SII-SWORD/CoKE huggingface dataset:
Pfam PF22094: CED4, winged-helix domain (domain)
This entry represents a WH-like (HTH superfamily) domain present in  CED4 proteins from nematodes. CDE4 together with EGL1, CED9, and CED3, forms a crucial component of the apoptotic signaling cascade necessary for triggering programmed cell death during both embryonic and postembryonic development. Molecular dynamics studies indicate that this WH domain may regulate CED4 dissociation from CED9.
Pfam PF11883: Domain of unknown function (DUF3403) (family)
This domain is functionally uncharacterised. This domain is found in eukaryotes.  This presumed domain is about 50 amino acids in length.  This domain is found associated with [pfam:PF00069], [pfam:PF08276], [pfam:PF00954], [pfam:PF01453].
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 PF10259: Rogdi leucine zipper containing protein (family)
This is a family of conserved proteins which have been suggested as containing leucine-zipper domains. A leucine zipper domain is a region of 30 amino acids with leucines repeating every seven or eight residues; these proteins do have many such leucines. The protein in Drosophila comes from the gene ROGDI.
Pfam PF24035: Domain of unknown function (DUF7344) (domain)
This is a presumed HTH domain found in a group of uncharacterised archaeal sequences.
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 PF02638: Glycosyl hydrolase-like 10 (domain)
This is family of bacterial glycosyl-hydrolase-like proteins falling into the family GHL10 as described above,.
Pfam PF21366: TRAFD1/XAF1, zinc finger (domain)
This is a TRAF (C2H2)-type zinc finger found in TRAD1 and XIAF1. TRAFD1 is a negative feedback regulator that controls excessive innate immune responses. XIAF1 seems to function as a negative regulator of members of the IAP (inhibitor of apoptosis protein) family. These proteins share amino acid identity with zinc fingers of TRAF6.
Pfam PF07159: CYRIA/CYRIB Rac1 binding domain (domain)
This domain has been annotated as Rac1-binding domain. It can be found in human CYRIA/CYRIB and at the N terminus of CYFIP1/2. CYFIP proteins are known RAC1 effectors that stimulate actin polymerization. In mice, CYRIB (also known as CYRI or FAM49B) negatively regulates RAC1-driven cytoskeletal remodelling and plays a role in restricting infection mediated by Mycobacterium tuberculosis and Listeria monocytogenes.
Pfam PF08583: Cytochrome c oxidase biogenesis protein Cmc1 like (family)
Cmc1 is a metallo-chaperone like protein which is known to localise to the inner mitochondrial membrane in Saccharomyces cerevisiae.  It is essential for full expression of cytochrome c oxidase and respiration.  Cmc1 contains two Cx9C motifs and is able to bind copper(I).  Cmc1 is thought to play a role in mitochondrial copper trafficking and transfer to cytochrome c oxidase.
Pfam PF09898: Uncharacterized protein conserved in bacteria (DUF2125) (family)
This domain, found in various hypothetical prokaryotic 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.
Pfam PF05324: Sperm antigen HE2 (family)
This family consists of several variants of the human and chimpanzee sperm  antigen proteins (HE2 and EP2 respectively). The EP2 gene codes for a  family of androgen-dependent, epididymis-specific secretory proteins.The  EP2 gene uses alternative promoters and differential splicing to produce a family of variant messages.  The translated putative protein variants differ significantly from each other. Some of these putative proteins have  similarity to beta-defensins, a family of antimicrobial peptides.
Pfam PF09591: Protein of unknown function (DUF2463) (family)
This protein is found in eukaryotic, parasitic microsporidia. 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 PF05227: CHASE3 domain (domain)
CHASE3 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria. Specifically, CHASE3 domains are found in histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins and predicted diguanylate cyclases/phosphodiesterases. This domain recognises pyrene (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF02885: Glycosyl transferase family, helical bundle domain (domain)
This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase.  All these proteins can transfer a phosphorylated ribose substrate.
Pfam PF07218: Rhoptry-associated protein 1 (RAP-1) (family)
This family consists of several rhoptry-associated protein 1 (RAP-1) sequences which appear to be specific to Plasmodium falciparum.
Pfam PF08348: YheO-like PAS domain (domain)
This family contains various hypothetical bacterial proteins that are similar to the E. coli protein YheO ([swissprot:P64624]). Their function is unknown, but are likely to be involved in signalling based on the presence of this PAS domain.
Wikipedia: A Per-Arnt-Sim (PAS) domain is a protein domain found in all kingdoms of life. Generally, the PAS domain acts as a molecular sensor, whereby small molecules and other proteins associate via binding of the PAS domain. Due to this sensing capability, the PAS domain has been shown as the key structural motif involved in protein-protein interactions of the circadian clock, and it is also a common motif found in signaling proteins, where it functions as a signaling sensor.
Pfam PF11455: Antitoxin MazE-like (family)
This entry includes MazE from Mycobacterium smegmatis. MazE is an antitoxin component of a type II toxin-antitoxin (TA) system.
Pfam PF13585: CHU_C Type IX secretion signal domain (domain)
This domain was initially identified from proteins from C. hutchinsonii giving rise to the CHU name. This domain adopts an immunoglobulin like domain that is foundat the C-terminus of various bacterial cell surface proteins. This domain was shown to be essential for localisation of the CHU_3220 protein. It is likely that this domain target the proteins containing it to the type IX secretion system. This domain is cleaved off the protein which is then anchored to the outer membrane.
Pfam PF14045: YIEGIA protein (family)
This family includes the B. subtilis YphB protein [swissprot:P50742], which is functionally uncharacterised. Its expression is regulated by the sporulation transcription factor sigma-F, however it is not essential for sporulation or germination. This is not a homologue of E.  coli YphB, which belongs to [pfam:PF01263].  This family of proteins is found in bacteria. Proteins in this family are typically between 276 and 300 amino acids in length and contain a conserved YIEGIA motif. Structure predictions show that these proteins contain an N-terminal transmembrane domain composed of five alpha helices. This domain is followed by a C-terminal domain that is likely cytosolic. Structure prediction shows that this family likely forms a homohexameric structure. Structure prediction also shows that this complex is capped by a homohexamer of proteins belonging to [pfam:PF21835] (pers. observation A Bateman).
Pfam PF16762: Ribbon-helix-helix domain (domain)
This ribbon-helix-helix domain binds to DNA and may be a part of a toxin-antitoxin system.
Pfam PF02430: Apical membrane antigen 1 (family)
Apical membrane antigen 1 (AMA-1) is a Plasmodium asexual blood-stage antigen. It has been suggested that positive selection operates on the AMA-1 gene in regions coding for antigenic sites.
Wikipedia: In molecular biology, apical membrane antigen 1 is a novel antigen of Plasmodium falciparum which has been cloned. It contains a hydrophobic domain typical of an integral membrane protein. The antigen is designated apical membrane antigen 1 (AMA-1) by virtue of appearing to be located in the apical complex. AMA-1 appears to be transported to the merozoite surface close to the time of schizont rupture.
Pfam PF12751: Vacuolar segregation subunit 7 (family)
Vac7 is localised at the vacuole membrane, a location which is consistent with its involvement in vacuole morphology and inheritance. Vac7 has been shown to function as an upstream regulator of the Fab1 lipid kinase pathway. The Fab1 lipid pathway is important for correct regulation of membrane trafficking events. It has been identified as a LEA-2 homologue together with TMEM106B from humans and Tag1 in yeast, all predicted to be lipid transfer proteins.
Pfam PF16419: CCR4-NOT transcription complex subunit 1 HEAT repeat (repeat)
This domain is a HEAT repeat found in fungal CCR4-NOT transcription complex subunit 1 at the N-terminus of PF16418.
Wikipedia: CCR4-NOT transcription complex subunit 1 is a protein that in humans is encoded by the CNOT1 gene.
Pfam PF10039: Predicted integral membrane protein (DUF2275) (family)
This domain, found in various hypothetical bacterial proteins and in the RNA polymerase sigma factor, 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 PF19128: Family of unknown function (DUF5811) (family)
This is a family of proteins of unknown function predominantly found in Halobacteria.
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 PF12291: Protein of unknown function (DUF3623) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 261 and 345 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 PF07013: Protein of unknown function (DUF1314) (family)
This family consists of several Alphaherpesvirus proteins of around 200 residues in length. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09233: Restriction endonuclease EcoRV (domain)
Members of this family of prokaryotic restriction endonucleases recognise the double-stranded sequence 5'-GATATC-3' and cleave after T-3. They catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
Wikipedia: EcoRV is a type II restriction endonuclease isolated from certain strains of Escherichia coli. It has the alternative name Eco32I.
Pfam PF19286: Zinc finger SWIM domain-containing protein 1/3, C-terminal (domain)
This is a presumed domain found at the C-terminal of Zinc finger SWIM domain-containing proteins 1 and 3. The function of ZSWIM3 is currently unknown. ZSWIM1 may play a role in the development or function of T helper cells. According to AlphaFold structure prediction, this domain may consist of two helices.
Pfam PF24395: OLD-like TOPRIM 1 (domain)
This entry represents a Toprim domain predicted to act as a nuclease like those seen in the OLD systems.
Pfam PF04859: Plant protein of unknown function (DUF641) (family)
Plant protein of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02909: Tetracyclin repressor-like, C-terminal domain (domain)
This entry represents the C-terminal domain found in the tetracycline transcriptional repressor TetR, which binds to the Tet(A) gene to repress its expression in the absence of tetracycline . Tet(A) is a membrane-associated efflux protein that exports tetracycline from the cell before it can attach to ribosomes and inhibit polypeptide chain growth. TetR occurs as a homodimer and uses two helix-turn-helix (HTH) motifs to bind tandem DNA operators, thereby blocking the expression of the associated genes, TetA and TetR. The structure of the class D TetR repressor protein  involves 10 Î±-helices, with connecting turns and loops. The three N-terminal helices constitute the DNA-binding HTH domain, which has an inverse orientation compared with HTH motifs in other DNA-binding proteins. The core of the protein, formed by helices 5-10, is responsible for dimerisation and contains, for each monomer, a binding pocket that accommodates tetracycline in the presence of a divalent cation.
Pfam PF08038: TOM7 family (family)
This family consists of TOM7 family of mitochondrial import receptors. TOM7 forms part of the translocase of the outer mitochondrial membrane (TOM) complex and it appears to function as a modulator of the dynamics of the mitochondrial protein transport machinery by promoting the dissociation of subunits of the outer membrane translocase.
Wikipedia: The translocase of the outer membrane (TOM) is a complex of proteins found in the outer mitochondrial membrane of the mitochondria. It allows movement of proteins through this barrier and into the intermembrane space of the mitochondrion. Most of the proteins needed for mitochondrial function are encoded by the nucleus of the cell. The outer membrane of the mitochondrion is impermeable to large molecules greater than 5000 daltons. The TOM works in conjunction with the translocase of the inner membrane (TIM) to translocate proteins into the mitochondrion. Many of the proteins in the TOM complex, such as TOMM22, were first identified in Neurospora crassa and Saccharomyces cerevisiae. Many of the genes encoding these proteins are designated as TOMM (translocase of the outer mitochondrial membrane) complex genes.
Pfam PF05304: Protein of unknown function (DUF728) (family)
This family consists of several uncharacterised tobravirus proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15473: PEST, proteolytic signal-containing nuclear protein family (family)
PCNP is a PEST-containing nuclear protein that is ubiquitinated by NIRF, a Np95/ICBP90-like RING finger protein. PEST sequences, which are rich in proline (P), glutamic acid (E), serine (S) and threonine (T), are found in a number of short-lived proteins, such as transcription factors and cell cycle-associated proteins. Their function is generally controlled by proteolysis, mostly via ubiquitin-mediated degradation. Thus, NIRF and PCNP are a ubiquitin ligase and its substrate, respectively, that may constitute a novel signalling pathway with some relation to cell proliferation.
Pfam PF01643: Acyl-ACP thioesterase N-terminal domain (domain)
This family consists of various acyl-acyl carrier protein (ACP) thioesterases (TE) these terminate fatty acyl group extension via hydrolysing an acyl group on a fatty acid. These proteins are usually composed of a pair of tandem HotDog domains. This entry represents the N-terminal one of the pair.
Pfam PF02221: ML domain (domain)
ML domain - MD-2-related lipid recognition domain. This family consists of proteins from plants, animals and fungi, including dust mite allergen Der P 2 ([swissprot:P49278]). It has been implicate in lipid recognition, particularly in the recognition of pathogen related products. A mutation in Npc2 ([swissprot:Q15668]) causes a rare form of Niemann-Pick type C2 disease. This domain has a similar topology to immunoglobulin domains.
Wikipedia: The MD-2-related lipid-recognition (ML) domain is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like beta-sandwich fold similar to that of immunoglobulin E-set domains. This domain is present in the following proteins:Epididymal secretory protein E1, which is known to bind cholesterol. Niemann-Pick disease type C2 is a fatal hereditary disease characterised by accumulation of low-density lipoprotein-derived cholesterol in lysosomes.
House dust mite allergen proteins such as Der f 2 from Dermatophagoides farinae and Der p 2 from Dermatophagoides pteronyssinus.
Pfam PF21878: C381 turret protein 1st galactose-binding domain-like (domain)
This entry represents the Sulfolobus turreted icosahedral virus (STIV) turret protein first jelly roll domain. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions of the membrane and various protein components involved. The turret protein is apposed on the penton base C-terminal jelly-roll ring and forms a pentamer consisting of three consecutive layers of jelly-rolls, with each jelly-roll exhibiting different orientations. The interior of the C381 pentamer harbors two rather large cavities, which exhibit an overall positive electrostatic potential, suggesting that the turrets may act as STIV receptor-binding proteins carrying out recognition and attachment to the host receptors. The turret protein shares similarity with many carbohydrate-binding modules as well as domains involved in protein-protein interactions.
Pfam PF05238: Kinetochore protein CHL4 like (family)
CHL4 is a protein involved in chromosome segregation. It is a component of the central kinetochore which mediates the attachment of the centromere to the mitotic spindle. CENP-N is one of the components that assembles onto the CENP-A-nucleosome-associated (NAC) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC.
Pfam PF11473: RNA binding protein B2 (family)
B2 is expressed by the insect Flock House virus (FHV) as a counter-defense mechanism against antiviral RNA silencing during infection. In vitro, B2 binds to dsRNA as a dimer and inhibits the cleavage of it by Dicer. B2 blocks cleavage of the FHV genome by Dicer and also the incorporation of FHV small interfering RNAs into the RNA-induced silencing complex.
Pfam PF17982: NSD Cys-His rich domain (domain)
This is an NSD-specific Cys-His rich region (C5HCH) domain. Family members include NSD3 (nuclear receptor SET domain-containing) proteins. This domain is located on the C-terminal of NSD1, 2 and 3 proteins. C5HCH domain lies adjacent to the fifth plant homeodomain (PHD5). The PHD5-C5HCH module of NSD3 (PHD5-C5HCHNSD3) recognises the H3 N-terminal peptide containing unmodified K4 and trimethylated K9. Moreover, it has been reported that the PHD5-C5HCH module of NSD1 (PHD5-C5HCH) was the sole region required for tight binding of the NUP98-NSD1 fusion protein to the HoxA9 gene promoter, implicating that PHD5-C5HCH might have chromatin targeting ability.
Pfam PF09812: Mitochondrial ribosomal protein L28 (family)
Members of this family are components of the mitochondrial large ribosomal subunit.  Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S).
Pfam PF10236: Mitochondrial ribosomal death-associated protein 3 (family)
This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
Wikipedia: 28S ribosomal protein S29, mitochondrial, also known as death-associated protein 3 (DAP3), is a protein that in humans is encoded by the DAP3 gene on chromosome 1. This gene encodes a 28S subunit protein of the mitochondrial ribosome (mitoribosome) and plays key roles in translation, cellular respiration, and apoptosis. Moreover, DAP3 is associated with cancer development, but has been observed to aid some cancers while suppressing others.
Pfam PF01417: ENTH domain (repeat)
The ENTH (Epsin N-terminal homology) domain is found in proteins involved in endocytosis and cytoskeletal machinery.  The function of the ENTH domain is unknown.
Wikipedia: The epsin N-terminal homology (ENTH) domain is a structural domain that is found in proteins involved in endocytosis and cytoskeletal machinery.