SII-SWORD/CoKE huggingface dataset:
Pfam PF06054: Competence protein CoiA-like family (family)
Many of the members of this family are described as transcription factors.  CoiA falls within a competence-specific operon in  Streptococcus.  CoiA is an uncharacterised protein.
Pfam PF03775: Septum formation inhibitor MinC, C-terminal domain (repeat)
In Escherichia coli [swissprot:P06138] assembles into a Z ring at midcell while assembly at polar sites is prevented by the min system. MinC [swissprot:P18196] a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with MinDE. MinC is an oligomer, probably a dimer. The C terminal half of MinC is the most conserved and interacts with MinD.  The N terminal half is thought interact with FtsZ.
Pfam PF19565: Family of unknown function (DUF6087) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a  protein from the kanamycin biosynthetic gene cluster from  Streptomyces kanamyceticus.
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 PF02981: FokI, recognition domain, subdomain 1 (domain)
Type IIS restriction endonuclease FokI is a member of an unusual class of bipartite restriction enzymes that recognises the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand. FokI contains amino- and carboxy-terminal domains corresponding to the DNA- recognition and cleavage functions, respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix- containing DNA-binding domain of the catabolite gene activator protein CAP. This entry represents the subdomain D1 of FokI. Subdomain D1 of the recognition domain covers the DNA major groove, recognizing base pairs at the 3' end of the recognition sequence (GGATG).
Pfam PF07286: D-glutamate cyclase (family)
This family includes mitochondrial D-glutamate cyclase which converts D-glutamate to 5-oxo-D-proline. This family also includes numerous uncharacterised proteins from bacteria.
Pfam PF00809: Pterin binding enzyme (domain)
This family includes a variety of pterin binding enzymes that all adopt a TIM barrel fold. The family includes dihydropteroate synthase [ec:2.5.1.15] as well as a group methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) [swissprot:Q46389] that catalyses a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. It transfers the N5-methyl group from methyltetrahydrofolate (CH3-H4folate) to a cob(I)amide centre in another protein, the corrinoid iron-sulfur protein. MeTr is a member of a family of proteins that includes methionine synthase and methanogenic enzymes that activate the methyl group of methyltetra-hydromethano(or -sarcino)pterin.
Wikipedia: Dihydropteroate synthase (DHPS) is an enzyme classified under EC 2.5.1.15. It produces dihydropteroate in bacteria, but it is not expressed in most eukaryotes including humans. This makes it a useful target for sulfonamide antibiotics, which compete with the PABA precursor.(2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate + 4-aminobenzoate (PABA)  diphosphate + dihydropteroate.
Pfam PF08502: LeuA allosteric (dimerisation) domain (domain)
This is the C-terminal regulatory (R) domain of alpha-isopropylmalate synthase, which catalyses the first committed step in the leucine biosynthetic pathway. This domain, is an internally duplicated structure with a novel fold. It comprises two similar units that are arranged such that the two -helices pack together in the centre, crossing at an angle of 34 degrees, sandwiched between the two three-stranded, antiparallel beta-sheets. The overall domain is thus constructed as a beta-alpha-beta three-layer sandwich.
Pfam PF20992: Nuclear cap binding complex subunit CBP66 second domain (domain)
This entry represents the second domain of the CBP66 component of the trypanasome nuclear cap binding complex. Trypanosomes have a different cap 4 structure for mRNAs. CBP66 is part of the complex that recognises this cap.
Pfam PF00661: Paramyxoviridae matrix protein N-terminal domain (domain)
This entry represents the N-terminal domain found in a variety of paramyxoviruses such as Morbillivirus, paramyxovirus, pneumovirus M proteins. The N-terminal domain of the NDV matrix protein consists of residues 1-181. It adopts a beta-sandwich fold in which the beta-strands in the opposing beta-sheets are approximately orthogonal to each other. Several alpha-helices are situated mostly on the surface of this beta-sandwich domain. The N-terminal domain is connected to a C-terminal domain with similar fold via a 16 amino acid linker. The two domains are related by an approximate fourfold rotation axis coincident with the twofold axis of the matrix protein dimer. The matrix protein dimer represents the physiologically relevant assembly unit. The N-terminal domain contributes to the highly positively charged surface that faces the viral membrane, enabling association with the negatively charged membrane.
Wikipedia: Viral matrix proteins are structural proteins linking the viral envelope with the virus core. They play a crucial role in virus assembly, and interact with the RNP complex as well as with the viral membrane. They are found in many enveloped viruses including paramyxoviruses, orthomyxoviruses, herpesviruses, retroviruses, filoviruses and other groups.
Pfam PF20506: Family of unknown function (DUF6732) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 73 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 PF24486: Domain of unknown function (DUF7583) (domain)
This is an Ig-like domain found in a group of uncharacterised sequences from nematodes. 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 PF14571: Stress-induced protein Di19, C-terminal (family)
C-terminal domain of Di19, a protein that increases the sensitivity of plants to environmental stress, such as salinity, drought, osmotic stress and cold. the protein is also induced by an increased supply of stress-related hormones such as abscisic acid ABA and ethylene. There is a zinc-finger at the N-terminus, zf-Di19, [pfam:PF05605].
Pfam PF06119: Nidogen-like (family)
This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function.
Pfam PF02590: Predicted SPOUT methyltransferase (family)
This family of proteins are predicted to be SPOUT methyltransferases.
Pfam PF00797: N-acetyltransferase (family)
Arylamine N-acetyltransferase (NAT) is a cytosolic enzyme of approximately 30kDa. It facilitates the transfer of an acetyl group from Acetyl Coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (M. tuberculosis, M. smegmatis etc) to man. It was the first enzyme to be observed to have polymorphic activity amongst human individuals. NAT is responsible for the inactivation of Isoniazid (a drug used to treat Tuberculosis) in humans. The NAT protein has also been shown to be involved in the breakdown of folic acid.
Wikipedia: An acetyltransferase is any of a class of transferase enzymes that transfers an acetyl group in a reaction called acetylation. In biological organisms, post-translational modification of a protein via acetylation can profoundly transform its functionality by altering various properties like hydrophobicity, solubility, and surface attributes. These alterations have the potential to influence the protein's conformation and its interactions with substrates, cofactors, and other macromolecules.
Pfam PF10877: Protein of unknown function (DUF2671) (family)
This family of proteins with unknown function appears to be restricted to Rickettsia spp.
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 PF04772: Influenza B matrix protein 2 (BM2) (family)
M2 is synthesised in the late phase of infection and incorporated into the virion.  It may be phosphorylated in vivo. The function of BM2 is unknown.
Wikipedia: The Matrix-2 (M2) protein is a proton-selective viroporin, integral in the viral envelope of the influenza A virus. The channel itself is a homotetramer, where the units are helices stabilized by two disulfide bonds, and is activated by low pH. The M2 protein is encoded on the seventh RNA segment together with the M1 protein. Proton conductance by the M2 protein in influenza A is essential for viral replication.
Pfam PF18042: ORF 12 gene product N-terminal (domain)
This is the N-terminal domain of Streptomyces clavuligerus ORF 12 gene product, which is directly involved in biosynthesis of Clavulanic acid (CA). The N-terminal domain consists of one four-stranded antiparallel beta-sheet surrounded by four alpha-helices and folds similarly to steroid isomerases and polyketide cyclases (PKTC). However, the N-terminal domain has no apparent polar-lined active-site pocket or conserved catalytic residues analogous to those of either the steroid isomerases or PKTCs. ORF 12 has 2 binding sites, CA is able to bind both to an active site and between the two domains. The active site pocket is lined by residues from both the N- and the C-terminal domains (His88, Ser173, Thr209, Ser234, Ser278, Met383, Phe374, Ala376 and Phe385). The C-2 carboxylate of CA is positioned deep in the pocket, making electrostatic interactions with Lys375, Arg418 and Lys89. Lys89 is located in strand beta-2 of the N-terminal domain and may also be involved in the beta-lactam core-binding region, including the residues Lys89 as well as Arg418.
Pfam PF03537: Glycoside-hydrolase family GH114 (domain)
This family is recognised as a glycosyl-hydrolase family, number 114. It is endo-alpha-1,4-polygalactosaminidase, a rare enzyme. It is proposed to be TIM-barrel, the most common structure amongst the catalytic domains of glycosyl-hydrolases.
Wikipedia: In biochemistry, glycoside hydrolases are a class of enzymes which catalyze the hydrolysis of glycosidic bonds in complex sugars. They are extremely common enzymes, with roles in nature including degradation of biomass such as cellulose (cellulase), hemicellulose, and starch (amylase), in anti-bacterial defense strategies, in pathogenesis mechanisms and in normal cellular function. Together with glycosyltransferases, glycosidases form the major catalytic machinery for the synthesis and breakage of glycosidic bonds.
Pfam PF03272: Putative mucin or carbohydrate-binding module (domain)
This family is the putative binding domain for the substrates of enhancin, and other similar metallopeptidases. This is not the enzymically active, peptidase, part of the proteins - see [pfam:PF13402].
Pfam PF12235: Fragile X-related 1 protein core C terminal (family)
This domain family is found in eukaryotes, and is typically between 126 and 160 amino acids in length. The family is found in association with [pfam:PF05641], [pfam:PF00013]. This family is the core C terminal region of the fragile X related 1 proteins FXR1P, FXR2 and FMR1. These different proteins have different regions at their very C-terminus. The Glutamine-arginine rich region facilitates protein interactions. This family contains two blocks of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs.
Pfam PF05233: PHB accumulation regulatory domain (domain)
The proteins this domain is found in are typically  involved in regulating polymer accumulation in bacteria, particularly poly-beta-hydroxybutyrate (PHB). The  N-terminal region is likely to be the DNA-binding domain ([pfam:PF07879]) while this domain probably binds PHB (personal obs:C Yeats).
Pfam PF21533: Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region (domain)
Histone-lysine N-methyltransferase EHMT1/EHMT2 mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. They interact to form an heterodimer. EHTM1 and EHTM2 contain ankyrin repeats (eight and seven ankyrin repeats, respectively), which bind the monomethylated RELA subunit of NF-kappa-B,  a SET domain which interacts with WIZ and a pre-SET domain that binds three zinc ions via cysteine residues. This entry represents a cysteine-rich region (CRR) found in the middle of the sequence, which is unique to EHTM1/2 and mediates protein-protein interactions and recruitment of the methyltransferases to specific sites in chromatin. This domain adopts an unusual compact fold with four bound zinc atoms that contains an embedded RING domain, which represents a novel zinc-binding motif.
Pfam PF23075: Zinc finger protein 462, C2H2 zinc finger (domain)
This domain is found in the human Zinc finger protein 462 and related proteins. This protein is involved in transcription by regulating chromatin structure and organisation. ZNF462 is a multidomain proteins that contains a number of classical C2H2 zinc fingers. This entry represents one of them.
Pfam PF24289: Domain of unknown function (DUF7477) (repeat)
This entry represents a domain consisting of a novel repeat fold which containing five repeats, each of them comprising three antiparallel beta-strands and a short alpha-helix, according to structure predictions (e.g SwissProt:S8CFV9). This domain is found in Casein kinase 1-like protein HD16 from rice, a protein involved in the regulation of flowering time through gibberellin (GA) signaling and independently of photoperiod.
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 PF23242: TRIP13-like, AAA+ ATPase lid C-terminal domain (domain)
This domain is found at the C-terminal end of human Pachytene checkpoint protein 2 homolog (TRIP13) and similar eukaryotic proteins. It is normally found associated to [pfam:PF00004] and is predicted to show an alpha-helical configuration.
Pfam PF11748: Protein of unknown function (DUF3306) (family)
This family of proteobacterial species 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 PF18390: Glycogen debranching enzyme C-terminal domain (domain)
This is the C-terminal domain of the glycogen debranching enzyme GlgX. GlgX hydrolyzes alpha-1,6-glycosidic linkages of phosphorylase-limit dextrin containing only three or four glucose subunits produced by glycogen phosphorylase. Sequence analysis suggests that GlgX is a debranching enzyme belonging to the glycoside hydrolase GH-13 family in the CAZy database.
Wikipedia: In molecular biology, glycoside hydrolase family 13 is a family of glycoside hydrolases.
Pfam PF11977: Zc3h12a-like Ribonuclease NYN domain (domain)
This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes. It has been suggested that this domain belongs to the PIN domain superfamily. This domain has also been identified as part  of the NYN domain family.
Pfam PF02984: Cyclin, C-terminal domain (domain)
Cyclins regulate cyclin dependent kinases (CDKs). [swissprot:P22674] is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the C-terminal domain.
Wikipedia: Cyclins are proteins that control the progression of a cell through the cell cycle by activating cyclin-dependent kinases (CDK).
Pfam PF02676: Methyltransferase TYW3 (family)
The methyltransferase TYW3 (tRNA-yW- synthesising protein 3) has been identified in yeast to be involved in wybutosine (yW) biosynthesis.  yW is a complexly modified guanosine residue that contains a tricyclic base and is found at the 3' position adjacent the anticodon of phenylalanine tRNA.  TYW3 is an N-4 methylase that methylates yW-86 to yield yW-72 in an Ado-Met-dependent manner.
Pfam PF04862: Protein of unknown function (DUF642) (domain)
This family represents a duplicated conserved region found in a number of uncharacterised plant proteins, potentially in the stem. There is a conserved CGP sequence motif.
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 PF01576: Myosin tail (coiled_coil)
The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.
Pfam PF04827: Plant transposon protein (family)
This family contains plant transposases which are putative members of the PIF / Ping-Pong family.
Pfam PF21980: Condensin complex protein MksE (family)
This entry represents a small family of MksE proteins. These proteins are part of MksBEF complex, which primarily function in structural chromosome maintenance. The N-terminal part of MksE is remotely related to the chromosome partition protein MukE and most likely adopts the same structure that consists of two winged helix domains (WHD).
Pfam PF19104: Family of unknown function (DUF5791) (family)
This is a family of proteins of unknown function predominantly found in Halobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF22334: Phage tubulin-like protein, C-terminal domain (domain)
This domain is found at the C-terminal end of Phage tubulin-like protein from the Pseudomonas phage phiKZ (TubZ) and similar viral sequences. TubZ is a tubulin-like GTPase that forms filaments, which are required for positioning viral DNA and capsids in the middle of the host cell for optimal replication. This protein adopts a tubulin/FtsZ protein family fold organised into two domains, a canonical N-terminal GTP-binding domain, and a C-terminal GTPase activation domain (this entry). This domain shows an alpha-beta structure.
Pfam PF09061: Stirrup (domain)
The Stirrup domain, found in the prokaryotic protein ribonucleotide reductase, has a molecular mass of 9 kDa and is folded into an alpha/beta structure. It allows for binding of the reductase to DNA via electrostatic interactions, since it has a predominance of positive charges distributed on its surface.
Wikipedia: In molecular biology, the protein domain Stirrup is a domain, found only in found in the domain, archaea. The Stirrup protein domain is found in prokaryotic protein ribonucleotide reductases. It obtains its name due to its resemblance to an old fashioned Japanese stirrup. Stirrip has a molecular mass of 9 kDa and is folded into an alpha/beta structure. It allows for binding of the reductase to DNA via electrostatic interactions, since it has a predominance of positive charges distributed on its surface.
Pfam PF21714: Circadian clock protein KaiA, N-terminal domain (domain)
This domain is found at the N-terminal end of Circadian clock protein KaiA from Synechococcus elongatus and similar bacterial proteins. KaiA is essential for circadian timekeeping. This protein organised into two domains. This entry represents the a pseudo-receiver domain, which has a similar fold with that of bacterial response regulators, with an alpha-beta structure.
Pfam PF23496: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7AMF2] from the parasite Babesia bovis.
Pfam PF22704: Alpha-galactosidase, CBM13 domain (domain)
This is a carbohydrate-binding module family 13 domain that is found in homologues of Alpha-galactosidase.
Pfam PF01349: Flavivirus non-structural protein NS4B (family)
Flaviviruses encode a single polyprotein.                 This is cleaved into three structural and seven non-structural proteins. The NS4B protein is small and poorly conserved among the Flaviviruses. NS4B contains multiple hydrophobic potential membrane spanning regions.  NS4B may form membrane components of the viral replication complex and could be involved in membrane localisation of NS3 and [pfam:PF00972].
Pfam PF16841: Ca-dependent carbohydrate-binding module xylan-binding (domain)
CBM60 is a family of xylan-binding modules found in conjunction with xylanase enzymes in many bacterial species that attack plant cell walls. Xylan is the major hemicellulose component of most plant cell walls, and is one of the most complex carbohydrates targeted by CBMs. CBM60 modules are evolutionarily related to CBM36 domains as both show circular permutation in the beta-barrel folds.  CBM60 targets xylan but is also able to bind cellulose and galactan and thus contribute towards breakdown of the plant cell wall. Recognition of the ligand is conferred primarily through the polar interactions of O2 (oxygen) and O3 of a single sugar with a protein-bound calcium ion.