SII-SWORD/CoKE huggingface dataset:
Pfam PF11490: DNA polymerase III polC-type N-terminus II (domain)
This is the second N-terminal domain, NII domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria.  Purine asymmetry is a characteristic of organisms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased. It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted hydrophobic surface patch suggests this domain may be involved in protein binding. This domain is associated with DNA_pol3_alpha [pfam:PF07733] and DNA_pol3_a_NI [pfam:PF14480].
Pfam PF07182: Protein of unknown function (DUF1402) (family)
This family consists of several hypothetical bacterial proteins of around 310 residues in length. Members of this family seem to be found exclusively in Agrobacterium, Rhizobium and Brucella species. 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 PF18759: Plavaka transposase (family)
A transposase with an RNaseH catalytic domain that often has a histone binding BAM/BAH domain at the C-terminus and is sometimes associated with TET/JBP family of dioxygenases in fungi.
Pfam PF03827: Orexin receptor type 2 (family)
The neuropeptide hormone orexin stimulates appetite and food consumption , and is found in the hypothalamus, which has been shown to be the 'feeding centre' and plays a central role in the integrated control of feeding and energy homeostasis . It also has a prominent role in promoting wakefulness . The orexin receptor (also referred to as the hypocretin receptor) is a rhodopsin-like G protein-coupled receptor that binds orexin. There are two subtypes; orexin receptor 1 (OX1) and orexin receptor 2 (OX2) .
This entry represents Orexin receptor 2, which is found throughout vertebrates and, like OX1, is expressed in brainstem and striatal nuclei, with additional expression in arousal promoting histaminergic nuclei . Both Orexin-A and B have nearly equal affinity for OX2 , and stimulate intracellular calcium levels through OX2-mediated induction of Gq and phospholipase C activity, but is also capable of activating Gs, Gi, and potentially ion channels . The OX2 receptor predominantly mediate the control of arousal induced by orexin neuropeptides .
Wikipedia: Orexin receptor type 2 (Ox2R or OX2), also known as hypocretin receptor type 2 (HcrtR2), is a protein that in humans is encoded by the HCRTR2 gene. It should not be confused for the protein CD200R1 which shares the alias OX2R but is a distinct, unrelated gene located on the human chromosome 3.
Pfam PF13182: Protein of unknown function (DUF4007) (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 284 and 326 amino acids in length. This domain is found associated with [pfam:PF01507] in some proteins, suggesting a functional link.
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 PF01166: TSC-22/dip/bun family (coiled_coil)
This entry includes a group of eukaryotic proteins that are evolutionary related and involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins included in this entry are:


 * Vertebrate proteins TSC22 1-4 , transcriptional regulators that act in different pathways, for instance, TSC22-1 acts on C-type natriuretic peptide (CNP) promoter , it also promotes CASP3-mediated apoptosis  and positively regulates TGF-beta signaling ; TSC22-3 (also known as DIP) protects T-cells from IL2 deprivation-induced apoptosis through the inhibition of FOXO3A transcriptional activity that leads to the down-regulation of the pro-apoptotic factor BCL2L11  and it also contributes to enhancement of TGF-beta signaling by binding to and modulating the transcription activator activity of SMAD4 .
 * Drosophila protein bunched  (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis.
 * Caenorhabditis elegans protein tsct-1 (also known as T18D3.7), whose function is unknown.
Pfam PF12317: Intraflagellar transport complex B protein 46 C terminal (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.
Pfam PF03413: Peptidase propeptide and YPEB domain (domain)
This region is likely to have an protease inhibitory function (personal obs:C Yeats). This model is likely to miss some members of this family as the separation from signal to noise is not clear. The name is derived from Peptidase & Bacillus subtilis YPEB.
Pfam PF20075: Domain of unknown function (DUF6471) (domain)
This domain of unknown function is found in uncharacterised proteins from bacteria (predominantly Proteobacteria) and eukaryotes. This domain is approximately 60 amino acids in length. There is a conserved motif KxxRG and a highly conserved L residue. It may be a DNA-binding domain.
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 PF00703: Glycosyl hydrolases family 2 (domain)
This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.
Wikipedia: In molecular biology, Glycoside hydrolase family 2 is a family of glycoside hydrolases EC 3.2.1., which are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of &gt;100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Pfam PF20304: Small protein from certain CxC ATPase-based DNA modification systems (family)
Analogous to an antitoxin, this small protein potentially acts as a negative regulatory component that might sense the presence of invaders by acting as a binding factor or substrate for invader-encoded enzymes like viral peptidases in certain CxC ABC ATPase-based DNA modification systems.
Pfam PF24213: Family of unknown function (DUF7434) (family)
This entry represents a small family of uncharacterised mycobacterial phage proteins. Structure prediction suggests that this protein forms a single alpha helix. It is quite hydrophobic with a negatively charged C-terminus. Some proteins are annotated as RDF proteins but there does not appear to be any evidence to support their function as recombination directionality factors.
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 PF18841: Beta solenoid repeat from Dextranase (repeat)
The crystal structures of Dex49A from Penicillium minioluteum and  of ATCC9642 isopullulanase from Aspergillus niger include  beta-solenoid repeats, sharing structural similarities. This Pfam  entry includes a single repeat unit of the repeat regions.
Pfam PF14569: Zinc-binding RING-finger (domain)
This RING/U-box type zinc-binding domain is frequently found in the catalytic subunit (irx3) of cellulose synthase. The enzymic class is [ec:2.4.1.12], whereby the synthase removes the glucose from UDP-glucose and adds it to the growing cellulose, thereby releasing UDP. The domain-structure is treble-clef like (PDB:1weo).
Wikipedia: A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells. Xenopus laevis TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein followed soon thereafter by the Krüppel factor in Drosophila. It often appears as a metal-binding domain in multi-domain proteins.
Pfam PF20854: LED repeat (repeat)
This entry represents a six residue tandem repeat found in Cerebellar degeneration-related antigen 1 (CDR1) from human. It is rich in Glu and Asp and usually flanked on the N-terminal by hydrophobic residues (Leu/Phe) and on the C-terminal by an aliphatic residue followed by and Asp residue.
Pfam PF22855: DNA (cytosine-5-)-methyltransferase, N-terminal (domain)
This entry represents the N-terminal domain of DNA (cytosine-5) -methyltransferase 3A from mouse, which is required for genome- wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. The dimethylation of lysine 44 in this domain represents a molecular link between the mechanisms that establish DNA methylation and H3K9 methylation.
Pfam PF22875: Glu2-Pro domain (domain)
This entry represents a novel glutamic protease unique to a few members of the family Secoviridae, such as Strawberry Mottle Virus (SMoV), which suggests it is a recent acquisition in the evolution of this family. This is a second protease required for processing of SMoV polyproteins. It has two highly conserved glutamic acid residues spaced by 82 residues that are strictly required for protease activity. This domain is predicted to share structural similarities fungal and bacterial glutamic proteases that adopt a lectin fold.
Pfam PF20827: PCF11, charged region (domain)
This entry represents the charged region found in the Pre-mRNA cleavage complex 2 protein (Pcf11) from human and the orthologues from vertebrates. PCF11 is a subunit and an essential component of the pre-mRNA cleavage complex II (CFII), the orthologue of yeast cleavage and polyadenylation factor IA (CFIA), which is involved in pre-mRNA 3' end processing and in transcription termination. PCF11-mediated termination is essential for vertebrate development.
Pfam PF11925: Protein of unknown function (DUF3443) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 400 to 434 amino acids in length. This protein has two conserved sequence motifs: NPV and DNNG.
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 PF07981: Plasmodium repeat_MYXSPDY (repeat)
This repeat is found in two hypothetical Plasmodium proteins.
Pfam PF04978: Protein of unknown function (DUF664) (family)
This family is commonly found in Streptomyces coelicolor and is of unknown  function. These proteins contain several conserved histidines at their N-terminus that may form a metal binding site.
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 PF19591: Family of unknown function (DUF6096) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and phage. Proteins in this family are typically between 124 and 138 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 PF21453: Infectious salmon anemia virus nucleoprotein, helical bundle (domain)
This entry represents the helical bundle of Infectious salmon anemia virus (ISAV) nucleoprotein that forms the head domain described in. The head and body domains from this protein affect the equilibrium-state RNA binding.
Pfam PF15917: Piezo TM25-28 (domain)
Piezo is a family of proteins that form mechanosensitive non-specific cation channels whose conductance is higher for Li+, intermediate for Na+ and lowest for Li+. Divalent ions except for Mn2+ permeate the channel but more slowly than monovalent ions and can reduce K+ currents. These channels have a homotrimeric three-blade propeller-shaped structure that use a cap-motion and plug-and-latch mechanism to gate their ion-conducting pathways. Each protomer consists of 38 TM helices (referred to THUs) that form unusual non-planar blades, and an extracellular cap-like structure ([pfam:PF12166]). This entry represents TM25-28, found in the central region of these proteins, following [pfam:PF24871] and associated with [pfam:PF12166] at the C-terminal.
Pfam PF09267: Dictyostelium STAT, coiled coil (coiled_coil)
Members of this family are found in Dictyostelium STAT proteins and adopt a structure consisting of four long alpha-helices, folded into a coiled coil. They are responsible for nuclear export of the protein.
Wikipedia: Members of the signal transducer and activator of transcription (STAT) protein family are intracellular transcription factors that mediate many aspects of cellular immunity, proliferation, apoptosis and differentiation. They are primarily activated by membrane receptor-associated Janus kinases (JAK). Dysregulation of this pathway is frequently observed in primary tumors and leads to increased angiogenesis which enhances the survival of tumors and immunosuppression. Gene knockout studies have provided evidence that STAT proteins are involved in the development and function of the immune system and play a role in maintaining immune tolerance and tumor surveillance.
Pfam PF14329: Domain of unknown function (DUF4386) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 214 and 245 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 PF19171: Family of unknown function (DUF5853) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Phycodnaviridae.
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 PF23085: PARP14, third RRM domain (domain)
This domain is found in human Protein mono-ADP- ribosyltransferase PARP14 and related proteins. PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins. In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation. The domain represented by this entry is an RRM domain found third in the human PARP14.
Pfam PF16474: Kinase non-catalytic C-lobe domain (domain)
The KIND domain (kinase non-catalytic C-lobe domain) evolved from a catalytic protein kinase fold and functions as an interaction domain. In SPIRE1 (protein spire homologue 1) this domain interacts with FMN2 (formin-2).
Pfam PF07292: Nmi/IFP 35 domain (NID) (domain)
This family represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi). This domain mediates Nmi-Nmi protein interactions and subcellular localisation. This domain is predicted to constitute a region that is swapped between tandem of RRM domains.
Pfam PF09645: F-112 protein (domain)
F-112 protein is of 70-110 residues and is found in viruses. Its winged-helix structure suggests a DNA-binding function.
Pfam PF17492: Delta Ctenitoxins (family)
This family includes peptides isolated from Phoneutria such as delta-ctenitoxins. Members of the CNTX-Pn1a family and its paralogs (delta-CNTX-Pn1b through delta-CNTX-Pn1e) of Phoneutria toxins have complex effects on sodium channels but their primary effect appears to be an inhibition of channel inactivation, a pharmacology similar to that of the delta-atracotoxins and delta-conotoxins. Orthologous toxins such as delta-CNTX-Pr1/PK1 and Pn2 are also family members, some of which act by blocking the calcium channels. Delta-CNTX-Pn1a and delta-CNTX-PN2a are 48-amino-acid polypeptides, with 5 disulfide bridges. The later has a complex pharmacology that results in inhibition of NaV channel inactivation and a hyperpolarizing shift in the channel activation potential.
Pfam PF16405: Domain of unknown function (DUF5013) (family)
This small family of proteins is functionally uncharacterised. This family is found in various Bacteroides and Parabacteroides species. Proteins in this family are around 400 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 PF21387: Baseplate structural protein gp6, C-terminal domain I (domain)
Baseplate structural protein gp6 is located next to the tail tube and is an intermediate (or inner) baseplate protein involved in tail assembly. Two molecules of gp6 form a complex with gp25 and gp7 which is involved sheath contraction. This domain has been described as C-terminal domain I, and adopts a 2-layer beta-sandwich fold.
Pfam PF14826: FACT complex subunit SPT16 N-terminal lobe domain (domain)
The FACT or facilitator of chromatin transcription complex binds to and alters the properties of nucleosomes. This family represents the N-terminal lobe of the NTD, or N-terminal domain, and acts as a protein-protein interaction domain presumably with partners outside of the FACT complex. Knockout of the whole NTD domain, 1-450 residues in UniProt:P32558, in yeast serves to tender the cells sensitive to DNA replication stress but is not lethal. The C-terminal half of NTD is structurally similar to aminopeptidases, and the most highly conserved surface residues line a cleft equivalent to the aminopeptidase substrate-binding site, family peptidase_M24, [pfam:PF00557].
Pfam PF17800: Nucleoplasmin-like domain (domain)
The nucleoplasmin-like NPL domain is present in Drosophila FKBP39 and a large number of chromatin-related proteins .
Pfam PF08606: Prp19/Pso4-like (domain)
This regions is found specifically in PRP19-like protein. The region represented by this family covers the sequence implicated in self-interaction and a coiled-coiled motif.  PRP19-like proteins form an oligomer that is necessary for spliceosome assembly.
Pfam PF23640: SH3BP4 UPA domain (domain)
This domain is found in SH3 domain-binding protein 4 (SH3BP4) and related proteins such as Metastasis-associated in colon cancer protein 1 (MACC1). SH3BP4 binds and negative regulates Rag GTPase complex. This binding abrogates the interaction of mTORC1 with Rag GTPase complex and the recruitment of mTORC1 to the lysosome, thus inhibiting amino acid-induced mTORC1 activation and cell growth and promoting autophagy. MACC1 acts as a transcription activator for MET and as a key regulator of HGF-MET signaling. It promotes cell motility, proliferation and tumor growth and metastasis in vivo. The domain represented by this entry is predicted to fold into a a beta-sandwich with Ig-like topology and significant similarity to UPA domain.
Pfam PF17462: Family of unknown function (DUF5424) (family)
This is a family of unknown function specific to Rickettsia amblyommii.
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 PF08229: ER membrane protein SH3 (domain)
This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs).  SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER.