SII-SWORD/CoKE huggingface dataset:
Pfam PF01327: Polypeptide deformylase (domain)
Peptide deformylase (PDF) is an essential metalloenzyme required for the removal of the formyl group at the N terminus of nascent polypeptide chains in eubacteria: 3.5.1.88 . The enzyme acts as a monomer and binds a single metal ion, catalysing the reaction: N-formyl-L-methionine + H2O = formate + methionyl peptide Catalytic efficiency strongly depends on the identity of the bound metal .
These enzymes utilize Fe(II) as the catalytic metal ion, which can be replaced with a nickel or cobalt ion with no loss of activity. There are two types of peptide deformylases, types I and II, which differ in structure only in the outer surface of the domain. Because these enzymes are essential only in prokaryotes (although eukaryotic gene sequences have been found), they are a target for a new class of antibacterial agents .
The structure of these enzymes is known . PDF, a zinc metalloenzyme from the mitochondrion, comprises an active core domain of 147 residues and a C-terminal tail of 21 residue. The 3D fold of the catalytic core has been determined by X-ray crystallography and NMR. Overall, the structure contains a series of anti-parallel Î²-strands that surround two perpendicular Î±-helices. The C-terminal helix contains the characteristic HEXXH motif of metalloenzymes, which is crucial for activity. The helical arrangement, and the way the histidine residues bind the zinc ion, is reminiscent of metalloproteases such as thermolysin or metzincins. However, the arrangement of secondary and tertiary structures of PDF, and the positioning of its third zinc ligand (a cysteine residue), are quite different. These discrepancies, together with notable biochemical differences, suggest that PDF constitutes a new class of zinc-metalloenzymes .
Pfam PF13535: ATP-grasp domain (domain)
This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Pfam PF02470: MlaD protein (domain)
This family of proteins contains MlaD, which is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane. The family also contains the mce (mammalian cell entry) proteins from Mycobacterium tuberculosis. The archetype (Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage. This family contains proteins of unknown function from other bacteria.
Pfam PF20263: LYR motif-containing protein 2-like (family)
This entry represents LYR motif-containing proteins, including LYR motif-containing protein 2 from animals, whose function is not clear, and Cup1 (caffeine unstable phenotype 1, previously known as uncharacterised protein C17G9.13c) from S. pombe. Cup1 has been characterised; it is a mitochondrial protein whose silencing by heterochromatin island formation results in caffeine resistance. LYR-motif containing proteins are basic polypeptides carrying a conserved tripeptide L-Y-R (leucine/tyrosine/arginine) sequence close to the N-terminus in addition to some basic arginine/lysine residues and a highly-conserved phenylalanine downstream of the LYR motif.
Pfam PF19690: Family of unknown function (DUF6191) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002014) is described by MIBiG as an example of the following biosynthetic classes, polyketide and NRP (non-ribosomal peptide). It includes a member of the pepticinnamin E biosynthetic gene cluster from Actinobacteria bacterium OK006. This family appears to be predominantly 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 PF09371: Tex-like protein N-terminal domain (domain)
This domain is found at the N-terminus of Tex protein [swissprot:Q45388] and other related proteins. Tex protein defines a family of prokaryotic transcriptional accessory factors. This domain is likely to be distantly related to PWI domain, an RNA/DNA binding domain. It is thought to be involved in ssDNA binding.
Pfam PF06740: Microtubule associated protein Futsch (repeat)
The Drosophila protein Futsch has homology to MAP1B and controls synaptic growth at the Drosophila neuromuscular junction through the regulation of the synaptic microtubule cytoskeleton. Ftusch protein colocalises with microtubules and identifies cytoskeletal loops that traverse the lateral margin of select synaptic boutons. Futsch mutations disrupt synaptic microtubule organisation. The N- and C-terminal domains of Futsch are homologous to the vertebrate MAP1B microtubule-associated protein. The central domain of Futsch is highly repetitive and it is represented in this entry.
Pfam PF14416: PMR5 N terminal Domain (domain)
The plant family with PMR5, ESK1, TBL3 etc have a N-terminal   C rich predicted sugar binding domain followed by the PC-Esterase (acyl esterase) domain.
Pfam PF10111: Glycosyltransferase like family 2 (family)
Members of this family of prokaryotic proteins include putative glucosyltransferase, which are involved in bacterial capsule biosynthesis.
Pfam PF13699: eCIS core domain (domain)
This entry represents a domain found in a group of prokaryotic proteins that was previously known as DUF4157. This domain has been recently identified as a highly conserved eCIS (extracellular Contractile Injection System) core domain. eCIS is a cell-free toxin-delivery system that evolved from a bacteriophage tail and is prevalent in prokaryotes. This eCIS core DUF4157 domain contains an HEXXH motif that is characteristic of many families of metallopeptidases and a putative metal-binding site for a divalent cation such as zinc. Proteobacterial members of this family are thought to be related to the type VI secretion system (T6SS). This region is responsible for the toxicity of the protein in the bacterial periplasm. eCIS-associated toxins carry DUF4157 domains in their N-terminus or are found adjacent to genes with this domain. No peptidase activity has been reported for this domain so far.
Pfam PF09586: Bacterial membrane protein YfhO (family)
This protein is a conserved membrane protein. The yfhO gene is transcribed in Difco sporulation medium and the transcription is affected by the YvrGHb two-component system. Some members of this family have been annotated as glycosyl transferases of the PMT family.
Pfam PF18208: Nicking enzyme C-terminal middle helical domain (domain)
This domain is found in nicking enzyme in S. aureus. NES initiates and terminates the transfer of plasmids that variously confer resistance to a range of drugs, including vancomycin and gentamicin. This domain is found in the C-terminal region of NES. The C-terminal region is required for conjugation and significantly impacts the catalytic activity of the N-terminal relaxase.
Pfam PF00421: Photosystem II protein (family)
This entry represents the intrinsic antenna proteins CP43 (PsbC) and CP47 (PsbB) found in the reaction centre of PSII. These polypeptides bind to chlorophyll a and beta-carotene and pass the excitation energy on to the reaction centre . This entry also includes the iron-stress induced chlorophyll-binding protein CP43' (IsiA), which evolved in cyanobacteria from a PSII protein to cope with light limitations and stress conditions. Under iron-deficient growth conditions, CP43' associates with PSI to form a complex that consists of a ring of 18 or more CP43' molecules around a PSI trimer, which significantly increases the light-harvesting system of PSI. IsiA can also provide photoprotection for PSII .
PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and Î²-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .
Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .
Wikipedia: Iron-starvation-induced protein A, also known as isiA, is a photosynthesis-related chlorophyll-containing protein found in cyanobacteria. It belongs to the chlorophyll-a/b-binding family of proteins, and has been shown to have a photoprotection role in preventing oxidative damage via energy dissipation. It was originally identified under Fe starvation, and thus received the name iron-starvation-induced protein A. However, the protein has more recently been found to respond to a variety of stress conditions such as high irradiance. It can aggregate with carotenoids and form rings around the PSI reaction center complexes to aid in photoprotective energy dissipation.
Pfam PF11017: Protein of unknown function (DUF2855) (family)
This family of 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 PF23137: HVO_0758 mu-protein (family)
This entry represents HVO_0758 mu-protein from halophilic mesophile archaeon Haloferax volcanii and related proteins. HVO_0758 is a small protein of 56 amino acid residues, containing two highly conserved CXXC and CPXC sequence motifs. The structure of this protein has a typical Zinc ribbon fold consisting of a small N-terminal alpha-helix and two knuckles at the tip of two beta-hairpins that contain the zinc coordinating residues. This protein plays an essential role in swarming behaviour and biofilm formation.
Pfam PF14064: HmuY protein (family)
HmuY is a novel heme-binding protein that recruits heme from host carriers and delivers it to its cognate outer-membrane transporter, the TonB-dependent receptor HmuR.              This family of proteins is found in bacteria. Proteins in this family are typically between 214 and 278 amino acids in length.
Pfam PF20621: Family of unknown function (DUF6806) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 210 amino acids in length and their N-terminal share a similar structure with the Crispr-associated endoribonuclease Cas2.
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 PF01039: Carboxyl transferase domain (family)
All of the members in this family are biotin dependent carboxylases.  The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxoacid as the acceptor molecule of carbon dioxide.  All of the members in this family utilise acyl-CoA as the acceptor molecule.
Wikipedia: In molecular biology, proteins containing the carboxyl transferase domain include biotin-dependent carboxylases. This domain carries out the following reaction: transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxo acid as the acceptor molecule of carbon dioxide. All of the members in this family use acyl-CoA as the acceptor molecule.
Pfam PF20287: SH3 fold domain associated with phage DNA polymerases (domain)
This is an SH3 fold domain related to nucleic acid binding toxins of uncharacterised function usually associated with a divergent Family B DNA polymerase in group 1/PhiKZ-like phages.
Pfam PF06002: Alpha-2,3-sialyltransferase (CST-I) (family)
This family consists of several alpha-2,3-sialyltransferase (CST-I) proteins largely found in Campylobacter jejuni.
Pfam PF05229: Spore Coat Protein U domain (domain)
This domain is found in a bacterial family of spore coat proteins, as well as a family of secreted pili proteins involved in motility and biofilm formation (). This family is distantly related to fimbrial proteins.
Pfam PF13531: Bacterial extracellular solute-binding protein (family)
This family includes bacterial extracellular solute-binding proteins.
Pfam PF22913: NBAS subunit of NRZ tethering complex, C-terminal (domain)
This domain is found at the C-terminal end of human NBAS subunit of NRZ tethering complex (NBAS) and similar sequences mainly found in vertebrates. NBAS is involved in Golgi-to-endoplasmic reticulum (ER) retrograde transport. This domain is predicted to adopt an all-alpha structure.
Pfam PF00542: Ribosomal protein L7/L12 C-terminal domain (domain)
This entry represents the C-terminal domain of the large ribosomal subunit protein bL12 (formerly known as L7/L12). bL12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of bL12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain . The bL12 dimer probably interacts with EF-Tu.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF02234: Cyclin-dependent kinase inhibitor (family)
Cell cycle progression is negatively controlled by cyclin-dependent  kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase.
Wikipedia: A cyclin-dependent kinase inhibitor protein (also known as CKIs, CDIs, or CDKIs) is a protein that inhibits the enzyme cyclin-dependent kinase (CDK) and Cyclin activity by stopping the cell cycle if there are unfavorable conditions, therefore, acting as tumor suppressors. Cell cycle progression is stopped by Cyclin-dependent kinase inhibitor protein at the G1 phase. CKIs are vital proteins within the control system that point out whether the processes of DNA synthesis, mitosis, and cytokines control one another. When a malfunction hinders the successful completion of DNA synthesis in the G1 phase, it triggers a signal that delays or halts the progression to the S phase. Cyclin-dependent kinase inhibitor proteins are essential in the regulation of the cell cycle. If cell mutations surpass the cell cycle checkpoints during cell cycle regulation, it can result in various types of cancer.
Pfam PF14922: Protein of unknown function (family)
This is a family of eukaryotic proteins. Most members carry a highly distinctive, conserved sequence motif of FWWh, where h represents a hydrophobic residue. The function of the family is not known.
Pfam PF20228: Family of unknown function (DUF6587) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Proteobacteria. Proteins in this family are typically between 80 and 101 amino acids in length and contain four conserved cysteine residues at the C-terminal.
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 PF14499: Domain of unknown function (DUF4437) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 152 and 283 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 PF04440: Dysbindin (Dystrobrevin binding protein 1) (family)
Dysbindin is an evolutionary conserved 40-kDa coiled-coil-containing protein that binds to alpha- and beta-dystrobrevin in muscle and brain. Dystrophin and alpha-dystrobrevin are co-immunoprecipitated with dysbindin, indicating that dysbindin is DPC-associated in muscle. Dysbindin co-localises with alpha-dystrobrevin at the sarcolemma and is up-regulated in dystrophin-deficient muscle. In the brain, dysbindin is found primarily in axon bundles and especially in certain axon terminals, notably mossy fibre synaptic terminals in the cerebellum and hippocampus. Dysbindin may have implications for the molecular pathology of Duchenne muscular dystrophy and may provide an alternative route for anchoring dystrobrevin and the DPC to the muscle membrane. Genetic variation in the  human dysbindin gene is also thought to be associated with Schizophrenia.
Pfam PF06024: Orf78 (ac78) (family)
Family members include Autographa californica nuclear polyhedrosis virus (AcMNPV), AC78 or Orf78. AC78 is a late gene in the viral life cycle and encodes an envelope structural protein that plays an essential role in embedding the occlusion-derived virus (ODV) in the occlusion body. Although AC78 is not essential for budding virus formation or nucleocapsid assembly and ODV formation, number are significantly reduced if the gene is knocked-out.
Pfam PF19973: Ternary complex associated domain 7 (domain)
Novel uncharacterised protein domain found associated with the vWA-MoxR-VMAP ternary systems
Pfam PF10995: Cellulose biosynthesis protein BcsE (family)
This family of proteins includes members involved in cellulose biosynthesis such as BcsE proteins found in Salmonella typhimurium. Family members carry a GIL domain on the C-terminal. The GIL domain, for GGDEF I-site like domain, is a c-di-GMP binding domain on the BcsE proteins of enterobacteria. It is not essential for cellulose synthesis but is critical for maximal cellulose production. Cellulose production in enterobacteria is controlled by a two-tiered c-di-GMP-dependent system involving BcsE and the PilZ domain containing glycosyltransferase BcsA. The RxGD motif of the GIL domain is required for c-di-GMP binding.
Pfam PF15272: Spindle pole body component BBP1, C-terminal (domain)
This C-terminal domain of BBP1, a spindle pole body component, carries coiled-coils that are necessary for the localisation of BBP1 to the spindle pole body (SPB). Although not a membrane protein itself, BBP1 binds to Mps2 as well as to Spc29 and the half-bridge protein Kar1, thus providing a model for how the SPB core is tethered within the nuclear envelope and to the half-bridge
Pfam PF17795: Major Vault Protein Repeat domain (domain)
This domain is found in the Major Vault Protein.
Pfam PF12104: T cell CD4 receptor C terminal region (domain)
This domain is the C terminal domain of the CD4 T cell receptor. The C terminal domain is the cytoplasmic domain which relays the signal for T cell activation. This process involves co-receptor internalisation. This domain is involved in binding to the N terminal of Lck co-receptor in a Zn2+ clasp structure.
Pfam PF19324: LETM1 domain-containing protein LETM2 N-terminus (family)
This family represents the N-terminal region of the LETM1-domain- containing protein LETM2, a mitochondrial protein that is expressed preferentially in spermatocytes and spermatozoa during developmental stages from spermatocyte to spermatozoon. LETM2 might contribute to the reorganisation of the inner and cristae membranes during spermatogenesis. Despite its name, it does not contain an EF-hand domain as LETM1, but it contains a putative leucine zipper coiled coil domain.
Pfam PF09069: EF-hand (domain)
Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain ([pfam:PF00397]), enhancing dystroglycan binding.