SII-SWORD/CoKE huggingface dataset:
Pfam PF16871: Domain of unknown function (DUF5077) (family)
This family is found at the N-terminal of DUF3472, [pfam:PF00958].
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 PF22409: Topoisomerase V, HHH domain (domain)
This entry represents a helix-hairpin-helix (HHH) domain of topoisomerase V (Topo-V), the only member of a novel topoisomerase subtype. Topo-V is unique as it is a bifunctional enzyme carrying both topoisomerase and DNA repair lyase activities within the same protein. This prptein contains a topoisomerase domain at the N-terminal, followed byt twelve tandem helix-hairpin-helix (HhH)2 domains.
Pfam PF12535: Hydrolase of X-linked nucleoside diphosphate N terminal (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 847 and 5344 amino acids in length. These enzymes hydrolyse the molecular motif of a nucleoside diphosphate linked to some other moiety, X.
Pfam PF00753: Metallo-beta-lactamase superfamily (domain)
Metallo beta lactamases exhibit low sequence identity between enzymes but they are structurally similar. They have a characteristic Î±-Î²/Î²-Î± sandwich fold in which the active site is at the interface between domains. Apart from the beta-lactamases and metallo-beta-lactamases, a number of other proteins contain this domain and share the same fold type . These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.
Wikipedia: The metallo-β-lactamase (MBL) superfamily constitutes a group of proteins found in all domains of life that share a characteristic αββα fold with the ability to bind transition metal ions. Such metal binding sites may have divalent transition metal ions like Zn(II), Fe(II)/Fe(III) and Mn(II), and are located at the bottom of a wide cleft able to accommodate diverse substrates. The name was adopted after the first members of the superfamily to be studied experimentally: a group of zinc-dependent hydrolytic enzymes conferring bacterial resistance to β-lactam antibiotics. These zinc-β-lactamases (ZBLs) inactivate β-lactam antibiotics through hydrolysis of the β-lactam ring. Early studies on MBLs were conducted on the enzyme βLII isolated from strain 569/H/9 of Bacillus cereus. It was named βLII because it was the second β-lactamase shown to be produced by the bacterium; the first one, βLI, was a non-metallic β-lactamase, i.e., insensitive to inhibition with EDTA.
Pfam PF17171: Glutathione S-transferase, C-terminal domain (domain)
This domain is closely related to PF00043.
Wikipedia: Glutathione S-transferase, C-terminal domain  is a structural domain of glutathione S-transferase (GST).
Pfam PF03396: Poxvirus DNA-directed RNA polymerase, 35 kD subunit (family)
DNA-directed RNA polymerases 2.7.7.6 (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.

RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.

Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:


 * RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.
 * RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.
 * RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.


Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.
The DNA-dependent RNA polymerase from vaccinia virions has a molecular weight of approximately 500kDa and can be dissociated into putative subunits of 140, 137, 37, 35, 31, 22, and 17kDa. This group represents a DNA-directed RNA polymerase, 35kDa subunit.
Pfam PF05000: RNA polymerase Rpb1, domain 4 (domain)
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases).  This domain, domain 4, represents the funnel domain.  The funnel contain the binding site for some elongation factors.
Pfam PF14305: TupA-like ATPgrasp (family)
A member of the ATP-grasp fold predicted to be involved in the biosynthesis of cell surface polysaccharides such as the O-antigen  in proteobacteria, the capsule in firmicutes and the polyglutamate chain of teichuronopeptide.
Pfam PF07977: FabA-like domain (domain)
This enzyme domain has a HotDog fold.
Pfam PF08811: Protein of unknown function (DUF1800) (family)
This is a family of large bacterial 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 PF02915: Rubrerythrin (domain)
This domain has a ferritin-like fold.
Pfam PF12886: Transducer of regulated CREB activity, C terminus (family)
This family includes the C terminal region 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). The C terminus region is negatively charged, resembling the transcription activation domains. When this domain, from all three human TORC proteins, was expressed as fusion proteins with the DNA-binding domain of GAL4 (GAL4-BD), and tested for induction of a minimal promoter linked to GAL4-binding sites (UAS-GAL4), UAS-GAL4 was potently induced by GAL4-BD fusions containing the C-terminal portion of all three human TORCs.
Pfam PF19630: Domain of unknown function (DUF6134) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 210 and 241 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 PF22420: Macrophage Locus Protein A, C-terminal domain (domain)
This entry represents the Macrophage Locus Protein A (MglA) C-terminal domain from Francisella tularensis. MglA interact with both RNA polymerase (RNAP) and the pathogenicity island (FPI) gene regulator to activate FPI transcription.
Pfam PF21253: Mannanase, galactose-binding domain-like (domain)
This is a galactose-binding domain-like found at the C-terminal of alkaline mannanases, such as [swissprot:Q4W8M3] from  Bacillus sp. JAMB-602 and related bacterial sequences which belong to the Glycoside Hydrolase Family 5 ([pfam:PF00150]).
Pfam PF17467: Viral Protein E7 (family)
This domain family is found in Vaccinia and Variola viruses. Family members include E7R gene product. Vaccinia virus (VV) is a large double-stranded DNA virus that replicates in the cytoplasm of infected cells. Many viruses express proteins that are modified by myristic acid. Myristic acid is a 14-carbon fatty acid that is cotranslationally transferred to the penultimate glycine residue found within the consensus sequence MGXXX(S/T/A/C/N) (where X is any amino acid) at the amino terminus of target proteins. E7R proteins in Vaccina virus have been shown to be myristylated. The expressed E7R protein has also been found to reside within mature infectious virions.
Pfam PF06200: tify domain (domain)
This short possible domain is found in a variety of plant transcription factors that contain GATA domains as well as other motifs. Although previously known as the Zim domain this is now called the tify domain after its most conserved amino acids. TIFY proteins can be further classified into two groups depending on the presence (group I) or absence (group II) of a C2C2-GATA domain. Functional annotation of these proteins is still poor, but several screens revealed a link between TIFY proteins of group II and jasmonic acid-related stress response.
Pfam PF14207: DpnD/PcfM-like protein (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 57 and 153 amino acids in length. There are two completely conserved residues (E and A) that may be functionally important.
Pfam PF11106: Exopolysaccharide production protein YjbE (family)
YjbE is part of a four gene operon which is involved in exopolysaccharide production. The expression of YjbE is higher than the rest of the operon yjbEFGH. It appears to be restricted to Enterobacteriaceae. YbjE is one of four gene-products expressed from an operon, yjbEFGH, which is regulated by the Rcs phosphorelay in a RcsA-dependent manner, similar to that of other exopolysaccharide biosynthetic pathways. It is highly possible that the yjbEFGH operon encodes a system involved in EPS secretion since none of the products is predicted to have enzymic activity, the products are all secreted and YbjH and F are predicted to be beta-barrel lipoproteins similar to porins. It may be that the operon products play some role in biofilm formation and/or matrix production.
Pfam PF16432: Domain of unknown function (DUF5029) (family)
This family consists of several uncharacterized proteins around 550 in length and is mainly found in Bacteroides fragilis and sp. 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 PF04019: Protein of unknown function (DUF359) (family)
This family of archaebacterial proteins are about 170 amino acids in length.  They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its 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 PF18427: DD-reactivating factor swiveling domain (domain)
AdoCbl-dependent diol dehydratase (DD) (EC 4.2.1.28) is one of the enzymes that catalyzes the conversion of 1,2-propanediol, 1,2-ethanediol, and glycerol to the corresponding aldehydes. A DD-reactivating factor (DDR) is responsible for the rapid reactivation of the inactivated holoDD in the presence of AdoCbl, ATP, and Mg2+. DDR exists as a dimer of heterodimer (alpha-beta)2. The alpha subunit has four domains: ATPase domain, swiveling domain, linker domain, and insert domain. The beta subunit, composed of a single domain, has a similar fold to the beta subunit of diol dehydratase (DD). This entry describes the swiveling domain of DDR, which structurally connects the beta subunit and the ATPase domain of the other alpha subunit. Furthermore, the beta subunit moves with the swiveling domain while the linker domain acts as a flat spring or a hinge for the domain movement of the swiveling domain.
Pfam PF06939: Protein of unknown function (DUF1286) (family)
This family consists of several hypothetical archaeal proteins of around 120 residues in length. All members of this family seem to be Sulfolobus species specific. 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 PF01104: Bunyavirus non-structural protein NS-s (family)
The NS-s protein is encoded by the S RNA. This segment also encodes for the N protein.  These two proteins are encoded by overlapping reading frames.
Pfam PF20787: SPP1 phage GP23.1 (family)
Gp23.1 from Bacillus subtilis SPP1 phage adopts a hexamer assembly and is likely to function as a chaperone. This family of highly conserved sequences is predominantly found in phages with long non-contractile tails and in bacterial prophages.
Pfam PF20527: Domain of unknown function (DUF6742) (domain)
This presumed domain family is functionally uncharacterised. This domain is found in eukaryotes and is around  40 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 PF00454: Phosphatidylinositol 3- and 4-kinase (family)
Some members of this family probably do not have lipid kinase activity and are protein kinases, e.g. [swissprot:P42345].
Wikipedia: Phosphoinositide 3-kinases (PI3Ks), also called phosphatidylinositol 3-kinases, are a family of enzymes involved in cellular functions such as cell growth, proliferation, differentiation, motility, survival and intracellular trafficking, which in turn are involved in cancer.
Pfam PF04564: U-box domain (domain)
The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process. This domain is related to the Ring finger [pfam:PF00097] but lacks the zinc binding residues.
Pfam PF16782: Nucleotide exchange factor SIL1 (repeat)
This family consists of fungal SIL1 nucleotide-exchange factor proteins.It interacts with Hsp70 (heat-shock protein of 70 kDa) Bip.
Pfam PF21209: Alpha-rhamnosidase-like, bacteroidetes, N-terminal (domain)
This domain is found in a group of alpha-rhamnosidases predominantly from Bacteroidetes, including the putative alpha-rhamnosidase from Bacteroides thetaiotaomicron, whose structure shows similarity with a galactose-binding domain.
Pfam PF06181: Urate oxidase N-terminal (family)
Cytochrome c urate oxidase (Uox) PuuD is involved in purine degradation. In contrast with soluble Uox it is a membrane protein with an 8-helix transmembrane N-terminal domain and a C-terminal cytochrome c.
Pfam PF03380: Caenorhabditis protein of unknown function, DUF282 (family)
This family consists of proteins of unknown function found in Caenorhabditis 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 PF16890: Domain of unknown function (DUF5083) (family)
This protein is believed to be involved in the type VII secretion system.
Pfam PF17316: Perilipin protein (family)
This family includes Pet10p and Sps4p which are yeast perilipin proteins.
Pfam PF07023: Protein of unknown function (DUF1315) (family)
This family consists of several bacterial proteins of around 90 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 PF03921: Intercellular adhesion molecule (ICAM), N-terminal domain (domain)
ICAMs normally functions to promote intercellular adhesion and signalling. However, The N-terminal domain of the receptor binds to the  rhinovirus 'canyon' surrounding the icosahedral 5-fold axes,  during the viral attachment process. This family is a family that is part of the Ig superfamily and is therefore related to the family ig ([pfam:PF00047]).
Wikipedia: In molecular biology, intercellular adhesion molecules (ICAMs) and vascular cell adhesion molecule-1 (VCAM-1) are part of the immunoglobulin superfamily. They are important in inflammation, immune responses and in intracellular signalling events. The ICAM family consists of five members, designated ICAM-1 to ICAM-5. They are known to bind to leucocyte integrins CD11/CD18 such as LFA-1 and Macrophage-1 antigen, during inflammation and in immune responses. In addition, ICAMs may exist in soluble forms in human plasma, due to activation and proteolysis mechanisms at cell surfaces.
Pfam PF02749: Quinolinate phosphoribosyl transferase, N-terminal domain (domain)
Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase [ec:2.4.2.19] is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide. The QA substrate is bound between the C-terminal domain of one subunit, and the N-terminal domain of the other. The N-terminal domain has an alpha/beta hammerhead fold.
Pfam PF08211: Cytidine and deoxycytidylate deaminase zinc-binding region (family)
This region contains the zinc-binding domain of cytidine and deoxycytidylate deaminase.
Pfam PF08332: Calcium/calmodulin dependent protein kinase II association domain (domain)
This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII).  These proteins also have a Ser/Thr protein kinase domain ([pfam:PF00069]) at their N-terminus.  The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers.
Wikipedia: Ca2+/calmodulin-dependent protein kinase II is a serine/threonine-specific protein kinase that is regulated by the Ca2+/calmodulin complex. CaMKII is involved in many signaling cascades and is thought to be an important mediator of learning and memory. 
CaMKII is also necessary for Ca2+ homeostasis and reuptake in cardiomyocytes, 
chloride transport in epithelia, 
positive T-cell selection, 
and CD8 T-cell activation.
Pfam PF07273: Protein of unknown function (DUF1439) (family)
This family consists of several hypothetical bacterial proteins of around 190 residues in length. Several members of this family are annotated as being putative lipoproteins and are often known as YceB. 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 PF05603: Hikeshi-like, N-terminal domain (domain)
This domain is found at the N-terminal end of Protein Hikeshi from humans and its orthologues OPI10 from other eukaryotes. Hikeshi is an specific nuclear import carrier for HSP70 proteins following heat-shock stress, which is required to protect cells from heat- shock damages. The N-terminal domain shows a jelly-roll/beta- sandwich fold with two layers of beta-sheets consisting of three and five and five antiparallel beta-strands.
Wikipedia: HIKESHI is a protein important in lung and multicellular organismal development that, in humans, is encoded by the HIKESHI gene. HIKESHI is found on chromosome 11 in humans and chromosome 7 in mice. Similar sequences (orthologs) are found in most animal and fungal species. The mouse homolog, lethal gene on chromosome 7 Rinchik 6 protein is encoded by the l7Rn6 gene.
Pfam PF08152: GUCT (NUC152) domain (domain)
This is the C terminal domain found in the RNA helicase II / Gu protein family.
Pfam PF01063: Amino-transferase class IV (domain)
The D-amino acid transferases (D-AAT) are required by bacteria to  catalyse the synthesis of D-glutamic acid and D-alanine, which are  essential constituents of bacterial cell wall and are the building block for other D-amino acids.  Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity.