SII-SWORD/CoKE huggingface dataset:
Pfam PF23983: Minor capsid protein P11, C-terminal conserved region (family)
This entry, previously known as DUF7306, represents a conserved region found C-terminal in the Minor capsid protein P11 and related phage proteins. P11 is one of the minor capsid proteins that constitute a network below the outer capsid shell, internal to the major capsid proteins and outside the lipid membrane. P11 plays crucial roles in determining the capsid size and binding neighbouring symmetrons together. The P11 proteins zip together most of the capsomers at the boundary of neighbouring tri- or penta- symmetrons via their C-terminal regions. The C-terminal regions of each P11 protein is located underneath the conjunction of a set of three neighbouring capsomers, gluing these capsomers together. These C-terminal regions are to a large extend unstructured.
Pfam PF18057: Domain of unknown function (DUF5594) (domain)
This domain was first discovered in BPSL1050, a highly immunoreactive protein found in Burkholderia pseudomallei. The domain's structure consists of three helical regions which pack onto an antiparallel beta sheet, formed by four strands. The beta sheet is solvent exposed on one side and packs tightly against the three helices on the other side, generating a network of hydrophobic and aromatic interactions that contribute to tight packing of the protein. Is is thought that the small loop L1, the main loop L2, and part of helix alpha-3 extending until Leu120 are the three main immunogenic sequences.
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 PF09150: Orange carotenoid protein, N-terminal (domain)
Members of this family adopt an alpha-helical structure consisting of two four-helix bundles. They are predominantly found in prokaryotic orange carotenoid protein, and carotenoid binding proteins.
Wikipedia: In molecular biology the orange carotenoid N-terminal domain is a protein domain found predominantly at the N-terminus of the Orange carotenoid protein (OCP), and is involved in non-covalent binding of a carotenoid chromophore. It is unique for being present in soluble proteins, whereas the vast majority of domains capable of binding carotenoids are intrinsic membrane proteins. Thus far, it has exclusively been found in cyanobacteria, among which it is widespread. The domain also exists on its own, in uncharacterized cyanobacterial proteins referred to as "Red Carotenoid Protein" (RCP). The domain adopts an alpha-helical structure consisting of two four-helix bundles.
Pfam PF01161: Phosphatidylethanolamine-binding protein (domain)
The PEBP (PhosphatidylEthanolamine-Binding Protein) family is a highly conserved group of proteins that have been identified in numerous tissues in a wide variety of organisms, including bacteria, yeast, nematodes, plants, drosophila and mammals. The various functions described for members of this family include lipid binding, neuronal development , serine protease inhibition , the control of the morphological switch between shoot growth and flower structures , and the regulation of several signalling pathways such as the MAP kinase pathway , and the NF-kappaB pathway . The control of the latter two pathways involves the PEBP protein RKIP, which interacts with MEK and Raf-1 to inhibit the MAP kinase pathway , and with TAK1, NIK, IKKalpha and IKKbeta to inhibit the NF-kappaB pathway. Other PEBP-like proteins that show strong structural homology to PEBP include Escherichia coli YBHB and YBCL , the Rattus norvegicus (Rat) neuropeptide HCNP, and Antirrhinum majus (Garden snapdragon) protein centroradialis (CEN). Although their overall structures are similar, the members of the PEBP family bind very different substrates including phospholipids, opioids, and hydrophobic odorant molecules as well as having different oligomerization states (monomer/dimer/tetramer).
Pfam PF06398: Integral peroxisomal membrane peroxin (family)
Peroxisomes play diverse roles in the cell, compartmentalising many activities related to lipid metabolism and functioning in the decomposition of toxic hydrogen peroxide. Sequence similarity was identified between two hypothetical proteins and the peroxin integral membrane protein Pex24p.
Pfam PF11188: Protein of unknown function (DUF2975) (family)
This family of bacterial proteins have no known function. These proteins are likely to be integral membrane proteins. The proteins contain a highly conserved glutamic acid close to their C-terminus.
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 PF05834: Lycopene cyclase protein (family)
This family consists of lycopene beta and epsilon cyclase proteins. Carotenoids with cyclic end groups are essential components of the photosynthetic membranes in all plants, algae, and cyanobacteria. These lipid-soluble compounds protect against photo-oxidation, harvest light for photosynthesis, and dissipate excess light energy absorbed by the antenna pigments. The cyclisation of lycopene (psi, psi-carotene) is a key branch point in the pathway of carotenoid biosynthesis. Two types of cyclic end groups are found in higher plant carotenoids: the beta and epsilon rings. Carotenoids with two beta rings are ubiquitous, and those with one beta and one epsilon ring are common; however, carotenoids with two epsilon rings are rare.
Pfam PF24491: Domain of unknown function (DUF7586) (domain)
This domain is found in bacterial uncharacterised proteins that probably belong to the penicillin-binding protein-type class of thioesterases. This domain is predicted to fold into a meander beta-barrel consisting of eight antiparallel beta-strands. It contains a semi-conserved GxWxW sequence motif near the N terminus.
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 PF23775: RIG second beta-propeller (repeat)
This entry represents the second beta-propeller found in Protein rigor mortis (RIG) from Drosophila melanogaster. RIG is a nuclear receptor-interacting protein required for the response to steroid hormone ecdysone during larval development. This domain acts as a specific protein-protein interaction domain. Also included in this entry are orthologues Gem-associated protein 5 (GEMI5) from animals. GEMI5 is a component of the survival of motor neurons (SMN) complex. The beta-propellers in GEMI5 bind small nuclear RNAs (snRNAs) playing a critical role in the assembly of the heptameric Sm protein core on snRNAs and the biogenesis of small nuclear ribonucleoproteins (snRNPs).
Pfam PF01195: Peptidyl-tRNA hydrolase (domain)
Peptidyl-tRNA hydrolase (3.1.1.29) (PTH) is a bacterial enzyme that cleaves peptidyl-tRNA or N-acyl-aminoacyl-tRNA to yield free peptides or N-acyl-amino acids and tRNA. The natural substrate for this enzyme may be peptidyl-tRNA which drop off the ribosome during protein synthesis . Bacterial PTH has been found to be evolutionary related to a yeast protein . This enzyme is interesting as a potential target for the discovery of new antimicrobial agents as it is critical for the viability of bacteria [cite:PUB00106491]}. It folds into a single Î±/Î² globular domain with seven Î²-strands forming a twisted mixed central Î²-sheet, surrounded by a total of six helices .
This group also contains chloroplast RNA splicing 2 (CRS2), which is closely related nuclear-encoded protein required for the splicing of nine group II introns in chloroplasts .
Pfam PF07989: Centrosomin N-terminal motif 1 (coiled_coil)
This domain has been identified in two microtubule associated proteins in Schizosaccharomyces pombe, Mto1 and Pcp1. Mto1 has been identified in association with spindle pole body and non-spindle pole body microtubules. The pericentrin homologue Pcp1 is also associated with the fungal centrosome or spindle pole body (SPB). Members of this family have been named centrosomins, and are an essential mitotic centrosome component required for assembly of all other known pericentriolar matrix proteins in order to achieve microtubule-organising activity in fission yeast. Cnn_1N is a short conserved motif towards the N-terminus.  Motif 1 is found to be necessary for proper recruitment of gamma-tubulin, D-TACC (the homolog of vertebrate transforming acidic coiled-coil proteins [TACC]), and Minispindles (Msps) to embryonic centrosomes but is not required for assembly of other centrosome components including Aurora A kinase and CP60 in Drosophila.
Pfam PF06772: Bacterial low temperature requirement A protein (LtrA) (family)
This family consists of several bacteria specific low temperature requirement A (LtrA) protein sequences which have been found to be essential for growth at low temperatures in Listeria monocytogenes.
Pfam PF11962: Peptidase_G2, IMC autoproteolytic cleavage domain (domain)
This domain is found at the very C-terminus of bacteriophage parallel beta-helical tailspike proteins. It carries the enzymic residues that induce autoproteolytic cleavage to bring about maturation of the folding process of the helix in a chaperone-like manner. The domain thus mediates the assembly of a large tailspike protein and then releases itself after maturation. These C-terminal regions that autoproteolytically release themselves after maturation are exchangeable between functionally unrelated N-terminal proteins and have been identified in a number of bacteriophage tailspike proteins.
Pfam PF23034: Domain of unknown function (DUF7035) (domain)
This domain is found in a group of uncharacterised proteins from Dictyostelia. It is predicted to adopt Ig-like fold with the fibronectin type III-like topology.
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 PF24176: TELO2-interacting protein 1 homologue second TPR domain (repeat)
This entry represents the second TPR domain found in TELO2-interacting protein 1 homologue (TTI1) from animals. TTI1 binds to TELO2 and TTI2 proteins to form the TTT complex, which plays a role in the assembly and stability of all phosphatidylinositol 3-kinase-related protein kinases (PIKKs), pivotal proteins in various pathways related to cell metabolism, proliferation and differentiation. This domain interacts with TELO2.
Pfam PF24409: wHTH-PRTase associated (domain)
This entry represents a wHTH domain found at the C-terminal of proteins containing PRTase-CE ([pfam:PF24390]) domain in the retron antiviral immunity system.
Pfam PF17326: Family of unknown function (DUF5365) (family)
This is a family of unknown function found in Bacillaceae.
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 PF00907: T-box (domain)
The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations.
Wikipedia: T-box refers to a group of transcription factors involved in embryonic limb and heart development. Every T-box protein has a relatively large DNA-binding domain, generally comprising about a third of the entire protein that is both necessary and sufficient for sequence-specific DNA binding. All members of the T-box gene family bind to the "T-box", a DNA consensus sequence of TCACACCT.
Pfam PF20150: 2EXR family (family)
This entry contains proteins with two conserved ExR motifs that may be functionally important. This entry represents a large and diverse family of proteins found in fungi.
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 PF08020: Protein of unknown function (DUF1706) (family)
This family contains many hypothetical proteins from bacteria and yeast.
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 PF00241: Cofilin/tropomyosin-type actin-binding protein (domain)
Severs actin filaments and binds to actin monomers.
Wikipedia: In molecular biology, ADF-H domain is an approximately 150 amino acid motif that is present in three phylogenetically distinct classes of eukaryotic actin-binding proteins.ADF/cofilins, which include ADF, cofilin, destrin, actophorin, coactosin, depactin and glia maturation factors (GMFs) beta and gamma. ADF/cofilins are small actin-binding proteins composed of a single ADF-H domain. They bind both actin-monomers and filaments and promote rapid filament turnover in cells by depolymerising/fragmenting actin filaments. ADF/cofilins bind ADP-actin with higher affinity than ATP-actin and inhibit the spontaneous nucleotide exchange on actin monomers
Twinfilins, which are actin monomer-binding proteins that are composed of two ADF-H domains
Abp1/Drebrins, which are relatively large proteins composed of an N-terminal ADF-H domain followed by a variable region and a C-terminal SH3 domain. Abp1/Drebrins interact only with actin filaments and do not promote filament depolymerisation or fragmentation. Although these proteins are biochemically distinct and play different roles in actin dynamics, they all appear to use the ADF-H domain for their interactions with actin.
Pfam PF18684: Pleurotolysin B C-terminal domain (domain)
This a trefoil C-terminal beta-rich domain found in PlyB, one of the components of pleurotolysin (Ply) pore-forming protein. Ply is a membrane attack complex/perforin-like family (MACPF) protein consisting of two components, PlyA and PlyB. PlyB and PlyA act together to form relatively small and regular pores in liposomes. The PlyB C-terminal trefoil sits on top of the PlyA dimer.
Pfam PF15403: HiaBD2_N domain of Trimeric autotransporter adhesin (GIN) (conserved_site)
HiaBD2_N may represent the GIN domain of the Head region of TAAs - trimeric autotransporter adhesins. Not all TAAs carry this domain; however, in those that do, the GIN in combination with the Trp-ring domain is necessary for adhesion to fibronectin in the host cell.
Wikipedia: In molecular biology, trimeric autotransporter adhesins (TAAs), are proteins found on the outer membrane of Gram-negative bacteria. Bacteria use TAAs in order to infect their host cells via a process called cell adhesion. TAAs also go by another name, oligomeric coiled-coil adhesins, which is shortened to OCAs. In essence, they are virulence factors, factors that make the bacteria harmful and infective to the host organism.
Pfam PF17849: Dis3-like cold-shock domain 2 (CSD2) (domain)
This domain has an OB fold and is found in the Dis3l2 protein. This domain along with CSD1 binds to RNA.
Pfam PF08127: Peptidase family C1 propeptide (conserved_site)
This motif is found at the N terminal of some members of the Peptidase_C1 family ([pfam:PF00112]) and is involved in activation of this peptidase.
Pfam PF24357: ABC transporter TMD0 domain (domain)
This transmembrane domain is found N-terminal in a number of ATP-binding cassette (ABC) transporters. It is composed of four or five helices arranged in a bundle.
Pfam PF01288: 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) (domain)
All organisms require reduced folate cofactors for the synthesis of a variety of metabolites. Most microorganisms must synthesise folatede novobecause they lack the active transport system of higher vertebrate cells which allows these organisms to use dietary folates. Enzymes involved in folate biosynthesis are therefore targets for a variety of antimicrobial agents such as trimethoprim or sulphonamides. 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (2.7.6.3) (HPPK) catalyses the attachment of pyrophosphate to 6-hydroxymethyl-7,8-dihydropterin to form 6-hydroxymethyl-7,8-dihydropteridine pyrophosphate. This is the first step in a three-step pathway leading to 7,8 dihydrofolate. Bacterial HPPK (gene folK or sulD)  is a protein of 160 to 270 amino acids. In the lower eukaryote Pneumocystis carinii, HPPK is the central domain of a multifunctional folate synthesis enzyme (gene fas) .
Wikipedia: E or e is the fifth letter and the second vowel letter of the Latin alphabet, used in the modern English alphabet, the alphabets of other western European languages and others worldwide. Its name in English is e ; plural es, Es, or E's.
Pfam PF11448: Protein of unknown function (DUF3005) (family)
This is a bacterial family of uncharacterised 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 PF18450: Zinc Finger domain (domain)
This is a C2H2 type zinc finger domain which can be found in Zinc finger and BTB domain-containing protein 21 (ZBTB21).
Wikipedia: A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells. Xenopus laevis TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein followed soon thereafter by the Krüppel factor in Drosophila. It often appears as a metal-binding domain in multi-domain proteins.
Pfam PF05970: PIF1-like helicase (family)
This family includes homologues of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated. This family includes a large number of largely uncharacterised plant proteins.  This entry includes a P-loop motif that is involved in nucleotide binding.
Pfam PF13915: Domain of unknown function (DUF4210) (domain)
This short domain is found in fungi, plants and animals, and the proteins appear to be necessary for chromosome segregation during meiosis.
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 PF07143: CrtC N-terminal lipocalin domain (domain)
This family contains the members of the old Pfam family DUF2006. Structural characterisation of family member [swissprot:Q82US3] (from DUF2006 now merged into this family) has revealed a lipocalin-like fold with domain duplication.
Pfam PF14702: Central domain of human glycogen debranching enzyme (domain)
This is a central domain of the eukaryotic variant of the glycogen debranching enzyme (GDE). The eukaryotic GDE performs two functions: 4-alpha-D-glucanotransferase, [ec:2.4.1.25], and Amylo-alpha-1,6-glucosidase, [ec:3.2.1.33], performed by the, respectively N- and C- terminal halves of eukaryotic GDE enzyme This central domain follows the glucanotransferase domain and precedes the glucosidase (GDE_N) domain. It is very likely that the current definition contains two or more domains, by analogy with bacterial GDEs, this domain should be involved in substrate- binding either for the N-terminal glucanotransferase and/or the the C-terminal glucosidase (or both).
Pfam PF06695: Putative small multi-drug export protein (family)
This family contains a small number of putative small multi-drug export proteins.
Pfam PF01518: Sigma NS protein (family)
This viral protein has a poly(C)-dependent poly(G) polymerase activity.