SII-SWORD/CoKE huggingface dataset:
Pfam PF01810: LysE type translocator (family)
This family consists of various hypothetical proteins and an l-lysine exporter LysE [swissprot:P94633] from Corynebacterium glutamicum which is proposed  to be the first of a novel family of translocators. LysE exports l-lysine from the cell into the surrounding medium and is predicted to span the membrane six times. The physiological function of the exporter is to excrete excess l-Lysine as a result of natural flux imbalances or peptide hydrolysis; and also after artificial deregulation of l-Lysine biosynthesis as used by the biotechnology. industry for the production of l-lysine.
Wikipedia: The resistance to homoserine/threonine (RhtB) family belongs to the lysine exporter (LysE) superfamily of transporters. Hundreds of sequenced proteins, derived from Gram-negative and Gram-positive bacteria as well as archaea, comprise the RhtB family, but few of these proteins are functionally characterized.
Pfam PF17709: Family of unknown function (DUF5554) (family)
This is a family of unknown function found in primates.
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 PF03905: Coronavirus non-structural protein NS4 (family)
This non-structural protein does not appear to be essential for viral growth in tissue culture and its physiological role is unknown.
Pfam PF07378: Flagellar protein FlbT (family)
This family consists of several FlbT proteins. FlbT is a post-transcriptional regulator of flagellin. FlbT is associated with the 5' untranslated region (UTR) of fljK (25 kDa flagellin) mRNA and that this association requires a predicted loop structure in the transcript. Mutations within this loop abolish FlbT association and result in increased mRNA stability. It is therefore thought that FlbT promotes the degradation of flagellin mRNA by associating with the 5' UTR.
Pfam PF14059: Domain of unknown function (DUF4251) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 164 and 196 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 PF16988: Vacuolar protein sorting 36 NZF-N zinc-finger domain (domain)
The vacuolar protein sorting 36 NZF-N zinc-finger domain interacts with the C-terminus of vacuolar protein sorting 28.
Pfam PF08798: CRISPR associated protein (domain)
This domain forms an anti-parallel beta strand structure with flanking alpha helical regions.
Wikipedia: CRISPR is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. Each sequence within an individual prokaryotic cell is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes and provide a form of heritable, acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
Pfam PF16030: Serine protease gd N-terminus (family)
This domain is found at the N-terminus of the serine protease gd (gastrulation defective) in insects.
Pfam PF15477: Small acidic protein family (family)
This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Pfam PF14117: Domain of unknown function (DUF4287) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 70 and 180 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 PF17515: Cypovirus polyhedrin (family)
This family is found in polyhedrin proteins of Cypoviruses. These viruses possess a single capsid layer with turrets and are commonly embedded in crystalline occlusion bodies called polyhedra, which are formed in the cell cytoplasm and mainly composed of a single virus-encoded protein, polyhedron. Cypoviruses have been classified into 21 distinct types. Within each type the amino acid sequence of polyhedrins are highly conserved, whilst between types there is little conservation. Structural analysis and comparison of the different polyhedrins reveals five variable regions: the N-terminal loop, connections between secondary structures (H2 and H3, beta-E and beta-F, beta-F and beta-G, beta-G and beta-H), and the C-terminal loop, which is designate V1-V5 respectively. V2 forms a cap at one end of the protein and is subdivided across two sections of the polypeptide, V2n and V2c. Differences in these regions give each polyhedrin its characteristic appearance. The base domain (residues 74-110) is a region that is neither required for proper folding of the protein, nor for crystal assembly, but fine-tunes the crystal, locking-down the structure, often in conjunction with NTPs. This region is also implicated in virion recognition and packaging.
Pfam PF22549: ARPP-2 (domain)
ARPP-2 (ARG and Rhodanese-Phosphatase-superfamily-associated Protein domain 2) shows a distinguishing group of absolutely conserved residues distinct from ARPP-1 ([pfam:PF20208]). ARPP-2 is typically found fused to a C-terminal HTH domain and adjacent to a Rot/TROVE domain fused to a vWA domain.
Pfam PF22305: BARF1 second Ig-like domain (domain)
This entry represents the second Immunoglobulin-like domain present in the BARF1 protein from Epstein-Barr virus.
Pfam PF11734: TilS substrate C-terminal domain (domain)
This domain is found in the tRNA(Ile) lysidine synthetase (TilS) protein.
Pfam PF02469: Fasciclin domain (domain)
This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria.
Wikipedia: In molecular biology, the fasciclin domain is an extracellular domain of about 140 amino acid residues. It has been suggested that the FAS1 domain represents an ancient cell adhesion domain common to plants and animals; related FAS1 domains are also found in bacteria.
Pfam PF22927: Integrator complex subunit 1, R3 domain (repeat)
Integrator (INT) complex is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. It binds the C-terminal domain (CTD) of RNA polymerase II (Pol II) and functions as an RNA endonuclease to cleave different classes of RNAs, regulating the transcription of both protein-coding genes and noncoding elements. Integrator also associates with protein phosphatase 2A (PP2A) core enzyme to form the INTAC complex which regulates transcription through dephosphorylation of Pol II CTD. This entry includes the Integrator complex subunit 1 (INTS1) which forms the backbone module of the complex (it consists of four modules: backbone, shoulder, phosphatase and endonuclease) through the association with INTS2 and INTS7 to form a rigid scaffold. The backbone and shoulder modules form a central cruciform scaffold. INTS1 contains four repetitive helix hairpin domains towards the C-terminal (R1-R4); this entry represents R3.
Pfam PF24595: Domain of unknown function (DUF7619) (domain)
This domain is found in uncharacterised proteins frequently in multiple copies. Some proteins containing this domain contain LPXTG cell wall anchor motif [pfam:PF00746] at the C-terminus. It is likely that some members of this entry contain an intramolecular isopeptide bond.
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 PF08057: Erythromycin resistance leader peptide (family)
This family consists of erythromycin resistance gene leader peptides.  These leader peptides are involved in the transcriptional attenuation control of the synthesis of the macrolide-lincosamide -streptogramin B resistance protein. It acts as a transcriptional attenuator, in contrast to other inducible erm genes. The mRNA leader sequence can fold in either of two mutually exclusive conformations, one of which is postulated to form in the absence of induction, and to contain two rho factor-independent terminators..
Pfam PF08063: PADR1 domain, zinc ribbon fold (domain)
This is the zinc ribbon fold of the PADR1 domain found in poly(ADP-ribose)-polymerases, referred to as the third zinc-binding domain of these proteins. The PADR1 domain is involved in protein-protein interactions that orchestrate PARP-1 activation and are critical to the DNA-dependent stimulation of PARP-1. PADR1 consists of an N-terminal helical region, the central zinc ribbon fold and a C-terminal tail.
Pfam PF09664: Protein of unknown function C-terminus (DUF2399) (domain)
Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Beta-proteobacteria). Just the C-terminal region is ioncluded here.
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 PF21336: Protein arginine N-methyltransferase 3, C2H2 zinc finger (domain)
This entry represents the  C2H2-type zinc finger from arginine N-methyltransferase 3 (ANM3). It catalyses both the monomethylation and asymmetric dimethylation of the guanidino nitrogens of arginine residues in target proteins.
Pfam PF02336: Capsid protein VP4 (domain)
Four different translation initiation sites of the densovirus capsid protein mRNA give rise to four viral  proteins, VP1 to VP4. This family represents VP4.
Pfam PF15584: Immunity protein 72 (family)
A predicted immunity protein with a mostly all-beta fold and GxxE, WxDxRY motifs and a glutamate residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox48 family. This domain is often fused to the Imm71 immunity domain.
Pfam PF18564: Glycoside hydrolase family 5 C-terminal domain (domain)
This is the C-terminal domain of endo-glycoceramidase II (EGC), a membrane-associated family 5 glycosidase [pfam:PF00150]. The C-terminal domain assumes a beta-sandwich fold, which resembles that of many carbohydrate-binding modules.
Pfam PF04533: Herpes virus U44 protein (family)
This is a family of proteins from dsDNA beta-herpesvirinae and gamma-herpesvirinae viruses. The function is not known, and the proteins are named variously as U44, BSRF1, UL71, and M71. The family BSRF1 has been merged into this.
Pfam PF22566: UBA-like domain (domain)
This entry represents a UBA-like domain.
Pfam PF21835: Capping complex subunit for YIEGIA (domain)
This entry contains a family of small protein of unknown function.  Proteins in this family are found in Firmicutes. These proteins adopt a beta sheet structure with four strands with an alpha helix packed on one face between the second and third strands. Using AlphaFold we can identify a likely hexameric ring complex. Additionally these proteins likely form a cap on a goblet like hexameric complex of [pfam:PF14045]. Analysis of genomic context suggests this larger complex is involved in spore germination and possibly phospholipid synthesis or regulation (pers.obs. Alex Bateman).
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 PF00685: Sulfotransferase domain (domain)
This entry includes a range of sulfotransferase proteins including flavonol 3-sulfotransferase, aryl sulfotransferases, alcohol sulfotransferases, estrogen sulfotransferases and phenol-sulphate phenol sulfotransferase. These enzymes are responsible for the transfer of sulphate groups to specific compounds .
Pfam PF22739: NACHT-associated inactive Restriction Endonuclease 2 (domain)
This entry represents a predicted sensor domain in bacterial NACHT conflict systems. It is likely to bind a ligand which could contribute to activation of enzymatic domains additionally fused to the N-terminus of the NACHT module.
Pfam PF06246: Isy1-like splicing family (family)
Isy1 protein is important in the optimisation of splicing.
Pfam PF18611: IL-3 receptor alpha chain N-terminal domain (domain)
Interleukin-3 (IL-3) is an activated T cell product that bridges innate and adaptive immunity and contributes to several immunopathologies. Structure of IL-3 receptor alpha chain (IL3Ra) in complex with the anti-leukemia antibody CSL362 reveals that the N-terminal domain (NTD), a domain also present in the granulocyte-macrophage colony-stimulating factor (GM-CSF), contains the CSL362 binding epitope. Furthermore, NTD of IL3Ra adopts a typical fibronectin type III (FnIII) fold.
Pfam PF20737: Glycoside hydrolase family 127 C-terminal domain (domain)
This entry represents the second beta sandwich domain found in enzymes belonging to the glycosyl hydrolase 127 family. The beta-sandwich domain is somewhat similar to the N-terminal domain of ErbB4 kinase and is involved in formation of a dimer, which is created by a crystallographic 2-fold axis.
Pfam PF18690: Family of unknown function (DUF5639) (domain)
This is a domain of unknown function which is mainly found in Deinococcus-Thermus. Some family members can be found in the C-terminal region of [pfam:PF01565].
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 PF03951: Glutamine synthetase, beta-Grasp domain (domain)
Glutamine synthetase (6.3.1.2) (GS)  plays an essential role in the metabolism of nitrogen by catalysing the condensation of glutamate and ammonia to form glutamine. This entry represents the glutamine synthetase N-terminal domain, which adopts a Î²-grasp fold  and contributes to the substrate binding pocket of the enzyme .
Wikipedia: Glutamine synthetase (GS) is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine:
Pfam PF05987: Bacterial protein of unknown function (DUF898) (repeat)
This entry consists of several bacterial proteins of unknown function. Some of the family members are described as inner membrane proteins. These proteins have a beta/alpha/alpha/beta/alpha hairpin structure that is repeated.
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 PF15700: Domain of unknown function (DUF4667) (family)
This family of proteins is found in fungi. Proteins in this family are typically between 172 and 313 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 PF22186: Hypothetical protein HI1480 (domain)
This entry represents the HI1480 protein from Haemophilus influenzae an apparent ORFan protein. The protein HI1480 from Haemophilus influenzae has been structurally characterized. It exhibits a unique amino acid sequence, lacking homology with known proteins. HI1480 adopts a novel alpha+beta fold and forms dimers of tightly associated dimers. The dimerization is facilitated by intermolecular interactions mediated by an antiparallel beta-barrel involving both monomers, while tetramer formation is mediated by helical regions of the dimers. Notably, the helical region contains a four-helix bundle reminiscent of anticodon binding domains found in class I tRNA synthetases, suggesting a potential active centre or catalytic site. Gel mobility shift assays demonstrate HI1480's ability to bind both DNA and RNA molecules, with a preference for double-stranded DNA over single-stranded DNA and higher affinity for longer DNA fragments.
Pfam PF05127: Helicase (domain)
This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble base to the active centre of the GCN5-related N-acetyltransferase (GNAT) domain. It is found in the bacterial exodeoxyribonuclease V alpha chain (RecD), which has 5'-3' helicase activity. It is structurally similar to the motor domain 1A in other SF1 helicases.
Pfam PF05450: Nicastrin large lobe (domain)
Nicastrin and presenilin are two major components of the gamma-secretase complex, which executes the intramembrane proteolysis of type I integral membrane proteins such as the amyloid precursor protein (APP) and Notch.  Nicastrin is synthesised in fibroblasts and neurons as an endoglycosidase-H-sensitive glycosylated precursor protein (immature nicastrin) and is then modified by complex glycosylation in the Golgi apparatus and by sialylation in the trans-Golgi network (mature nicastrin). A region featured in this family has a fold similar to human transferrin receptor (TfR, [swissprot:P02786]) and a bacterial aminopeptidase ([swissprot:P80561]). It is implicated in the pathogenesis of Alzheimer's disease.
Wikipedia: Gamma secretase is a multi-subunit protease complex, an integral membrane protein, that cleaves single-pass transmembrane proteins at residues within the transmembrane domain. Proteases of this type are known as intramembrane proteases. The most well-known substrate of gamma secretase is amyloid precursor protein, a large integral membrane protein that, when cleaved by both gamma and beta secretase, produces a short 37-43 amino acid peptide called amyloid beta whose abnormally folded fibrillar form is the primary component of amyloid plaques found in the brains of Alzheimer's disease patients. Gamma secretase is also critical in the related processing of several other type I integral membrane proteins, such as Notch, ErbB4, E-cadherin, N-cadherin, ephrin-B2, or CD44.
Pfam PF24441: Family of unknown function (DUF7560) (family)
This entry represents a small family of uncharacterised proteins found in archaea. They contain two pairs of conserved cysteines that are likely involved in metal coordination. It is predicted they may structurally resemble Zinc-beta ribbon 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 PF16169: Domain of unknown function (DUF4872) (family)
Members of this family are often found in the gene neighbourhood, or fused to, non-ribosomal peptide synthetases.
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 PF16092: Cilia- and flagella-associated protein 61, N-terminal domain (domain)
This entry represents the N-terminal domain of proteins described as cilia- and flagella-associated protein. Proteins containing this domain includes FAP61 from Chlamydomonas reinhardtii. FAP61 is part of the calmodulin and spoke-associated complex (CSC) required for wild-type motility and for the stable assembly of a subset of radial spokes in motile cilia.
Pfam PF17876: Cold shock domain (domain)
Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding.
Pfam PF20121: Family of unknown function (DUF6511) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 87 and 141 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.