SII-SWORD/CoKE huggingface dataset:
Pfam PF23715: Family of unknown function (DUF7157) (domain)
This domain is found at the C-terminal end of a group of uncharacterised sequences from actinobacteria.
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 PF07258: COMM domain (domain)
The leucine-rich, 70-85 amino acid long COMM domain is predicted to form a beta-sheet and an extreme C-terminal alpha- helix. The COMM domain containing proteins are about 200 residues in length and passed the C-terminal COMM domain.
Pfam PF10797: Protein of unknown function (family)
This family is conserved in Firmicutes and Proteobacteria. The function is not known but several members are annotated as being homologues of E coli YhfT, a protein thought to be involved in fatty acid oxidation.
Pfam PF01995: NrpR regulatory domains NRD1 and 2 (domain)
This entry comprises two domains found in the nitrogen regulatory protein NrpR that bind DNA and repress transcription of nitrogen assimilation genes. The two NrpR regulatory domains (NRD1 and NRD2) that sense and bind 2-oxoglutarate (2OG) are both structurally and functionally homologous and share a high degree of sequence conservation. Mutational analysis of NrpR from Methanococcus maripaludis (MmNrpR) indicated that the two most critical residues for 2OG binding are Cys389 and His435 (Cys395 and His441, respectively in thermophilic archaeon Methanocaldococcus jannaschii (MjNrpR)). Both the Cys395 and His441 are conserved among NrpR proteins from diverse species.
Pfam PF07603: Lcl C-terminal domain (domain)
This domain is found C-terminal in the Legionella collagen-like protein (Lcl) and related proteins mainly from bacteria. Lcl is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans (GAGs) on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. This domain has a structural similarity to C-type lectins and is involved in glycan recognition.
Pfam PF15292: Treslin, M domain (domain)
This entry represents the M domain of treslin, a checkpoint regulator which plays a role in DNA replication preinitiation complex formation. Treslin is the metazoan counterpart of Sld3 from yeast, which are the hub proteins mediating protein associations critical for the helicase formation. Treslin, as Sld3, interacts with TopBP1 in a Cdk2-dependent manner, which then collaborate in the Cdk2-mediated loading of Cdc45 onto replication origins. Treslin and Sld3 differ in their molecular sizes and amino acid sequences, however, they share a conserved Sld3/Treslin domain (STD). According to their similarities, it has been suggested that helicase activation in mammals has diverged in complexity during evolution from that in yeasts and may involve additional partners that interact with TopBP1. This domain adopts a Ku70-like beta-barrel fold which engage in homotypic interactions with MTBP, which is also essential for replication in human cells.
Pfam PF10403: Rad4 beta-hairpin domain 1 (domain)
This short domain is found in the Rad4 protein. This domain binds to DNA.
Pfam PF20512: Phosphomannose isomerase type I, helical insertion domain (domain)
This entry represents the alpha-helical insertion domain of Phosphomannose isomerase type I enzymes (EC 5.3.1.8), in which the helices are packed closely, connected by short turns and loops. This domain packs closely against the catalytic domain, interrupting it.
Pfam PF03125: Sre G protein-coupled chemoreceptor (family)
Caenorhabditis elegans Sre proteins are candidate chemosensory receptors. There are four main recognised groups of such receptors: Odr-10, Sra, Sro, and Srg. Sre (this family), Sra [pfam:PF02117] and Srb [pfam:PF02175] comprise the Sra group. All of the above receptors are thought to be G protein-coupled seven transmembrane domain proteins. The existence of several different chemosensory receptors underlies the fact that in spite of having only 20-30 chemosensory neurones, C. elegans detects hundreds of different chemicals, with the ability to discern individual chemicals among combinations.
Pfam PF15207: TMEM240 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 54 and 175 amino acids in length. The function of this family is unknown.
Pfam PF14746: WASH complex subunit 7, C-terminal (family)
This family is the conserved C-terminal region of proteins that form subunit 7 of the WASH complex. In species such as Drosophila this protein is the only component of the 'complex'. This complex is a nucleation promoting factor necessary for the activation of Arp2/3 that nucleates and organises actin filaments by associating with a pre-existing filament to induce the assembly of a branching filament.  WASH thus effectively nucleates actin on endosomes. The C-terminus is predicted to include a transmembrane region.
Pfam PF09954: Uncharacterized protein conserved in bacteria (DUF2188) (domain)
This domain represents a ribosome-associating protein predicted to mediate translation inhibition alongside repair of DNA damage or restriction in conflict contexts. A subset of this family contains a conserved histidine residue, raising the possibility that it directly acts as a RNase or in RNA end-processing.
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 PF24387: Archaeo-eukaryotic primase 1D-like (family)
This entry represents a nucleotidyltransferase of the archaeo-eukaryotic primase superfamily predicted to produce an oligo/cyclic nucleotide signal that activates the associated effectors in the associated prokaryotic antiviral immunity system. These feature a single aspartate in the DXD active site.
Pfam PF16852: Herpes viral adaptor-to-host cellular mRNA binding domain (conserved_site)
HHV-1_VABD is the short region of the Herpes simplex 1 virus' specific signature adaptor protein that binds to the cellular mRNA export factor such as mouse REF.
Pfam PF20774: Immune inhibitor A-like metallopeptidase, VEG domain (domain)
Immune inhibitor A(InhA)-type metallopeptidases are potential virulence factors secreted by members of the Bacillus cereus group (BCG) and belong to the thuringilysin family within the metzincin clan of metallopeptidases, M6 in the MEROPS database. The structure of these proteins consists of four domains: a pro-peptide, a catalytic domain, a domain reminiscent of viral envelope glycoproteins (VEG), and a MAM domain grafted into the latter. This entry represents the VEG domain found at the C-terminal of InhA and PrtV peptidases (a slightly more distant thuringilysin family members). It consists of a central parallel beta-sandwich comprised by an upper five-stranded mixed sheet and a lower four-stranded antiparallel sheet.
Pfam PF08394: Archaeal TRASH domain (domain)
This region is found in the C-terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module.
Pfam PF20442: BREX system Lon protease-like protein BrxL N-terminal (domain)
This entry represents the N-terminal domain of BREX system Lon protease-like protein BrxL from Bacillus cereus and similar proteins. BrxL is part of a type 1 BREX system, which contains a C-terminal Lon-like protease domain ([pfam:PF05362]). BREX systems (bacteriophage exclusion) provide immunity against bacteriophage, a system that allows phage adsorption but prevents phage DNA replication, without degradation of the phage DNA.
Pfam PF05317: Thermopsin (family)
This family consists of several thermopsin proteins from archaebacteria. Thermopsin is a thermostable acid protease which is capable of hydrolysing the following bonds: Leu-Val, Leu-Tyr, Phe-Phe, Phe-Tyr, and Tyr-Thr. The specificity of thermopsin is therefore similar to that of pepsin, that is, it prefers large hydrophobic residues at both sides of the scissile bond.
Pfam PF07544: RNA polymerase II transcription mediator complex subunit 9 (family)
This family of Med9 proteins is conserved in yeasts. It forms part of the middle region of Mediator. Med9 has two functional domains. The species-specific amino-terminal half (aa 1-63) plays a regulatory role in transcriptional regulation, whereas this well-conserved carboxy-terminal half (aa 64-149) has a more fundamental function involved in direct binding to the amino-terminal portions of Med4 and Med7 and the assembly of Med9 into the Middle module. Also, some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter.
Wikipedia: Mediator is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes. It was discovered in 1990 in the lab of Roger D. Kornberg, recipient of the 2006 Nobel Prize in Chemistry. Mediator complexes interact with transcription factors and RNA polymerase II. The main function of mediator complexes is to transmit signals from the transcription factors to the polymerase.
Pfam PF20711: Family of unknown function (DUF6825) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in plants and cyanobacteria. Proteins in this family are typically between 108 and 202 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 PF13606: Ankyrin repeat (repeat)
Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities.
Wikipedia: The ankyrin repeat is a 33-residue motif in proteins consisting of two alpha helices separated by loops, first discovered in signaling proteins in yeast Cdc10 and Drosophila Notch. Domains consisting of ankyrin tandem repeats mediate protein–protein interactions and are among the most common structural motifs in known proteins. They appear in bacterial, archaeal, and eukaryotic proteins, but are far more common in eukaryotes. Ankyrin repeat proteins, though absent in most viruses, are common among poxviruses. Most proteins that contain the motif have four to six repeats, although its namesake ankyrin contains 24, and the largest known number of repeats is 34, predicted in a protein expressed by Giardia lamblia.
Pfam PF09498: Protein of unknown function (DUF2388) (family)
This family consists of small hypothetical proteins, about 100 amino acids in length. The family includes five members (three in tandem) in Pseudomonas aeruginosa PAO1 and in Pseudomonas putida (strain KT2440), four in Pseudomonas syringae DC3000, and single members in several other Proteobacteria. The function is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF07296: TraP protein (family)
This family consists of several bacterial conjugative transfer TraP proteins from Escherichia coli and Salmonella typhimurium. TraP appears to play a minor role in conjugation and may interact with TraB, which varies in sequence along with TraP, in order to stabilise the proposed transmembrane complex formed by the tra operon products.
Pfam PF24812: TTC3-like, winged helix turn helix domain (domain)
This domain is found in human E3 ubiquitin-protein ligase TTC3, which catalyses the formation of 'Lys-48'-polyubiquitin chains. This domain is predicted to adopt a winged helix turn helix (wHTH) fold.
Pfam PF11511: Intrinsic membrane protein PufX (family)
PufX organises RC-LH1, the photosynthesis reaction centre-light harvesting complex 1 core complex of Rhodobacter sphaeroides. It also facilitates the exchange of quinol for quinone between the reaction centre and cytochrome bc(1) complexes. In organic solvent, PufX contains two hydrophobic helices which are flanked by unstructured regions and connected by a helical bend.
Pfam PF01566: Natural resistance-associated macrophage protein-like (family)
The natural resistance-associated macrophage protein (NRAMP) family consists of animal NRAMP1, NRAMP2, yeast proteins Smf1 and Smf2 and bacterial homologues. The NRAMP family includes functional related proteins defined by a conserved hydrophobic core of ten transmembrane domains. These membrane proteins are divalent cation transporters which have a high degree of sequence conservation, particularly, the residues contributing to ion interaction are stongly conserved (DPNG and MPH motifs). NRAMP1 is an integral membrane protein expressed exclusively in cells of the immune system and is recruited to the membrane of a phagosome upon phagocytosis, where it plays an essential role in host defense against pathogens. Mutations in NRAMP1 may genetically predispose an individual to susceptibility to diseases including leprosy and tuberculosis. NRAMP2 (DMT1) is a multiple divalent cation transporter broadly expressed in the duodenum, kidney, brain, testis and placenta. It transports Fe2+, Mn2+ and Cd+2, whereas Zn2+ is a poor substrate. Ca+2 and Mg+2 are not transported, which is important because their high concentrations in duodenum, where NRAMP2 is expressed at high levels, would interfere with the absorption of Fe2+. It is the major transferrin-independent iron uptake system in mammals. NRAMP related members of this family have substrate specificity for Mn2+ and/or Mg2+, such as the yeast proteins Smf1 and Smf2 and a group of bacterial transporters (NrmT, for Nramp-related magnesium transporter).
Wikipedia: Natural resistance-associated macrophage proteins (Nramps), also known as metal ion (Mn2+-iron) transporters (TC# 2.A.55), are a family of metal transport proteins found throughout all domains of life. Taking on an eleven-helix LeuT fold, the Nramp family is a member of the large APC Superfamily of secondary carriers. They transport a variety of transition metals such as manganese, cadmium, and manganese using an alternating access mechanism characteristic of secondary transporters.
Pfam PF21671: Protein CPL1-like (domain)
This domain is found in CPL1 from Cryptococcus neoformans and similar fungal proteins. CPL1 is a virulence factor which promotes fungal virulence by enhancing type 2 inflammation in the mouse host.
Pfam PF06940: Domain of unknown function (DUF1287) (domain)
This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. This family is related to [pfam:PF00877].
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 PF13281: MAP3K TRAFs-binding domain (repeat)
This entry corresponds to the TNF receptor-associated factors (TRAFs)-binding domain found at the N-terminus of some MAP3Ks, like Apoptosis signal-regulating kinases (ASK). This domain is flanked by a thioredoxin-binding domain and a PH-like domain. It includes seven tetratricopeptide repeats (TPRs) and, together with the PH-like domain, constitutes the central regulatory domain of ASK1.
Pfam PF16994: Glycosyl-transferase family 4 (family)
This family belongs to the Pfam clan GT-B that contains diverse glycosyltransferases that possess a Rossmann-like fold.
Pfam PF13304: AAA domain, putative AbiEii toxin, Type IV TA system (domain)
Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF19563: Family of unknown function (DUF6085) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001905) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a  protein from the violapyrone B biosynthetic gene cluster from  Streptomyces somaliensis and appears to be predominantly found in Actinobacteria and Caudovirale bacteriophages.
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 PF10268: Predicted transmembrane protein 161AB (family)
Transmemb_161AB is a family of conserved proteins found from worms to humans. Members are putative transmembrane proteins but otherwise the function is not known.
Pfam PF17099: Tryptophan transporter TrpP (family)
TrpP is a bacterial transmembrane protein that is probably involved in tryptophan uptake. Its expression is regulated by tryptophan-activated RNA-binding regulatory protein (TRAP).
Pfam PF12881: NUT protein (family)
This family includes the NUT protein. The gene encoding for NUT protein (Nuclear Testis protein) is found fused to BRD3 or BRD4 genes, in some aggressive types of carcinoma, due to chromosomal translocations. Proteins of the BRD family contain two bromodomains that bind transcriptionally active chromatin through associations with acetylated histones H3 and H4. Such proteins are crucial for the regulation of cell cycle progression. On the other hand, little is known about NUT protein. NUT is known to have a Nuclear Export Sequence (NES) as well as a Nuclear Localisation Signal (NLS), both located towards the C-terminal end of the protein. A fused NUT-GFP protein showed either cytoplasmic or nuclear localisation, suggesting that it is subject to nuclear/cytoplasmic shuttling. Consistent with this possibility, treatment with leptomycin B an inhibitor of CRM1-dependent nuclear export resulted in re-distribution of NUT-GFP to the nucleus. Inspection of NUT revealed a C-terminal sequence similar to known nuclear export sequences (NES) which are often regulated by phosphorylation. This family carries some natively unstructured sequence.
Pfam PF22893: Ubiquitin-like domain (domain)
This domain has a ubiquitin like structure. It is found in a range of fungal proteins.
Pfam PF21821: Dit-like phage tail protein (domain)
This entry represents a large family of proteins that have a RIFT-like barrel structure which is related to the Dit phage protein from SPP1.
Pfam PF09842: Predicted membrane protein (DUF2069) (family)
This domain, found in various prokaryotes, 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.
Pfam PF09517: Eco29kI restriction endonuclease (family)
This family includes the Eco29kI (recognises and cleaves CCGC^GG ) restriction endonuclease.
Pfam PF15341: Ribosome biogenesis protein SLX9 (family)
SLX9 is present in pre-ribosomes from an early stage and is implicated in the processing events that remove the ITS1 spacer sequences. In eukaryotes, biogenesis of ribosomes starts in the nucleolus with transcription by RNA polymerase I of a large precursor RNA molecule, called 35S pre-rRNA in yeast, in which the 18S, 5.8S, and 25S mature rRNAs reside, while RNA polymerase III transcribes a 3'-extended pre-5S rRNA. The 35S precursor also contains external transcribed spacer elements (5' and 3'-ETS) at either end as well as internal transcribed spacers (ITS1 and ITS2) that separate the mature sequences.
Pfam PF10674: Ycf54 protein (family)
Ycf54 is found encoded in the chloroplast genomes of algae, also found in plants and cyanobacteria. It is a component of the MgPME-cyclase complex and plays two roles: first, it plays a critical role in the assembly/stability of the Mg-cyclase complex and its constituents; secondly, it is required for normal Pchlide formation. This protein is required for optimal MgPME-cyclase activity, although it is not absolutely essential.
Pfam PF06857: Malonate decarboxylase delta subunit (MdcD) (family)
This family consists of several bacterial malonate decarboxylase delta subunit (MdcD) proteins.  Malonate decarboxylase of Klebsiella pneumoniae consists of four different subunits and catalyses the conversion of malonate plus H+ to acetate and CO2. The catalysis proceeds via acetyl and malonyl thioester residues with the phosphribosyl-dephospho-CoA prosthetic group of the acyl carrier protein (ACP) subunit. MdcC is the (apo) ACP subunit. The family also contains the CitD family of citrate lyase acyl carrier proteins.
Pfam PF02427: Photosystem I reaction centre subunit IV / PsaE (domain)
PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains.
Pfam PF07947: YhhN family (family)
The members of this family are similar to the hypothetical protein yhhN expressed by E. coli ([swissprot:P37616]). Many are annotated as possible transmembrane proteins, and in fact they all have a high proportion of hydrophobic residues. A human member of this family, formerly known as TMEM86B, is a lysoplasmalogenase that catalyzes the hydrolysis of the vinyl ether bond of lysoplasmalogen. Putative conserved active site residues have been proposed for the YhhN family.
Pfam PF15388: Protein Family FAM117 (disordered)
This protein family is a domain of unknown function found in eukaryotes. Proteins in this family are typically between 269 and 453 amino acids in length. There are two conserved sequence motifs: RRT and TQT.
Pfam PF09690: Plasmodium yoelii subtelomeric region (PYST-C1) (domain)
This group of sequences are defined by the N-terminal domain of a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologues to these genes in any other organism. The C-terminal portions of the genes that contain this domain are divergent and some contain other yoelii-specific paralogous domains such as PYST-C2 (IPR006491).