SII-SWORD/CoKE huggingface dataset:
Pfam PF02305: Capsid protein (F protein) (domain)
This is a family of proteins from single-stranded DNA bacteriophages. Protein F is the major capsid component, sixty copies of which are found in the virion.
Pfam PF04177: TAP42-like family (repeat)
The TOR signalling pathway activates a cell-growth program in response to nutrients. TIP41 ([pfam:PF04176]) interacts with TAP42 and negatively regulates the TOR signaling pathway.
Pfam PF10191: Golgi complex component 7 (COG7) (repeat)
COG7 is a component of the conserved oligomeric Golgi complex which is required for normal Golgi morphology and localisation. Mutation in COG7 causes a congenital disorder of glycosylation.
Pfam PF17175: Modulator of levamisole receptor-1 (family)
MOLO1 is a one-pass transmembrane protein that contains a single extracellular globular domain. It is a positive regulator of levamisole-sensitive acetylcholine receptors in Caenorhabditis elegans, UniProtKB:Q19280. These receptors are Cys-loop ligand-gated ion channels, and the MOLO1 domain is an auxiliary subunit of the gated channel. The proteins carry a Rossmann fold.
Pfam PF08275: DNA primase catalytic core, N-terminal domain (domain)
DNA primase (DNAG) is a a nucleotidyltransferase which synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division. Primases comprise three domains: a zinc-binding domain at the N-terminal ([pfam:PF01807]), a polymerase domain (catalytic core), and a domain that interacts with the replicative helicase ([pfam:PF01807]). The catalytic core consists of an alpha+beta domain at the N-terminal (this entry) and a TOPRIM domain at the C-terminal ([pfam:PF13155]).
Wikipedia: DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA segment called a primer complementary to a ssDNA template. After this elongation, the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA.
Pfam PF12197: LCI fold (domain)
This domain is found in bacteria, and is approximately 40 amino acids in length. This domain is found in bacillus cereus group bacteria and functionally related to antimicrobial activity. It has been reported linked to CHAP, PGBD and SH3 domains in a putative cysteine protease. This domain consists of three antiparallel beta-strands in a beta1-beta3-beta2 topology.
Pfam PF08576: Eukaryotic protein of unknown function (DUF1764) (family)
This is a family of eukaryotic proteins of unknown function. This family contains many hypothetical proteins.
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 PF12209: Leucine permease transcriptional regulator helical domain (domain)
This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found in association with [pfam:PF03399]. This domain is a helical domain in the middle of leucine permease transcriptional regulator.
Pfam PF10580: Gap junction protein N-terminal region (domain)
Neuromodulin (also known as growth-associated protein 43 or GAP-43) is a component of the motile growth cones. It is membrane protein whose expression is widely correlated with successful axon elongation . It is a crucial component of an effective regeneration response in the nervous system . Although its function is uncertain, the N-terminal region is well conserved and contains both a calmodulin binding domain, and sites for acylation, membrane attachment and protein kinase C phosphorylation. Structure predictions suggest that the C-terminal region may exist as an extended, negatively-charged rod with some similarity to the side arms of neurofilaments, indicating that the biological role of neuromodulin may depend on its ability to form a dynamic membrane-cytoplasm-calmodulin complex .
This entry represents the neuromodulin N-terminal domain.
Pfam PF19306: Large helicase-related protein, winged helix domain (domain)
This domain is found in Large helicase-related protein from Escherichia coli (Lhr), DEAD/DEAH box helicase from Mycolicibacterium smegmatis ([swissprot:A0QT91]) and similar prokaryotic sequences. Lhr is a DNA damage-inducible superfamily 2 helicase that uses adenosine triphosphate (ATP) hydrolysis to drive unidirectional 3' to 5' translocation along single -stranded DNA (ssDNA). These proteins have an N-terminal helicase domain (Lhr-Core) and a C-terminal domain (Lhr-CTD). This entry represents the third domain in the Lhr-Core, which has a winged helix (WH) domain fold. It is found associated to [pfam:PF00270] and [pfam:PF00271].
Pfam PF08055: Tryptophan leader peptide (family)
This family consists of the tryptophan (trp) leader peptides. Tryptophan accumulation is the principal event resulting in downregulation of transcription of the structural genes of the trp operon. The leader peptide of the trp operon forms mutually exclusive secondary structures that would either result in the termination of transcription of the trp operon when tryptophan is in plentiful supply or vice versa.
Pfam PF23783: TiaS C-terminal zinc ribbon domain (domain)
This entry represents the zinc ribbon domain (ZRD) found at the the C-terminal of tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS. TiaS is an archaeal ATP-dependent agmatine transferase that catalyses the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2). This modified base specifically recognises AUA codons. TiaS consists of four domains, the TCKD domain ([pfam:PF22641]) at the N-terminal followed by the FLD domain ([pfam:PF08489]), an OB fold domain and a C-terminal ZRD. The ZDR domain is responsible for the recognition of the acceptor arm of tRNA(Ile2).
Pfam PF17180: Zinc-binding domain (domain)
This domain is found in homologues of human ZCCHC24 protein. It is predicted to adopt zinc ribbon fold.
Pfam PF09943: Uncharacterized protein conserved in archaea (DUF2175) (family)
This domain, found in various hypothetical archaeal 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 PF20680: Domain of unknown function (DUF6817) (domain)
This presumed domain is functionally uncharacterised, found in bacteria and plants. It is approximately 160 amino acids in length and it has two conserved sequence motifs, HL and GLxHxxY. Several members of this entry also has TPR regions.
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 PF22808: RhopH3 C-terminal domain (domain)
This domain is found C-terminal in homologues of RhopH3. RhopH3 is conserved and restricted to Plasmodium spp. and it is a component of the RhopH complex that is essential for the pathogen erythrocyte invasion and for remodelling its host cells to achieve tissue adherence and nutrient acquisition.
Pfam PF05436: Mating factor alpha precursor N-terminus (family)
This family contains the N-terminal regions of the Saccharomyces mating factor alpha precursor protein. All proteins in this family contain one or more copies [pfam:PF04648] further toward their C terminus.
Pfam PF19885: Family of unknown function (DUF6358) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 62 and 77 amino acids in length. There are two conserved sequence motifs: FILN and VVLIYLK. This family is related to [pfam:PF17259].
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 PF21444: CofB, pilin domain (domain)
This domain is found in CofB from Escherichia coli and in similar proteins predominantly from proteobacteria. CofB is a minor pilin, required for assembly of Type IV pili. This entry represents the pilin domain, which is located in the N-terminal region of the protein. It shows a canonical T4b pilin fold seen in the major pilins, with an alpha-helical backbone and a five-stranded anti- parallel beta-sheet.
Pfam PF21280: Archaeal helicase, domain 4 (domain)
This entry includes archaeal helicases from the helicase superfamily 2, and represents domain 4 described in. This domain folds into a seven alpha-helix bundle structure and seems to be unique within this helicase family. The central helix acts as a ratchet and mediates stacking interactions on base moieties of the DNA.
Pfam PF19872: Family of unknown function (DUF6345) (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, in particular the  kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. This family appears to be predominantly found in bacteria and  archaea.
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 PF04138: GtrA/DPMS, transmembrane domain (domain)
Members of this entry are  integral membrane proteins with three or four transmembrane spans. They are involved in the synthesis of cell surface polysaccharides. The GtrA family are a subset of this family. GtrA is predicted to be an integral membrane protein with 4 transmembrane spans. It is involved is in O antigen modification by Shigella flexneri bacteriophage X (SfX), but does not determine the specificity of glucosylation.  Its function remains unknown, but it may play a role in translocation of undecaprenyl phosphate linked glucose (UndP-Glc) across the cytoplasmic membrane. Another member of this family is a DTDP-glucose-4-keto-6-deoxy-D-glucose reductase, which catalyses the conversion of dTDP-4-keto-6-deoxy-D-glucose to dTDP-D-fucose, which is involved in the biosynthesis of the serotype-specific polysaccharide antigen of Actinobacillus actinomycetemcomitans Y4 (serotype b). This family also includes the teichoic acid glycosylation protein, GtcA, which is a serotype-specific protein in some Listeria innocua and monocytogenes strains.  Its exact function is not known, but it is essential for decoration of cell wall teichoic acids with glucose and galactose.
Pfam PF19972: Ternary complex associated domain 3 (domain)
Novel uncharacterised protein domain found associated with the vWA-MoxR-VMAP ternary systems
Pfam PF11108: Viral glycoprotein L (family)
GL forms a complex with gH, a glycoprotein known to be essential for entry of HSV-1 into cells and virus-induced cell fusion. It is a hetero-oligomer of gH and gL which is incorporated into virions and transported to the cell surface which acts during entry of virus into cells
Pfam PF18024: Helix-turn-helix domain (domain)
The TyrR protein of Haemophilus influenzae is a 36-kD transcription factor whose major function is to control the expression of genes important in the biosynthesis and transport of aromatic amino acids. This entry represents the C-terminal helix-turn-helix DNA-binding domain of TyrR and related proteins.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF18702: Domain of unknown function (DUF5642) (domain)
This is a domain of unknown function found in actinobacteria.
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 PF06044: Dam-replacing family (family)
Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements.  The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis.
Pfam PF03585: Herpesvirus ICP4-like protein C-terminal region (family)
The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection.  ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer.  ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the C-terminal region that probably acts as an enhancer for the N-terminal region.
Pfam PF22439: Turkey Adenovirus 3 Fibre protein-like, head domain (domain)
This entry represents the C-terminal Head Domain of the Fibre protein from Turkey Adenovirus 3, also known as turkey hemorrhagic enteritis virus (THEV) ([swissprot:Q2TLC1]).
Pfam PF02197: Regulatory subunit of type II PKA R-subunit (domain)
Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity :


 * Serine/threonine-protein kinases
 * Tyrosine-protein kinases
 * Dual specificity protein kinases (e.g. MEK -phosphorylates both Thr and Tyr on target proteins)


Protein kinase function is evolutionarily conserved from Escherichia coli to human . Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases .
In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits . In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively.

Two types of regulatory (R) subunits exist -types I and II -which differ in molecular weight, sequence, autophosphorylation capability, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents the dimerization-anchoring domain of types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins.The dimerization-anchoring domain is located within the first 45 residues of each regulatory subunit, and forms a high affinity binding site for A-kinase-anchoring proteins (AKAPs) .
Pfam PF03997: VPS28 protein (family)
The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, Vps23, Vps28, and Vps37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions .
Pfam PF18781: Phage spike trimer (repeat)
This Pfam entry includes some phage spike repeats that fail to be  detected with the [pfam:PF18715] model.
Pfam PF10574: Arp2/3-interacting proteins Arpin (family)
This family includes proteins such as Arp2/3-interacting proteins (Arpin). Arpin regulates actin polymerization by inhibiting the actin-nucleating activity of the Arp2/3 complex. It induces cell turning by pausing cell migration.
Pfam PF19302: Domain of unknown function (DUF5915) (domain)
This presumed domain is found at the C-terminus of isoleucyl tRNA ligase enzymes.
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 PF13188: PAS domain (domain)
PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Heme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. This domain recognises oxygen and CO (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Wikipedia: A Per-Arnt-Sim (PAS) domain is a protein domain found in all kingdoms of life. Generally, the PAS domain acts as a molecular sensor, whereby small molecules and other proteins associate via binding of the PAS domain. Due to this sensing capability, the PAS domain has been shown as the key structural motif involved in protein-protein interactions of the circadian clock, and it is also a common motif found in signaling proteins, where it functions as a signaling sensor.
Pfam PF12938: M domain of GW182 (domain)
This entry represents the M (middle region) domain of GW182 . GW182 (also known as Gawky) plays a role in RNA-mediated gene silencing by micro-RNAs (miRNAs) .
Pfam PF15411: Pleckstrin homology domain (domain)
This Pleckstrin homology domain is found in some fungal species.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF19472: Family of unknown function (DUF6009) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000965) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a  protein from the C-1027 biosynthetic gene cluster from  Streptomyces globisporus.
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 PF24837: AMIN-like domain (domain)
This entry represents a family of extracellular likely lipoproteins that adopt a structure similar to the AMIN domain. However, there are some topological differences between the two families.
Pfam PF10573: Uncharacterised protein family UPF0561 (family)
This family of proteins has no known function.
Pfam PF20603: Bacterial hydrolase (family)
This family of proteins, found in bacteria, is thought to have a hydrolase activity.
Pfam PF09080: K cyclin, C terminal (domain)
Members of this family adopt a secondary structure consisting of a five alpha-helix cyclin fold. Interaction with cyclin dependent kinases (CDKs) at a PSTAIRE sequence motif within the catalytic cleft of CDK results in the regulation of CDK activity.
Wikipedia: Cyclins are proteins that control the progression of a cell through the cell cycle by activating cyclin-dependent kinases (CDK).
Pfam PF04126: Cyclophilin-like (family)
This domain has a cyclophilin-like fold, consisting of an eight-stranded beta-barrel with an alpha helix located between the beta-2 and beta-3 strands and a 310 helix located between the beta-7 and beta-8 strands. The catalytic site found in human cyclophilin is not conserved in this domain, suggesting a different function for this domain.
Pfam PF01731: Arylesterase (repeat)
This family consists of arylesterases (Also known as serum paraoxonase) [ec:3.1.1.2]. These enzymes hydrolyse organophosphorus esters such as paraoxon and are found in the liver and blood. They confer resistance to organophosphate toxicity. Human arylesterase (PON1) [swissprot:P27169] is associated with HDL and may protect against LDL oxidation.