SII-SWORD/CoKE huggingface dataset:
Pfam PF04320: YggL 50S ribosome-binding protein (family)
This family represents bacterial proteins predominantly found in Gammaproteobacteria. YggL from E.coli has been characterised and it interacts with ribosome subunits 50S and 70S. It is a 50S-binding protein likely to be involved in particle assembly. It is a small protein extremely conserved in Gammaproteobacteria but also present in orders Burkholderiales and Neisseriales from Betaproteobacteria.
Pfam PF03274: Foamy virus BEL 1/2 protein (family)
Foamy virus (FV) gene expression is strictly dependent on their transactivator proteins called Bel1/Tas. The presence of a functionally active, internal promoter, besides the conventional LTR promoters, is unique to FVs. The nuclear Bel1/Tas protein of primate prototype FV binds DNA target sites directly and consists of at least two functional domains, an N-terminal/central DNA binding and a C-terminal activation domain .
Pfam PF19196: Family of unknown function (DUF5871) (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 PF17818: Keratinocyte-associated gene product (family)
This entry includes Keratinocyte-associated transmembrane protein 2 found in humans. Functional studies show that KCP2 localises to the endoplasmic reticulum, consistent with a role in protein biosynthesis, and has a functional KKxx retrieval signal at its cytosolic C-terminus.
Pfam PF22410: DNA primase DnaG, helical domain (domain)
DnaG from Aquifex aeolicus is a RNA polymerase that catalyses the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. This entry represents an helical domain found towards the C-terminal, after the TOPRIM domain.
Pfam PF24961: NfeD integral membrane domain (domain)
This entry represents the central integral membrane domain found in the NfeD protein.
Pfam PF08543: Phosphomethylpyrimidine kinase (family)
This enzyme [ec:2.7.4.7] is part of the Thiamine pyrophosphate (TPP) synthesis pathway, TPP is an essential cofactor for many enzymes.
Pfam PF18665: Tetracyclin repressor-like, C-terminal domain (domain)
IcaR belongs to the tetracycline repressor (TetR) family of proteins, which are involved in a wide variety of gene regulations. It binds to a 42 bp region immediately upstream of the icaA gene. This entry represents the C-terminal domain which is involved in dimerization.
Pfam PF16517: Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain (domain)
The Nore1-SARAH, C-terminal, domain of Nore1, the tumour-suppressor, a novel Ras effector, has a characteristic coiled-coil structure. It is a small helical module that is important in signal-transduction networks.  The recombinant SARAH domain of Nore1 crystallises as an anti-parallel homodimer with representative characteristics of coiled coils. The central function of the SARAH domain seems to be the mediation of homo- and hetero-oligomerisation between SARAH domain-containing proteins. Nore1 forms homo- and hetero complexes through its C-terminal SARAH (Sav/Rassf/Hpo) domain.
Pfam PF24790: SAC9 first GBDL domain (domain)
This domain is found toward the C terminus of the SAC9 from Arabidopsis thaliana which is a probable phosphoinositide phosphatase that is involved in modulating phosphoinositide signals during the stress response. SAC9 contains three domains (GBDL) with topology similar to the galactose binding domains (GBD), in particular to the anaphase promoting complex subunit 10. These domains are located in the second half of the protein. The domain represented by this entry is the first of the three.
Pfam PF15243: Anaphase-promoting complex subunit 15 (family)
This is a component of the anaphase promoting complex/cyclosome.
Pfam PF00948: Flavivirus non-structural Protein NS1 (family)
The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins.  Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication.
Pfam PF23647: Trafficking protein particle complex subunit 13, middle domain (domain)
Trafficking protein particle complex subunit 13 (TRAPPC13) is involved in regulating autophagy and survival in response to small molecule compound-induced Golgi stress. It is the mammal homologue of Trs65 from yeast, part of TRAPPII complex which interacts with COPI-coated vesicles in mammalian cells and aids in endosome-to-Golgi transport. This entry represents the middle domain of TRAPPC13 which may have a beta-sandwich fold.
Pfam PF11516: Protein of unknown function (DUF3220) (family)
This family of proteins with unknown function appears to be restricted to Bordetella.
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 PF23692: YmjE-like (family)
This protein family includes Protein YmjE from Escherichia coli, a 54-residues long sequence predicted to adopt an alpha helical configuration.
Pfam PF19617: Family of unknown function (DUF6122) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 104 and 120 amino acids in length. There are two conserved sequence motifs: HYG and RCSI.
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 PF12539: Chromosome segregation protein Csm1/Pcs1 (family)
Saccharomyces cerevisiae Csm1 is part of the monopolin complex. Csm1 forms a complex with Mde4 and promotes monoorientation during meiosis.  Csm1 also plays a mitotic role in DNA replication.  This family also contains the Schizosaccharomyces pombe homologue to Csm1, Pcs1.  Pcs1 forms a complex with Mde4 and acts in the central kinetochore domain to clamp microtubule binding sites together.  The two complexes (Csm1/Lrs4 and Pcs1/Mde4) contribute to the prevention of merotelic attachment.
Pfam PF22426: Maltogenic amylase, N-terminal domain (domain)
This entry represents the second beta-sandwich domain present in Staphylothermus marinus maltogenic amylase (SMMA). SMMA is a extreme thermophile maltogenic amylase with an optimal temperature of 100 C, which hydrolyzes alpha(1-4)glycosyl linkages in cyclodextrins and in linear malto-oligosaccharides.
Pfam PF23220: Pre-mRNA-splicing factor SYF1 middle HAT repeat (repeat)
Syf1 is a component of the spliceosome and is involved in pre-RNA splicing. It has HAT (Half A TPR) repeats which have a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs. This entry represents HAT repeats from the middle region of Syf1.
Pfam PF00302: Chloramphenicol acetyltransferase (domain)
Chloramphenicol acetyltransferase (CAT) (2.3.1.28)  catalyzes the acetyl-CoA dependent acetylation of chloramphenicol (Cm), an antibiotic which inhibits prokaryotic peptidyltransferase activity. Acetylation of Cm by CAT inactivates the antibiotic. A histidine residue, located in the C-terminal section of the enzyme, plays a central role in its catalytic mechanism.

The crystal structure of the type III enzyme from Escherichia coli with chloramphenicol bound has been determined. CAT is a trimer of identical subunits (monomer Mr 25,000) and the trimeric structure is stabilised by a number of hydrogen bonds, some of which result in the extension of a Î²-sheet across the subunit interface. Chloramphenicol binds in a deep pocket located at the boundary between adjacent subunits of the trimer, such that the majority of residues forming the binding pocket belong to one subunit while the catalytically essential histidine belongs to the adjacent subunit. His195 is appropriately positioned to act as a general base catalyst in the reaction, and the required tautomeric stabilisation is provided by an unusual interaction with a main-chain carbonyl oxygen .
Wikipedia: Chloramphenicol acetyltransferase is a bacterial enzyme that detoxifies the antibiotic chloramphenicol and is responsible for chloramphenicol resistance in bacteria. This enzyme covalently attaches an acetyl group from acetyl-CoA to chloramphenicol, which prevents chloramphenicol from binding to ribosomes. A histidine residue, located in the C-terminal section of the enzyme, plays a central role in its catalytic mechanism.
Pfam PF20648: Family of unknown function (DUF6809) (family)
This family of proteins is functionally uncharacterised. Proteins in this family are found in bacteria, are typically around 85 amino acids in length and have a conserved motif FxxGF.
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 PF04668: Twisted gastrulation (Tsg) protein conserved region (family)
Tsg was identified in Drosophila as being required to specify the dorsal-most structures in the embryo, for example amnioserosa. Biochemical experiments have revealed three key properties of Tsg: it can synergistically inhibit Dpp/BMP action in both Drosophila and vertebrates by forming a tripartite complete between itself, SOG/chordin and a BMP ligand; Tsg seems to enhance the Tld/BMP-1-mediated cleavage rate of SOG/chordin and may change the preference of site utilisation; Tsg can promote the dissociation of chordin cysteine-rich-containing fragments from the ligand to inhibit BMP signalling.
Pfam PF14358: Domain of unknown function (DUF4405) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 50 amino acids in length. There are two conserved histidines that may be functionally important. This family is N-terminally truncated compared to other members of the clan.
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 PF12548: Sulfatase protein (family)
This domain family is found in eukaryotes, and is typically between 144 and 173 amino acids in length. The family is found in association with [pfam:PF00884].
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 PF10274: Parkin co-regulated protein (repeat)
This family of proteins is transcribed anti-sense along the DNA to the Parkin gene product and the two appear to be transcribed under the same promoter. The protein has predicted alpha-helical and beta-sheet domains which suggest its function is in the ubiquitin/proteasome system.  Mutations in parkin are the genetic cause of early-onset and autosomal recessive juvenile parkinsonism.
Pfam PF19151: Sublancin (family)
This family represents sublancin, a small bacteriocin active against  Gram-positive bacteria. This family appears to be restricted to  Bacilli. Sublancin was thought to be a lantibiotic but was later  shown to be an S-linked glycopeptide. Glycosylation is  essential for its antimicrobial activity. Sublancin is  biosynthesised as a precursor peptide bearing an N-terminal leader  peptide, and a C-terminal core peptide that is converted into the  mature peptide. Sublancin comprises two alpha helices and a  well-defined inter-helical loop. Sublancin inhibits B.cereus  spore outgrowth, after the germination stage, approximately  1000-fold better than it inhibits exponential growth of the same  cells and inhibits B.subtilis strain ATCC6633 and B. megaterium strain 14581.
Pfam PF13551: Winged helix-turn helix (domain)
This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.
Pfam PF14484: Fish-specific NACHT associated domain (family)
This domain is frequently found associated with the NACHT domain ([pfam:PF05729]) in fish and other vertebrates.
Pfam PF14403: Circularly permuted ATP-grasp type 2 (domain)
Circularly permuted ATP-grasp prototyped by Roseiflexus RoseRS_2616  that is associated in gene neighborhoods with a GCS2-like COOH-NH2  ligase, alpha/beta hydrolase fold peptidase, GAT-II -like  amidohydrolase, and M20 peptidase. Members of this family are  predicted to be involved in the biosynthesis of small peptides.
Pfam PF01597: Glycine cleavage H-protein (domain)
This is a family of glycine cleavage H-proteins, part of the glycine  cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. A lipoyl group is attached to a completely conserved lysine residue. The H protein shuttles the methylamine group of glycine from the P protein to the T protein.
Wikipedia: The glycine cleavage system (GCS) is also known as the glycine decarboxylase complex or GDC. The system is a series of enzymes that are triggered in response to high concentrations of the amino acid glycine. The same set of enzymes is sometimes referred to as glycine synthase when it runs in the reverse direction to form glycine. The glycine cleavage system is composed of four proteins: the T-protein, P-protein, L-protein, and H-protein. They do not form a stable complex, so it is more appropriate to call it a "system" instead of a "complex". The H-protein is responsible for interacting with the three other proteins and acts as a shuttle for some of the intermediate products in glycine decarboxylation. In both animals and plants, the glycine cleavage system is loosely attached to the inner membrane of the mitochondria. Mutations in this enzymatic system are linked with glycine encephalopathy.
Pfam PF16576: Barrel-sandwich domain of CusB or HlyD membrane-fusion (domain)
This entry represents a domain comprising the combined domains 2 and 3 of the membrane-fusion proteins CusB and HlyD. It is formed by a barrel-sandwich domain which is inserted in a RIFT-like domain. The barrel-sandwich domain, itself, contains an insert of a three-helical bundle subdomain. CusB and HlyD proteins are membrane fusion proteins of the CusCFBA copper efflux system in E.coli and related bacteria.  The whole molecule hinges between D2 and D3. Efflux systems of this resistance-nodulation-division group - RND - have been developed to excrete poisonous metal ions, and in E.coli the only one that deals with silver and copper is the CusA transporter. The transporter CusA works in conjunction with a periplasmic component that is a membrane fusion protein, eg CusB, and an outer-membrane channel component CusC in a CusABC complex driven by import of protons.
Pfam PF18424: Alpha-Dystroglycan N-terminal domain 2 (domain)
This is the second N-terminal domain found in alpha-Dystroglycan (DG). The murine skeletal muscle N-terminal alpha-DG region, contains two autonomous domains; the first identified as an Ig-like and the second resembling ribosomal RNA-binding proteins. This domain is similar to the small subunit ribosomal protein S6 of Thermus thermophilus (S6 domain). It is suggested that the S6 domain may be of functional relevance for LARGE (like-acetylglucosaminyltransferase) recognition along the alpha-DG maturation pathway.
Pfam PF23950: MLLE-related domain (domain)
This entry represents a domain related to the MLLE domain found in a set of plant proteins. This domain is likely to form a peptide binding domain.
Pfam PF02491: SHS2 domain inserted in FTSA (domain)
FtsA is essential for bacterial cell division, and co-localises to  the septal ring with FtsZ. The SHS2 domain is inserted in to the RNAseH fold of FtsA, and is involved in protein-protein interaction.
Wikipedia: FtsA is a bacterial protein that is related to actin by overall structural similarity and in its ATP binding pocket.
Pfam PF00933: Glycosyl hydrolase family 3 N terminal domain (domain)
O-Glycosyl hydrolases (3.2.1.) 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 glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Glycoside hydrolase family 3 GH3 comprises enzymes with a number of known activities; beta-glucosidase (3.2.1.21); beta-xylosidase (3.2.1.37); N-acetyl beta-glucosaminidase (3.2.1.52); glucan beta-1,3-glucosidase (3.2.1.58); cellodextrinase (3.2.1.74); exo-1,3-1,4-glucanase (3.2.1). These enzymes are two-domain globular proteins that are N-glycosylated at three sites . This domain is often N-terminal to the glycoside hydrolase family 3, C-terminal domain IPR002772.
Wikipedia: In molecular biology, glycoside hydrolase family 3 is a family of glycoside hydrolases. Glycoside hydrolases EC 3.2.1. 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 over 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 PF20596: Putative adhesive domain (group 11) (family)
This domain is found N-terminal to repeating stalk domains in Firmicutes and Actinobacteria surface proteins. The structure model resembles a receptor binding domain in cattle suggesting protein binding function. The structure model also resembles partly a galactose binding Yersinia pestis antigen.
Pfam PF11040: Dispersed gene family protein 1 C-terminal domain (domain)
This entry represents the C-terminal domain present in DGF-1 from Typanosoma, one of the most abundant proteins in T. cruzi genome and it seems to have a preferential expression in amastigotes (intracellular replicative forms that develop in the mammalian host). The function of this protein is not yet clear, however, it is likely to play a role in cell-to-cell interactions or signal transduction. This is the transmembrane segment of these proteins.
Pfam PF10417: C-terminal domain of 1-Cys peroxiredoxin (domain)
This is the C-terminal domain of 1-Cys peroxiredoxin (1-cysPrx), a member of the peroxiredoxin superfamily which protect cells against membrane oxidation through glutathione (GSH)-dependent reduction of phospholipid hydroperoxides to corresponding alcohols. The C-terminal domain is crucial for providing the extra cysteine necessary for dimerisation of the whole molecule. Loss of the enzyme's peroxidase activity is associated with oxidation of the catalytic cysteine, upstream of this domain; and glutathionylation, presumably through its disruption of protein structure, facilitates access for GSH, resulting in spontaneous reduction of the mixed disulfide to the sulfhydryl and consequent activation of the enzyme.  The domain is associated with family AhpC-TSA, [pfam:PF00578], which carries the catalytic cysteine.
Pfam PF04263: Thiamin pyrophosphokinase, catalytic domain (domain)
Family of thiamin pyrophosphokinase ([ec:2.7.6.2]). Thiamin pyrophosphokinase (TPK) catalyses the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.
Pfam PF21545: T7SS, ESX-1 secretion system protein EccA1, N-terminal domain (repeat)
This domain is found at the N-terminal end of ESX-1 secretion system protein EccA1 from Mycobacterium tuberculosis and similar proteins predominantly from Actinobacteria. EccA1 is part of the ESX-1 specialised secretion system (a cluster of the type VII secretion system, T7SS). EccA1 contains a C-terminal ATPase domain ([pfam:PF00004] and [pfam:PF17866]) and a tetratricopeptide repeat (TPR) containing N-terminal domain (this entry). The six tandem TPR motifs of this domain packed in parallel create a series of repeating antiparallel alpha-helices that give rise to an overall superhelix structure.
Pfam PF06523: Protein of unknown function (DUF1106) (family)
This family consists of several hypothetical bacterial proteins found in Escherichia coli and Citrobacter rodentium. 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 PF24630: TASOR PIN domain (domain)
This is a domain found in TASOR proteins, a key component of the HUSH complex, a vertebrate-specific multiprotein complex that mediates epigenetic repression of both exogenous and endogenous genetic elements. The HUSH complex regulates H3K9me3 deposition by promoting recruitment of SETDB1 and also recruits MORC2 to compact chromatin. TASOR is crucial in early embryonic development and contains a catalytically-inactive PARP domain, necessary for epigenetic regulation of target elements. This entry represents a PIN domain found towards the C terminus of TASOR and TASOR2 and shares detectable similarity to the PIN domain of SMG5.
Pfam PF25121: ESF1 RRM domain (domain)
This domain is found in the yeast Pre-rRNA-processing protein ESF1 and related eukaryotic proteins. ESF1 is involved in the 18S rRNA synthesis and required for the early cleavages at sites A0, A1 and A2. this domain has a detectable similarity to known RNA binding domains.