SII-SWORD/CoKE huggingface dataset:
Pfam PF08056: Tryptophan operon leader peptide (family)
This family consists of the tryptophan operon  leader peptides. The tryptophan operon is regulated  by transcription attenuation in response to changes  in the level of tryptophan. The transcript of the  leader peptide can adopt alternative mutually-exclusive  secondary structures that would either result in  termination of transcription of the tryptophan structural  genes or in transcription of the entire operon.
Pfam PF23408: TMEM126-like protein (domain)
This entry represents a family of proteins from nematodes that have sequence and structural similarity to the TMEM126 family of integral membrane proteins that are involved in the assembly of complex I.  Therefore these proteins may have a similar function. However, it has also been suggested that this assembly function was only acquired by the TMEM126B proteins.
Pfam PF22553: T3SS (YopN, CesT) and YbjN peptide-binding chaperone 2 (domain)
This domain is observed in host systems predicted to counter viral ribosylating toxins. They are predicted to function as peptide-binding chaperone domains that target proteins modified by ADPr and potentially misfolded as a consequence.
Pfam PF03516: Filaggrin (repeat)
Filaggrins are filament-associated proteins that interact with keratin intermediate filaments of terminally differentiating mammalian epidermis via disulphide bond formation . Filaggrin-2 is essential for normal cell-cell adhesion in the cornified cell layers and important for proper integrity and mechanical strength of the stratum corneum of the epidermis . They show wide species variations and their aberrant expression has been implicated in a number of keratinising disorders. The proteins are synthesised as large, insoluble, highly-phosphorylated precursors, containing multiple tandem repeats of 324 amino acids, which are not separated by a large linker. The precursor is deposited as keratohyalin granules. During terminal differentiation, it is dephosphorylated and proteolytically cleaved.
Pfam PF03208: PRA1 family protein (family)
This family includes the PRA1 (Prenylated rab acceptor) protein which is a Rab guanine dissociation inhibitor (GDI) displacement factor.  This family also includes the glutamate transporter EAAC1 interacting protein GTRAP3-18.
Pfam PF11859: Protein of unknown function (DUF3379) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 234 to 251 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 PF11339: Protein of unknown function (DUF3141) (family)
This family of proteins with unknown function appears to be restricted to Proteobacteria.
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 PF11149: Protein of unknown function (DUF2924) (family)
This bacterial 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 PF07854: Protein of unknown function (DUF1646) (family)
Some of the members of this family are hypothetical bacterial and archaeal proteins, but others are annotated as being cation transporters expressed by the archaebacterium Methanosarcina mazei ([swissprot:Q8PXG5], [swissprot:Q8PXG7] and [swissprot:Q8PXG8]).
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 PF19447: Family of unknown function (DUF5985) (family)
This family of uncharacterised proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length and contain three transmembrane helices.
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 PF12016: Stonin 2 (family)
Stonin 2 is involved in clathrin mediated endocytosis. It binds to Eps15 by its highly conserved NPF motif. The complex formed has been shown to directly associate with the clathrin adaptor complex AP-2, and to localize to clathrin-coated pits (CCPs). In addition, stonin2 was recently identified as a specific sorting adaptor for synaptotagmin, and may thus regulate synaptic vesicle recycling.
Pfam PF24169: Straight fiber protein PB4 first Fn3-like domain (domain)
This entry represents the N-terminal Fn3-like domain of the Straight fiber protein PB4 found in T5-like phages. PB4 along with PB3, forms the central straight fiber, bearing the receptor binding protein PB5 at its C terminus. Upon PB5 binding to the host receptor FhuA, the central fiber reorganises and undergoes structural rearrangements that lead to its bending, bringing PB3 close to the host membrane for anchoring. The PB4-PB3 interactions are ensured by the proximal loops of the first of the three Fn3-like domains of PB4. These interactions are disrupted upon binding to the host receptor and the string of PB4 Fn3-like domains undergoes drastic conformational changes.
Pfam PF06431: Polyomavirus large T antigen C-terminus (family)
The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses . Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA . T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see [prositedoc:PDOC00553], IPR001623), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see [prositedoc:PDOC51206], IPR010932) .
This entry represents the helicase domain of LTag, which assembles into a hexameric structure containing a positively charged central channel that can bind both single- and double-stranded DNA . ATP binding and hydrolysis trigger large conformational changes which are thought to be coupled to the melting of origin DNA and the unwinding of duplex DNA . These conformational changes cause the angles and orientations between regions of a monomer to alter, creating what was described as an "iris"-like motion in the hexamer. In addition to this, six Î² hairpins on the channel surface move longitudinally along the central channel, possibly serving as a motor for pulling DNA into the LTag double hexamer for unwinding.
Pfam PF10997: Alternate to MurJ (family)
This bacterial family of proteins has no known function. However, family members include lipid II flippase Amj, which is required for bacterial cell wall synthesis. It transports lipid-linked peptidoglycan precursors from the inner to the outer surface of the cytoplasmic membrane.
Pfam PF00227: Proteasome subunit (domain)
The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria. The second is call beta-proteobacteria proteasome homologue (BPH).
Pfam PF13262: Protein of unknown function (DUF4054) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 120 and 152 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 PF20532: Family of unknown function (DUF6747) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There are two conserved sequence motifs: YFKAF and FRVSTG.
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 PF03884: DNA gyrase inhibitor YacG (domain)
YacG inhibits all the catalytic activities of DNA gyrase by preventing its interaction with DNA. It acts by binding directly to the C-terminal domain of GyrB, which probably disrupts DNA binding by the gyrase. YacG has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins. The conserved four cysteine motif in this protein (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.
Pfam PF09229: Activator of Hsp90 ATPase, N-terminal (domain)
Members of this family, which are predominantly found in the protein 'Activator of Hsp90 ATPase' adopt a secondary structure consisting of an N-terminal alpha-helix leading into a four-stranded meandering antiparallel beta-sheet, followed by a C-terminal alpha-helix. The two helices are packed together, with the beta-sheet curving around them. They bind to the molecular chaperone HSP82 and stimulate its ATPase activity.
Pfam PF15200: Keratinocyte differentiation-associated (family)
Keratinocyte differentiation-associated protein (KRTDAP) is secreted by keratinocytes and may serve as a soluble regulator of keratinocyte differentiation .
Wikipedia: Keratinocyte differentiation-associated protein is a protein that in humans is encoded by the KRTDAP gene.
Pfam PF12930: Family of unknown function (DUF3836) (family)
Family of uncharacterised proteins found in Bacteroidales species.
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 PF15235: G protein-regulated inducer of neurite outgrowth C-terminus (family)
This represents the C-terminus of the G protein-regulated inducer of neurite outgrowth proteins.
Pfam PF21293: Ribonuclease D, C-terminal HRDC domain (domain)
Ribonuclease D is a bacterial 3'-5' exonuclease that acts on tRNA. It contributes to the 3' maturation of several stable RNAs. It consists of a catalytic domain ([pfam:PF01612]) and two alpha- helical domains at the C-terminal that closely resemble the HRDC domain seen in RecQ-family helicases. This is the second HRDC domain from RNAse D. The first one is included in [pfam:PF00570].
Pfam PF08258: WWamide peptide (family)
This family contain neuropeptides, isolated from ganglia of the African giant snail, Achatina fulica.  Each peptide has a Trp residue at both the N- and C-termini.  Purified WWamide-1, -2 and -3 showed an inhibitory effect on the phasic contractions of the anterior byssus retractor muscle (ABRM).
Pfam PF16415: CCR4-NOT transcription complex subunit 1 CAF1-binding domain (repeat)
This is the CAF1-binding domain of CCR4-NOT transcription complex. It adopts a MIF4G (middle portion of eIF4G) fold.
Wikipedia: CCR4-NOT transcription complex subunit 1 is a protein that in humans is encoded by the CNOT1 gene.
Pfam PF01408: Oxidoreductase family, NAD-binding Rossmann fold (domain)
This entry represents the N-terminal domain of a group of enzymes that utilise NADP or NAD, known as the GFO/IDH/MOCA family, which includes enzymes that catalyse different chemical reactions such as oxidation and reduction of carbohydrates, oxidation of trans-dihydrodiols, reduction of biliverdin and hydrolysation of glycosidic bonds. This domain adopts a a typical Rossmann fold.
Pfam PF16331: TolA binding protein trimerisation (domain)
This is the N-terminal domain of the YbgF protein. YbgF binds to TolA. This domain mediates trimerisation.
Pfam PF19348: Family of unknown function (DUF5926) (domain)
This entry represents a presumed domain that is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 294 and 327 amino acids in length. Many proteins in this family are annotated at Topoisomerase II, but the source of this annotation is unclear.
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 PF20286: Divergent Family B DNA polymerase (family)
This family represents a Divergent Family B DNA polymerase found in PhiKZ/ group 1 phages.
Pfam PF15927: Cancer susceptibility candidate 1 N-terminus (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 200 amino acids in length. The family is found in association with [pfam:PF12366]. There are two completely conserved residues (N and W) that may be functionally important.
Pfam PF17176: tRNA-binding domain (domain)
This domain, found at the C-terminus of tRNA(Met) cytidine acyltransferase, may be involved in tRNA-binding. This family represents the tRNA-binding domain proteins not captured by [pfam:PF13725].
Pfam PF24885: Nephrocystin-3 TPR domain (repeat)
This entry represents the TPR domain found at the C-terminal of nephrocystin-3 (NPHP3), a protein required for normal ciliary development and function. It inhibits disheveled-1-induced canonical Wnt-signaling activity and may also play a role in the control of non-canonical Wnt signaling which regulates planar cell polarity.
Pfam PF16817: Domain of unknown function (DUF5073) (domain)
This domain of unknown function is a membrane protein found in Mycobacterium.
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 PF18738: DZIP3/ hRUL138-like HEPN (domain)
DZIP3/ hRUL138-like HEPN nuclease. Fusion to TPR, Zn-ribbon, RING, Ankyrin, CARD, NACHT ATPase, DEATH and LRR in various animal lineages.
Pfam PF24264: Family of unknown function (DUF7465) (family)
This entry represents a small family of uncharacterised phage proteins. The family includes Phage Bxb1 protein 85 [swissprot:Q9B036].
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 PF09312: SurA N-terminal domain (domain)
This domain is found at the N-terminal of the chaperone SurA, a chaperone that assists correct folding of outer membrane proteins (OMPs) in Gram-negative bacteria. This is the helical domain found at the N-terminal of SurA that, together with the C-terminal, forms a core domain which contains OMP binding sites. OMP binding induces conformational changes of SurA domains that protect OMPs from misfolding and aggregation. The C-terminal of the SurA protein folds back and forms part of this domain also but is not included in the current alignment.
Pfam PF14315: Domain of unknown function (DUF4380) (family)
This family of proteins is found in bacteria, archaea and eukaryotes.  Proteins in this family are typically between 288 and 372 amino acids in length. There are two completely conserved residues (G and E) that may be functionally important.
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 PF03778: Protein of unknown function (DUF321) (conserved_site)
This family may be related to the FARP (FMRFamide) family, [pfam:PF01581].
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 PF00083: Sugar (and other) transporter (family)
This entry represents a subfamily of the major facilitator superfamily. Members in this family include sugar transporters, which are responsible for the binding and transport of various carbohydrates, organic alcohols, and acids in a wide range of prokaryotic and eukaryotic organisms . Most but not all members of this family catalyse sugar transport .
Wikipedia: Glucose transporters are a wide group of membrane proteins that facilitate the transport of glucose across the plasma membrane, a process known as facilitated diffusion. Because glucose is a vital source of energy for all life, these transporters are present in all phyla. The GLUT or SLC2A family are a protein family that is found in most mammalian cells. 14 GLUTS are encoded by the human genome. GLUT is a type of uniporter transporter protein.
Pfam PF09098: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding (domain)
Members of this family are predominantly found in the prokaryotic protein quinohemoprotein amine dehydrogenase. They have a predominantly alpha-helical structure and can be divided into two subdomains, each binding a haem C group via a conserved CXXCH motif.
Pfam PF09497: Transcription mediator complex subunit Med12 (domain)
Med12 is a negative regulator of the Gli3-dependent sonic hedgehog signalling pathway via its interaction with Gli3 within the RNA polymerase II transcriptional Mediator. A complex is formed between Med12, Med13, CDK8 and CycC which is responsible for suppression of transcription. This subunit forms part of the Kinase section of Mediator.
Wikipedia: Mediator of RNA polymerase II transcription, subunit 12 homolog , also known as MED12, is a human gene found on the X chromosome.
Pfam PF11489: Altered inheritance of mitochondria protein 21 (disordered)
This is a family of proteins conserved in yeasts. Saccharomyces cerevisiae Aim21 may be involved in mitochondrial migration along  actin filament. It may also interact with ribosomes.
Pfam PF09552: BstXI restriction endonuclease (family)
This family includes the BstXI (recognises and cleaves CCANNNNN^NTGG) restriction endonuclease.
Pfam PF18614: RNase II-type exonuclease C-terminal S1 domain (domain)
This entry describes the C-terminal S1 domain found in type 2 RNase exonucleases. DrR63 proteins from Deinococcus radiodurans are an RNase II-type enzymes (DrII). Structure analysis of DrII indicates that it has an N-terminal HTH domain which interacts with a flexible loop that connects two beta-strands from the conserved C-terminal S1 domain, forming a beta-wing fold common in wHTH domains.
Pfam PF08928: PoNe immunity protein (PoNi), N-terminal (domain)
This entry represents the N-terminal domain of the PoNe immunity proteins (PoNi) which antagonise the DNAse toxin PoNe (Polymorphic Nuclease effector). PoNi proteins may directly interact with PoNe.
Pfam PF07423: Domain of unknown function (DUF1510) (domain)
This domain is found in hypothetical bacterial proteins of around 200 residues in length. The function of this domain 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 PF15521: Novel toxin 11 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin contains two structural domains, an N-terminal alpha/beta domain and a C-terminal all-beta domain. The domain contains conserved GxR, RxxxoH GxE and GxxH motifs and a conserved histidine residue. In bacterial polymorphic toxin systems, the toxin is usually exported by the Photorhabdus virulence cassette (PVC)-type export system.