulum (ER)-to-Golgi vesicle trafficking. SidM consists of an N-terminal helical domain (this entry), a Rab1-activation domain ([pfam:PF20851]), and a C- terminal phosphatidylinositol 4-phosphate-binding (P4M) domain ([pfam:PF14860]). The N-terminal is mostly alpha-helical, but also shows a short two-stranded beta-sheet.
Pfam PF19897: Family of unknown function (DUF6370) (family)
This family of proteins is found in bacteria and it is functionally uncharacterised. Proteins in this family are approximately 110 amino acids in length. Some of the members included in this family are thought to be glutaminyl-tRNA synthetases. There are some conserved sequence motifs: CGxC, YFVD/EG and GDAH.
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 PF01277: Oleosin (family)
Oleosins  are the proteinaceous components of plants' lipid storage bodies called oil bodies. Oil bodies are small droplets (0.2 to 1.5 mu-m in diameter) containing mostly triacylglycerol that are surrounded by a phospholipid/ oleosin annulus. Oleosins may have a structural role in stabilising the lipid body during dessication of the seed, by preventing coalescence of the oil. They may also provide recognition signals for specific lipase anchorage in lipolysis during seedling growth. Oleosins are found in the monolayer lipid/ water interface of oil bodies and probably interact with both the lipid and phospholipid moieties. Oleosins are proteins of 16 Kd to 24 Kd and are composed of three domains: an N-terminal hydrophilic region of variable length (from 30 to 60 residues); a central hydrophobic domain of about 70 residues and a C-terminal amphipathic region of variable length (from 60 to 100 residues). The central hydrophobic domain is proposed to be made up of Î²-strand structure and to interact with the lipids . It is the only domain whose sequence is conserved.
Wikipedia: Oleosins are structural proteins found in vascular plant oil bodies and in plant cells. Oil bodies are not considered organelles because they have a single layer membrane and lack the pre-requisite double layer membrane in order to be considered an organelle. They are found in plant parts with high oil content that undergo extreme desiccation as part of their maturation process, and help stabilize the bodies.
Pfam PF13668: Ferritin-like domain (domain)
This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins.
Pfam PF23667: CDCP1 CUB domain (domain)
This domain is found in the human CUB domain-containing protein 1 (CDCP1) and related proteins. CDCP1 may be involved in cell adhesion and cell matrix association. It also play a role in the regulation of anchorage versus migration or proliferation versus differentiation via its phosphorylation. CDCP1 contains a tandem of CUB domains. This entry represents the first of the tandem.
Pfam PF11057: Cortexin of kidney (family)
In the middle of cortexin protein there is a single membrane-spanning domain which indicates that this protein may be a membrane protein involved in intracellular or extracellular signalling of the kidney or brain, since it is expressed specifically in the kidneys and brain only. The protein is highly conserved among species. Cortexin is also thought to be important to neurons of both the developing and adult cerebral cortex.
Pfam PF16188: C-terminal region of peptidase_M24 (domain)
This is a short region at the C-terminus of a number of metallo-peptidases of the M24 family.
Pfam PF03863: Phage maturation protein (family)
This entry represents assembly/maturation protein (A-protein, MP) from Enterobacteria phages, including bacteriophage MS2. The single-stranded RNA genome of bacteriophage MS2 is 3,569 nt long and encodes four gene products: maturation protein, coat protein, and lysis and replicase proteins . The maturation protein is a necessary constituent in the assembly process of the virus . It is located on the surface of the phage particle  and influences the global arrangement of the virus coat . It binds to sequences located toward each end of the genome, hence circularizing it . The single-copy viral maturation protein breaks the symmetry of the capsid, suggesting an exit route for the genome during infection, and it is involved in receptor and genome binding .
Pfam PF02900: Catalytic LigB subunit of aromatic ring-opening dioxygenase (domain)
Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) . These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar.

Class III enzymes usually have two subunits, designated A and B. Enzymes that belong to the extradiol class III family include Protocatechuate 4,5-dioxygenase (4,5-PCD; LigAB) (1.13.11.8) ; and 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarBaBb) .

The crystal structure of dioxygenase LigAB revealed that the molecule is an alpha2beta2 tetramer. The active site contains a non-heme iron coordinated by His12, His61, Glu242, and a water molecule located in a deep cleft of the beta subunit, which is covered by the alpha subunit .

This entry represents the structural domain of subunit B.
Pfam PF13047: Protein of unknown function (DUF3907) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. There is a conserved AYTG sequence motif.
Pfam PF21899: Tarsal-less (Tal)/polished rice (Pri) peptide (family)
This entry represents Peptide tarsal-less AA from Drosophila melanogaster and simal sequences from Drosophilidae. This protein is required in early stages of leg development for the intercalation of the tarsal segments during the mid-third instar stage and later for tarsal joint formation . It is one of four peptides (tal-1A, tal-2A, tal-3A and tal-AA) produced from a polycistronic gene that function redundantly in several developmental processes .
Pfam PF23616: GEX2 N-terminal Ig-like domain (domain)
This domain is found N-terminal in the Arabidopsis GAMETE EXPRESSED 2 (GEX2) and related proteins. GEX2 is localised at the sperm membrane and contains a number of extracellular Ig-like domains. GEX2 is required for gamete attachment. The domain represented by this entry adopts a beta-sandwich structure with an Ig-like topology.
Pfam PF21432: 56B-like, Ribbon-helix-helix (domain)
This entry includes Sulfolobus virus proteins, including 56B from Sulfolobus virus SIRV1, which have a ribbon-helix-helix fold, very similar to that of bacterial RHH proteins. 56B binds DNA.
Pfam PF21357: Eukaryotic translation initiation factor 3 subunit E, C-terminal (domain)
Eukaryotic translation initiation factor 3 subunit E (EIF3E) is a component of the EIF3 complex, involved in protein synthesis. This is the C-terminal helical tail of EIF3E.
Pfam PF05253: U11-48K-like CHHC zinc finger (domain)
This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.
Pfam PF19589: Family of unknown function (DUF6095) (family)
This family of predicted integral membrane proteins is functionally uncharacterised. This family of proteins is found in Bacteroidetes. Proteins in this family are approximately 70 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 PF10502: Signal peptidase, peptidase S26 (domain)
This is a family of membrane signal serine endopeptidases which function in the processing of newly-synthesised secreted proteins.  Peptidase S26 removes the hydrophobic, N-terminal, signal peptides as proteins are translocated across membranes. The active site residues take the form of a catalytic dyad that is Ser, Lys in subfamily S26A; the Ser is the nucleophile in catalysis, and the Lys is the general base.
Wikipedia: Signal peptidases are enzymes that convert secretory and some membrane proteins to their mature or pro forms by cleaving their signal peptides from their N-termini.
Pfam PF16769: MCM3AP domain of GANP (family)
MCM3AP_GANP is the C-terminal domain of germinal centre-associated proteins, GANPs in higher eukaryotes.  GANP forms part of the TREX-2 complex which in higher eukaryotes requires the MCM3AP domain of GANP to facilitate its localisation to the Nuclear pore complex and nuclear envelope. TREX-2 complex links transcription with nuclear messenger RNA export.
Pfam PF05205: COMPASS (Complex proteins associated with Set1p) component shg1 (family)
The Shg1 subunit is one of the eight subunits of the COMPASS complex, complex associated with SET1, conserved in yeasts and in other eukaryotes up to humans. It is associated with the region of the Set1 protein that is N-terminal to the C-terminus, ie Set1-560-900. The function of Shg1 seems to be to slightly inhibit histone 3 lysine 4 (H3K4) di- and tri-methylation, and it is a pioneer protein. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for silencing of genes close to the telomeres of chromosomes.
Pfam PF20682: Hantavirus glycoprotein Gc, C-terminal (domain)
The medium (M) genome segment of hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins Gn and Gc (also known as G1 and G2, respectively) as a polyprotein precursor. Gn and Gc forms homotetramers at the surface of the virion, which attach the virion to host cell receptors including integrin beta3/ITGB3 and induce internalisation, predominantly through clathrin-dependent endocytosis. This protein has a typical class II fusion protein fold consisting of a central beta-sandwich domain (termed domain I) made of eight beta-strands arranged in two antiparallel beta-sheets; domain II which has an elongated shape with two subdomains (a central, opened beta-barrel proximal to domain I and a distal beta-sandwich 'tip') and the C-terminal domain III, represented in this entry, which has a Ig-like fold.
Pfam PF22227: DNA polymerase III gamma subunit-related, C-terminal domain (domain)
This entry represents the C-terminal domain of DNA polymerase III gamma subunit from Thermotoga maritima. This domain consists of a five alpha-helix bundle (PDB:2gno).
Pfam PF22243: DUF5018-related (domain)
This domain is found in the putative secreted protein BF4250 from Bacteroides fragilis ([swissprot:Q5L7M9]) and similar bacterial functionally uncharacterised proteins. This domain seems to be related to [pfam:PF16410].
Pfam PF17274: Family of unknown function (DUF5339) (family)
This is a family of unknown function that can be found mostly in Proteobacteria. Some of the family members are predicted to contain a coiled coil region.
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 PF09737: De-etiolated protein 1 Det1 (family)
This is the C-terminal conserved 400 residues of Det1 proteins of approximately 550 amino acids.  Det1 (de-etiolated-1) is an essential negative regulator of plant light responses, and it is a component of the Arabidopsis CDD complex containing DDB1 and COP10 ubiquitin E2 variant. Mammalian Det1 forms stable DDD-E2 complexes, consisting of DDB1, DDA1 (DET1, DDB1 Associated 1), and a member of the UBE2E group of canonical ubiquitin conjugating enzymes and modulates Cul4A function.
Pfam PF19444: MTP large subunit, lipid-binding domain (domain)
Microsomal triglyceride transfer protein (MTP) is essential in lipid metabolism, especially in the biogenesis of very low-density lipoproteins and chylomicrons via the transfer of neutral lipids and the assembly of apoB-containing lipoproteins. It is a heterodimer consisting of a large MTP alpha-subunit and a protein disulfide isomerase (PDI) beta-subunit. The MTP large subunit has and N-terminal beta-barrel domain, a central alpha-helical domain and a C-terminal 2-beta-sheet domain. This is the highly conserved MTP C-terminal domain involved in lipid-binding and transfer activity, with preference of neutral 3 chain-containing lipids. The beta-sheets are named A and C and form a sandwich comprising the lipid-binding site between them. Half of the A-sheet interacts with the beta-barrel. This domain also interacts with a' and b' domains of PDI.
Pfam PF12388: Dual-action HEIGH metallo-peptidase (family)
The catalytic triad for this family of proteases is HE-H-H, which in many members is in the sequence motif HEIGH.
Pfam PF21880: Domain of unknown function (DUF6916) (domain)
This is a domain of unknown function found in bacterial proteins. It is predicted to adopt a RIFT-type beta(6)-barrel topology with a greater similarity to FAD-binding domains.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24027: Family of unknown function (DUF7338) (family)
This entry represents a family of uncharacterised proteins from phage.  Structure prediction shows the proteins to be composed of an alpha helical N-terminal domain and a C-terminal domain composed of a 5 stranded beta meander.
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 PF09965: Uncharacterized protein conserved in bacteria (DUF2199) (family)
This domain, found in various hypothetical bacterial 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.