SII-SWORD/CoKE huggingface dataset:
Pfam PF06724: Domain of Unknown Function (DUF1206) (family)
This region consists of two a pair of transmembrane helices and occurs three times in each of the family member 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 PF11216: Protein of unknown function (DUF3012) (family)
This family of proteins with unknown function is restricted to Gammaproteobacteria.
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 PF10464: Peptidase U40 (family)
This family contains P5 murein endopeptidase from bacteriophage phi-6.  P5 murein endopeptidase has lytic activity against several gram-negative bacteria.  It is thought that the enzyme cleaves the cell wall peptide bridge formed by meso-2,6-diaminopimelic acid and D-Ala
Pfam PF24624: Phage integrase, N-terminal domain (domain)
This domain is found at the N-terminal end of phage integrases, including the member from Escherichia phage P2. This protein is necessary for integration of the phage into the host genome by site-specific recombination.
Pfam PF22037: PSD13 N-terminal repeats (repeat)
This entry represents the N-terminal helical repeats of PSD13 from human and its orthologues from yeast, RPN9. These proteins are a component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This domain mediates interaction with the ubiquitin receptor Rpn10 (also known as PSMD4 in human).
Pfam PF07663: Sorbitol phosphotransferase enzyme II C-terminus (family)
The Gut family consists only of glucitol-specific permeases, but these occur both in Gram-negative and Gram-positive bacteria. Escherichia coli contains IIA protein, IIC protein and IIBC protein.

This entry represents the C-terminal conserved region of the IIBC component.
Pfam PF09068: EF hand (domain)
Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain ([pfam:PF00397]), enhancing dystroglycan binding.
Pfam PF02018: Carbohydrate binding domain (domain)
This family includes diverse carbohydrate binding domains.
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 PF22093: Cell wall binding protein Cwp8 domain 2 (domain)
Cwp8 is a member of the C. difficile cell wall protein (CWP) family. It consists of several domains. This entry represents the domain 2 that is a part of the N-terminal elongated part of the molecule. This domain is composed of a three-stranded antiparallel beta-sheet, an alpha-helix packed on it and a short beta-hairpin located at the edge of the sheet.
Pfam PF12832: MFS_1 like family (family)
This family contains proteins related to the MFS superfamily.
Pfam PF03546: Treacher Collins syndrome protein Treacle (family)
Treacher Collins Syndrome (TCS) is an autosomal dominant disorder of craniofacial development, the features of which include conductive hearing loss and cleft palate ; it is the most common of the human mandibulo-facial dysostosis disorders . The TCS locus has been mapped to human chromosome 5q31.3-32 and the mutated gene identified (TCOF1) . To date, 35 mutations have been reported in TCOF1, all but one of which result in the introduction of a premature-termination codon into the predicted protein, Treacle. The observed mutational spectrum supports the hypothesis that TCS results from haploinsufficiency.

Treacle is a low complexity protein of 1,411 amino acids whose predicted protein structure contains a set of highly polar repeated motifs . These motifs are common to nucleolar trafficking proteins in other species and are predicted to be phosphorylated by casein kinase. In concert with this observation, the full-length TCOF1 protein sequence also contains putative nuclear and nucleolar localisation signals . Throughout the open reading frame are found mutations in TCS families and several polymorphisms. It has thus been suggested that TCS results from defects in a nucleolar trafficking protein that is critically required during human craniofacial development.
Pfam PF22156: Thiaminase I-like, N-terminal domain (domain)
This domain is found at the the N-terminal end of Thiaminase I from the amoeba Naegleria gruberi ([swissprot:D2V4Z5]) and similar eukaryotic sequences. This enzyme catalyse the elimination of the thiazole ring moiety from thiamin through substitution of the methylene group. This domain has thiaminase I activity by itself. It consists of a seven-stranded beta-sheet surrounded by eight alpha-helices.
Pfam PF17270: Family of unknown function (DUF5336) (family)
This Actinobacterial family of proteins has no known function. Most of the family members are predicted to have have 4 trans-membrane regions.
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 PF03100: CcmE domain (domain)
CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.
Pfam PF11907: Domain of unknown function (DUF3427) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 243 to 275 amino acids in length. This domain is found associated with [pfam:PF04851], [pfam:PF00271].
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 PF05009: Epstein-Barr virus nuclear antigen 3 (EBNA-3) (family)
This family contains EBNA-3A, -3B, and -3C which are latent infection nuclear proteins important for Epstein-Barr virus (EBV)-induced B-cell immortalisation and the immune response to EBV infection.
Pfam PF10561: C2orf69 (family)
This family includes C2orf69 from human, previously known as UPF0565, which is an important regulator of human mitochondrial function and may also influence other metabolic pathways.
Pfam PF10282: Lactonase, 7-bladed beta-propeller (repeat)
This entry contains bacterial 6-phosphogluconolactonases (6PGL)YbhE-type ([ec:3.1.1.31]) which hydrolyse 6-phosphogluconolactone to 6-phosphogluconate. The entry also contains the fungal muconate lactonising enzyme carboxy-cis,cis-muconate cyclase ([ec:5.5.1.5]) and muconate cycloisomerase ([ec:5.5.1.1]), which convert cis,cis-muconates to muconolactones and vice versa as part of the microbial beta-ketoadipate pathway.                          Structures of proteins in this family have revealed a 7-bladed beta-propeller fold.
Wikipedia: Lactonase (EC 3.1.1.81, acyl-homoserine lactonase; systematic name N-acyl-L-homoserine-lactone lactonohydrolase) is a metalloenzyme, produced by certain species of bacteria, which targets and inactivates acylated homoserine lactones (AHLs). It catalyzes the reactionan N-acyl-L-homoserine lactone + H2O  an N-acyl-L-homoserine
Pfam PF02980: FokI, recognition domain, subdomain 2 (domain)
Type IIS restriction endonuclease FokI is a member of an unusual class of bipartite restriction enzymes that recognises the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand. FokI contains amino- and carboxy-terminal domains corresponding to the DNA- recognition and cleavage functions, respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP. This entry represents the subdomain D2 of FokI. D1 and D2 make almost all of the base-specific contacts with the DNA.
Pfam PF16130: Domain of unknown function (DUF4842) (domain)
This domain is found on the C-terminal of large number of uncharacterized proteins with broad phylogenetic distribution, which includes human gut Bacteroides, g-proteobacteria (Vibrio and Shewanella) and also spirochetes from Leptospira genus. Solved structure of Bacteroides ovatus protein BACOVA_00967 shows a large beta barrel with an immunoglobulin-like fold and significant structural similarity to collagen-binding domain of adhesin from S. aureus (1amx), but with several additional long loops and secondary structure elements.  Function of this domain is unknown.
Pfam PF15686: Lysine-rich CEACAM1 co-isolated protein family (family)
LYRIC is a family of proteins found in eukaryotes. It is a type-1b membrane protein with a single transmembrane domain and localises to the endoplasmic reticulum and the nuclear envelope. It is also found in the nucleolus, suggesting functional relationships between these two cellular compartments. It is found to be colocalised with tight junction proteins ZO-1 and occludin in polarised epithelial cells, suggesting that LYRIC is part of the tight junction complex. LYRIC has been shown to promote tumour cell migration and invasion by activating the transcription factor NF-kappaB.
Pfam PF18619: GPCR-Autoproteolysis-INducing (GAIN) subdomain A (domain)
GPR56 is a a cell-surface G protein-coupled receptor (GPCR) which belongs to the adhesion G protein-coupled receptor (aGPCR) family, a large family of chimeric proteins that have both adhesion and signaling functions and play critical roles in diverse neurobiological processes including brain development, synaptogenesis, and myelination. This entry represents GPCR-Autoproteolysis-INducing (GAIN) subdomain A, including PLL-GAIN linker (F161-D175) region.
Pfam PF02258: Shiga-like toxin beta subunit (domain)
This family represents the B subunit of shiga-like toxin (SLT or verotoxin) produced by some strains of E.coli associated with hemorrhagic colitis and hemolytic uremic syndrome. SLT's are composed of one enzymatic A subunit and five cell binding B subunits.
Wikipedia: Shiga toxins are a family of related toxins with two major groups, Stx1 and Stx2, expressed by genes considered to be part of the genome of lambdoid prophages. The toxins are named after Kiyoshi Shiga, who first described the bacterial origin of dysentery caused by Shigella dysenteriae. Shiga-like toxin (SLT) is a historical term for similar or identical toxins produced by Escherichia coli. The most common sources for Shiga toxin are the bacteria S. dysenteriae and some serotypes of Escherichia coli, which include serotypes O157:H7, and O104:H4.
Pfam PF13740: ACT domain (domain)
ACT domains bind to amino acids and regulate associated enzyme domains.
Pfam PF12462: DNA helicase IV / RNA helicase N terminal (family)
This domain family is found in bacteria, and is approximately 170 amino acids in length. This family is found in bacterial DNA helicase IV, at the N-terminus of [pfam:PF00580].
Pfam PF05722: Ustilago B locus mating-type protein (family)
This family consists of several Ustilago mating-type proteins. The b locus of the phytopathogenic fungus Ustilago maydis encodes a multiallelic recognition function that controls the ability of the fungus to form a dikaryon and complete the sexual stage of the life cycle. The b locus has at least 25 alleles and any combination of two different alleles, brought together by mating between haploid cells, allows the fungus to cause disease and undergo sexual development within the plant.
Pfam PF17567: Family of unknown function (DUF5473) (family)
This is a family of unknown function found in Human adenovirus.
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 PF21200: Alpha-L-iduronidase C-terminal domain (domain)
This entry represents the C-terminal Ig-fold domain of Alpha-L-iduronidase enzyme.
Pfam PF09535: Protein of unknown function (Gmx_para_CXXCG) (family)
This entry consists of at least 10 paralogous proteins from Myxococcus xanthus and that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment.
Pfam PF00394: Multicopper oxidase (domain)
Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.
Wikipedia: In molecular biology, multicopper oxidases are enzymes which oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. There are three spectroscopically different copper centres found in multicopper oxidases: type 1, type 2 and type 3. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology with the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel.
Pfam PF00305: Lipoxygenase (domain)
Lipoxygenases (1.13.11.-) are a class of iron-containing dioxygenases which catalyses the hydroperoxidation of lipids, containing a cis,cis-1,4-pentadiene structure. They are common in plants where they may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. In mammals a number of lipoxygenases isozymes are involved in the metabolism of prostaglandins and leukotrienes . Sequence data is available for the following lipoxygenases:


 * Plant lipoxygenases (1.13.11.12). Plants express a variety of cytosolic isozymes as well as what seems to be a chloroplast isozyme .
 * Mammalian arachidonate 5-lipoxygenase (1.13.11.34).
 * Mammalian arachidonate 12-lipoxygenase (1.13.11.31).
 * Mammalian arachidonate 15-lipoxygenase B (also known as erythroid cell-specific 15-lipoxygenase; 1.13.11.33).


The iron atom in lipoxygenases is bound by four ligands, three of which are histidine residues . Six histidines are conserved in all lipoxygenase sequences, five of them are found clustered in a stretch of 40 amino acids. This region contains two of the three iron-ligands; the other histidines have been shown  to be important for the activity of lipoxygenases.
This entry represents the C-terminal region of these proteins.
Wikipedia: Lipoxygenases (LOX) are a family of (non-heme) iron-containing enzymes, more specifically oxidative enzymes, most of which catalyze the dioxygenation of polyunsaturated fatty acids in lipids containing a cis,cis-1,4-pentadiene into cell signaling agents that serve diverse roles as autocrine signals that regulate the function of their parent cells, paracrine signals that regulate the function of nearby cells, and endocrine signals that regulate the function of distant cells.
Pfam PF18739: Apea-like HEPN (domain)
Apea-like HEPN nuclease. In epsilonproteobacteria embedded in R-M operons.
Pfam PF03433: EspA-like secreted protein (family)
EspA is the prototypical member of this family. EspA, together with EspB, EspD and Tir are exported by a type III secretion system.  These proteins are essential for attaching and effacing lesion formation. EspA is a structural protein and a major component of a large, transiently expressed, filamentous surface organelle which forms a direct link between the bacterium and the host cell.
Pfam PF20986: Domain of unknown function (DUF6849) (domain)
This domain is found in uncharacterised archaeal proteins. It is found C-terminal to [pfam:PF02933], in CDC48 proteins. Its 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 PF00820: Borrelia lipoprotein (family)
This family of lipoproteins is found in Borrelia spirochetes. The function of these proteins is uncertain.
Pfam PF03957: Jun-like transcription factor (family)
The c-Jun NH(2)-terminal kinase (JNK) is a member of an evolutionarily conserved sub-family of mitogen-activated protein (MAP) kinases .
Pfam PF23913: Family of unknown function (DUF7255) (family)
This entry represents uncharacterised bacterial proteins that were predicted to possess defence functions. They contain highly conserved aspartate and histidine residues that may have functional role.
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 PF00013: KH domain (domain)
KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.
Wikipedia: The K Homology (KH) domain is a protein domain that was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. An evolutionarily conserved sequence of around 70 amino acids, the KH domain is present in a wide variety of nucleic acid-binding proteins. The KH domain binds RNA, and can function in RNA recognition. It is found in multiple copies in several proteins, where they can function cooperatively or independently. For example, in the AU-rich element RNA-binding protein KSRP, which has 4 KH domains, KH domains 3 and 4 behave as independent binding modules to interact with different regions of the AU-rich RNA targets. The solution structure of the first KH domain of FMR1 and of the C-terminal KH domain of hnRNP K determined by nuclear magnetic resonance (NMR) revealed a beta-alpha-alpha-beta-beta-alpha structure. Autoantibodies to NOVA1, a KH domain protein, cause paraneoplastic opsoclonus ataxia. The KH domain is found at the N-terminus of the ribosomal protein S3. This domain is unusual in that it has a different fold compared to the normal KH domain.
Pfam PF11739: Intermembrane phospholipid transport protein YdbH (repeat)
This entry represents the YdbH protein from E.coli and related proteins. YdbH is one of the six AsmA-like paralogues in E.coli (YhdP, TamB, YdbH, AsmA, YicH, and YhjG) that have a variable size but share similar predicted structure. In-depth functional characterisation of AsmA-like proteins revealed that YdbH together with the other largest paralogs (YhdP and TamB) are redundant in performing a function that is essential for growth and OM lipid homeostasis in E. coli. Current model based on these analyses suggests that TamA-TamB, YhdP, and YdbH form bridge-like structures that mediate the diffusional flow of phospholipids between the IM and OM.
Pfam PF08222: CodY helix-turn-helix domain (domain)
This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF13786: Domain of unknown function (DUF4179) (family)
This presumed domain is functionally uncharacterised.
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 PF09984: Single cache domain 4 (domain)
Members of this family of domains are found in various BarA-like signal transduction histidine kinases, which are involved in the regulation of carbon metabolism via the csrA/csrB regulatory system. The role of this domain has not, as yet, been established.
Pfam PF11965: Domain of unknown function (DUF3479) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is about 160 amino acids in length. This domain is found associated with [pfam:PF02514].
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.