SII-SWORD/CoKE huggingface dataset:
Pfam PF15801: zf-MYND-like zinc finger, mRNA-binding (domain)
zf-C6H2 is an unusual zinc-finger similar to zf-MYND, [pfam:PF01753].This zinc-finger is found at the N-terminus of Pfam families Exo_endo_phos [pfam:PF03372] and Peptidase_M24 [pfam:PF00557]. The domain is missing in prokaryotic methionine aminopeptidases, and is a unique type of zinc-finger domain. It consists of a C2-C2 zinc-finger motif similar to the RING finger family followed by a C2H2 motif similar to zinc-fingers involved in RNA-binding. In yeast the domain chelates zinc in a 2:1 ratio. The domain is found in yeast, plants and mammals. The domain is necessary for the association of the methionine aminopeptidase with the ribosome and the normal processing of the peptidase.
Wikipedia: In molecular biology the MYND-type zinc finger domain is a conserved protein domain. The MYND domain is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface.
Pfam PF25131: Large ribosomal subunit protein bL9m N-terminal domain (domain)
This is a presumed domain found at the very N-terminal of Large ribosomal subunit protein bL9m from animals, a structural component of the large subunit of the ribosome. According to structure predictions, it may consist in a hairpin with two beta-sheets at each ends connected by a loop.
Pfam PF25065: Med14 RM domain (repeat)
This entry represents a domain found in the human Mediator of RNA polymerase II transcription subunit 14 (Med14) and related proteins. Med14 is a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. The major portion of Med14 exists in the Head-Shoulder module of the Mediator and consists of nine tandem repeats (RM1 to RM9), which are arranged in an atypical right-handed helix. This entry represents repeat RM3.
Pfam PF11394: Type VI lipase adapter protein Tla3, N-terminal (domain)
This  entry represents the N-terminal domain of Type VI lipase adapter protein Tla3, an adapter protein that targets and loads the Tle3 toxin onto the H2 type VI secretion system (H2-T6SS) machinery through an interaction with the TTR domain of VgrG2b and it seems specific for Tle3. This domain and its C-terminal ([pfam:PF20995]) are both required for the interaction with the toxin.
Pfam PF04589: RFX1 transcription activation region (family)
The RFX family is a family of winged-helix DNA binding proteins. RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region  ([pfam:PF02257]) in some mammalian RFX proteins, and is thought to activate  transcription when associated with DNA.  Deletion analysis has identified  the region 233-351 in human RFX1 ([swissprot:P22670]) as being required for  maximal activation.
Pfam PF05999: Herpesvirus U5-like family (family)
This family of Herpesvirus includes U5, U7 and UL27. UL27 promotes a cell cycle arrest in G0/G1 by inducing the proteasomal degradation of host histone acetyltransferase KAT5/Tip60.
Pfam PF13151: Protein of unknown function (DUF3990) (family)
A family of uncharacterised proteins found by clustering human gut metagenomic 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 PF14134: Domain of unknown function (DUF4301) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 505 and 516 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 PF09045: L27_2 (domain)
The L27_2 domain is a protein-protein interaction domain capable of organising scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer.
Wikipedia: The L27 domain is a protein domain that is found in receptor targeting proteins Lin-2 and Lin-7, as well as some protein kinases and human MPP2 protein. The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices.
The L27_2 domain is a protein-protein interaction domain capable of organising scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer.
Pfam PF19132: Family of unknown function (DUF5815) (family)
This is a family 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 PF01635: Coronavirus M matrix/glycoprotein (family)
This family consists of various coronavirus matrix proteins which are transmembrane glycoproteins. The membrane (M) protein is the most abundant structural protein and defines the shape of the viral envelope, being the central organiser of coronavirus assembly. M proteins play a critical role in protein-protein interactions (as well as protein-RNA interactions) since virus-like particle (VLP) formation in many CoVs requires only the M and envelope (E) proteins for efficient virion assembly. Interaction of spike (S) with M is necessary for retention of S in the ER-Golgi intermediate compartment (ERGIC)/Golgi complex and its incorporation into new virions; binding of M to nucleocapsid (N) proteins stabilises the nucleocapsid. Together, M and E protein make up the viral envelope and their interaction is sufficient for the production and release of virus-like particles (VLPs).
Pfam PF11016: Protein of unknown function (DUF2854) (family)
This family of 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 PF15476: Histone deacetylase complex subunit SAP25 (family)
SAP25 is a family of proteins found in eukaryotes. SAP25 is a core component of the mSin3 co-repressor complex whose subcellular location is regulated by PML. mSin3, the transcriptional co-repressor, is associated with histone deacetylases (HDACs) and is utilised by many DNA-binding transcriptional repressors. SAP25 is a nucleo-cytoplasmic shuttling protein that is actively exported from the nucleus by a CRM1-dependent mechanism. It binds to the PAH1 domain of mSin3A, associates with the mSin3A-HDAC complex in vivo, and represses transcription when tethered to DNA.
Pfam PF15898: cGMP-dependent protein kinase interacting domain (coiled_coil)
This domain is found at the C-terminus of protein phosphatase 1 regulatory subunits 12A, 12B and 12C. In protein phosphatase 1 regulatory subunit 12A it has been found to bind to cGMP-dependent protein kinase 1 via a leucine zipper motif located at the C-terminus of this domain.
Pfam PF02661: Fic/DOC family (family)
This family consists of the Fic (filamentation induced by cAMP) protein and doc (death on curing).  The Fic protein is involved in cell division and is suggested to be involved in the synthesis of PAB or folate, indicating that the Fic protein and cAMP are involved in a regulatory mechanism of cell division via folate metabolism.  This family contains a central conserved motif HPFXXGNG in most members.  The exact molecular function of these proteins is uncertain.  P1 lysogens of Escherichia coli carry the prophage as a stable low copy number plasmid. The frequency with which viable cells cured of prophage are produced is about 10(-5) per cell per generation.  A significant part of this remarkable stability can be attributed to a plasmid-encoded mechanism that causes death of cells that have lost P1. In other words, the lysogenic cells appear to be addicted to the presence of the prophage. The plasmid withdrawal response depends on a gene named doc (death on curing) that is represented by this family. Doc induces a reversible growth arrest of E. coli cells by targetting the protein synthesis machinery. Doc hosts the C-terminal domain of its antitoxin partner Phd (prevents host death) through fold complementation, a domain that is intrinsically disordered in solution but that folds into an alpha-helix on binding to Doc.This domain forms complexes with Phd antitoxins containing [pfam:PF02604].
Wikipedia: In molecular biology, the Fic/DOC protein family is a family of proteins which catalyzes the post-translational modification of proteins using phosphate-containing compound as a substrate. Fic domain proteins typically use ATP as a co-factor, but in some cases GTP or UTP is used. Post-translational modification performed by Fic domains is usually NMPylation, however they also catalyze phosphorylation and phosphocholine transfer. This family contains a central conserved motif HPFX[D/E]GNGR in most members and it carries the invariant catalytic histidine. Fic domain was found in bacteria, eukaryotes and archaea and can be found organized in almost hundred different multi-domain assemblies.
Pfam PF19538: Family of unknown function (DUF6062) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 234 and 254 amino acids in length. This family contains two repeated domains that each contain a conserved CXXC and GXCXXH sequence motif. This suggests that these proteins are likely to be metal binding.
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 PF12885: Transducer of regulated CREB activity middle domain (family)
This family includes the region between the N and C terminus of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerisation domain of CREB (cAMP Response Element-Binding). Although the C- and N- terminal domains of these proteins have been well characterised, no functional role has been assigned to the central region, yet.
Pfam PF19290: PmbA/TldA metallopeptidase central domain (domain)
This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the glutamic acid is a substrate-binding residue and the two histidines are zinc ligands. The third zinc ligand is a cysteine, C-terminal to the HEXXXH motif. The TldE (also known as PmbA) by itself has no catalytic activity, does not bind zinc, and does not carry the HEXXXH motif. TldD and TldE were originally identified as regulators of DNA gyrase. Later, they are shown to be metalloproteases involved in CcdA degradation.
Pfam PF21039: Centrosomal protein CEP104, ZnF (domain)
Centrosomal protein CEP104 localises to the distal end of centrioles that interacts through its N- and C-terminal region, respectively, with the distal end proteins Cep97 and CP110. It is required for ciliogenesis and for structural integrity at the ciliary tip, being involved in regulating microtubule length in cilia. This is a multidomain protein that consists of an N-terminal all-beta domain, a central all-alpha-helical HEAT repeat domain and a C-terminal array of four zinc finger domains, the latter represented in this entry. This ZnF domain interacts with kinase Nek1 which competes with CP110.
Pfam PF03609: PTS system sorbose-specific iic component (family)
Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Mannose (Man) family is unique in several respects among PTS permease families .


 * It is the only PTS family in which members possess a IID protein.
 * It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue.
 * Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.


The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine.
Pfam PF01439: Metallothionein (family)
Members of this family are metallothioneins. These proteins are cysteine rich proteins that bind to heavy metals. Members of this family appear to be closest to Class II metallothioneins, seed [pfam:PF00131].
Pfam PF04741: InvH outer membrane lipoprotein (family)
This family represents the Salmonella outer membrane lipoprotein InvH. The molecular function of this protein is unknown, but it is required for the localisation to outer membrane of InvG, which is involved in a type III secretion apparatus mediating host cell invasion.
Pfam PF08281: Sigma-70, region 4 (domain)
Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
Wikipedia: A sigma factor is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it. They are also found in plant chloroplasts as a part of the bacteria-like plastid-encoded polymerase (PEP).
Pfam PF22839: Domain of unknown function (DUF7015) (domain)
This domain of unknown function is found at the C-terminal of a group of bacterial proteins and, according to structure predictions, it may adopt a beta-barrel structure. It is often associated with an Ig-like domain ([pfam:PF08522]).
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 PF17161: Domain of unknown function (DUF5123) (repeat)
This function of this domain is not known. It is found in proteins from Bacteroidetes.
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 PF01020: Ribosomal L40e family (family)
Bovine L40 has been identified as a secondary RNA binding protein. L40 is fused to a ubiquitin protein.
Pfam PF10646: Sporulation and spore germination (domain)
The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. The domain is found in a number of different bacterial species both alone and in association with other domains such as Amidase_3 [pfam:PF01520], Gmad1 and Gmad2.  It is predicted to have a novel alpha-beta fold.
Pfam PF16916: Dimerisation domain of Zinc Transporter (domain)
ZT_dimer is the dimerisation region of the whole molecule of zinc transporters since the full-length members form a homodimer during activity. The domain lies within the cytoplasm and exhibits an overall structural similarity with the copper metallochaperone Hah1 UniProtKB:O00244, exhibiting an open alpha-beta domain with two alpha helices (H1 and H2) aligned on one side and a three-stranded mixed beta-sheet (S1 to S3) on the other side. The N-terminal part of the members is the Cation_efflux family, [pfam:PF01545].
Pfam PF00782: Dual specificity phosphatase, catalytic domain (domain)
Ser/Thr and Tyr protein phosphatases. The enzyme's tertiary fold is highly similar to that of tyrosine-specific phosphatases, except for a "recognition" region.
Wikipedia: Protein tyrosine phosphatases (EC	3.1.3.48, systematic name protein-tyrosine-phosphate phosphohydrolase) are a group of enzymes that remove phosphate groups from phosphorylated tyrosine residues on proteins:[a protein]-tyrosine phosphate + H2O = [a protein]-tyrosine + phosphate
Pfam PF23958: Family of unknown function (DUF7287) (family)
This entry includes uncharacterised archaeal proteins including Uncharacterized protein AF_0763 from Archaeoglobus fulgidus [[swissprot:O29495]].
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 PF03076: Equine arteritis virus GP3 (family)
This protein is encoded by ORF3 of equine arteritis virus. The function is unknown.
Pfam PF10732: Protein of unknown function (DUF2524) (coiled_coil)
This family of proteins with unknown function appears to be restricted to Bacillaceae bacteria.
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 PF04597: Ribophorin I (family)
Ribophorin I is an essential subunit of oligosaccharyltransferase (OST), which is also known as Dolichyl-diphosphooligosaccharide--protein glycosyltransferase, ([ec:2.4.1.119]).  OST catalyses the transfer of an oligosaccharide from dolichol pyrophosphate to selected asparagine residues of nascent polypeptides as they are translocated into the lumen of the rough endoplasmic reticulum. Ribophorin I and OST48 are though to be responsible for OST catalytic activity. Both yeast and mammalian proteins are glycosylated but the sites are not conserved.  Glycosylation may contribute towards general solubility but is unlikely to be involved in a specific biochemical function Most family members are predicted to have a transmembrane helix at the C terminus of this region.
Pfam PF17634: Gene product 67 (family)
This is a family of unknown function found in Myoviridae such as Enterobacteria phages. Family members such as Gp67, is a prohead core (scaffold) protein.
Pfam PF06962: Putative rRNA methylase (family)
This family contains a number of putative rRNA methylases. Note that many family members are hypothetical proteins.