SII-SWORD/CoKE huggingface dataset:
Pfam PF24741: AlkZ related (family)
This entry represents uncharacterised bacterial proteins that have a detectable similarity to AlkZ-like proteins [pfam:PF06224]. AlkZ adopts a unique fold in which three tandem winged helix-turn-helix (HTH) motifs scaffold a positively charged concave surface shaped for binding to duplex DNA. In contrast, the members of this family contain two instead of three tandem HTH motifs. They still probably retain the basic interface to bind DNA however it is unclear whether these proteins possess enzymatic activity.
Pfam PF24405: Pua-like (domain)
Members of the PUA family play a crucial role in binding and recognising RNA and DNA with modified bases. They are often linked with Calcineurin-CE domains, indicating their function as sensors in prokaryotic antiviral immunity by recognising modified DNA in invasive DNA elements.
Pfam PF10273: Pre-rRNA-processing protein TSR2 (family)
This entry represents the central conserved section of a family of proteins described as pre-rRNA-processing protein TSR2. The region has a distinctive WGG motif but the function is unknown.
Pfam PF23335: IFT80 second beta-propeller (repeat)
This entry represents the second beta-propeller of the Intraflagellar transport protein 80 homolog (IFT80) from human and related proteins. IFT80 is a component of the intraflagellar transport (IFT) complex B, which is essential for the development and maintenance of motile and sensory cilia. It is required for initiation of the ciliary axoneme. It has an unique architecture consisting of two beta-propellers followed by an alpha-solenoid structure. This beta-propeller is involved in dimerization together with the alpha-solenoid.
Pfam PF20607: Family of unknown function (DUF6800) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length and have conserved Arginine residues. This family may have an alpha-helical structure.
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 PF08904: EipB-like (family)
This entry includes a group of bacterial proteins, including EipB from Brucella. EipB is a periplasmic protein that functions as part of a system required for cell envelope homeostasis. It adopts a beta-spiral fold, consisting of 14 beta-strands and 2 alpha-helices.
Pfam PF00669: Bacterial flagellin N-terminal helical region (family)
Flagellins polymerise to form bacterial flagella. This family includes flagellins and hook associated protein 3. Structurally this family forms an extended helix that interacts with [pfam:PF00700].
Pfam PF11154: Protein of unknown function (DUF2934) (family)
This bacterial 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 PF14954: Limb expression 1 (family)
This entry represents the limb expression 1 (LIX1) family.
Pfam PF19393: Family of unknown function (DUF5968) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000566) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
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 PF17523: MinK-related peptide, potassium channel accessory sub-unit protein 4 (family)
MinK-related peptides (MiRPs or KCNEs) are single-transmembrane proteins that associate with pore-forming ion-channel sub-units to form stable complexes with channel properties markedly distinct from those of the isolated pore-forming sub-units. MPS-4 is expressed exclusively in the C. elegans nervous system and is essential for neuronal excitability.
Pfam PF22061: CSN7 helical bundle subdomain (repeat)
This entry represents the helical bundle subdomain (HB) found at the N-terminal of CSN7 (COP9 signalosome complex subunit 7) proteins. This HB constitutes a functional subdomain that, with the C-terminal winged helix subdomain, constitutes the PCI domain, which mediate interactions with other COP9 signalosome components. The COP9 signalosome complex (CSN) that regulates the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes which leads to a decrease in Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. This complex is involved in various cellular and developmental processes.
Pfam PF09255: Caf1 Capsule antigen (domain)
Members of this family are predominantly found in the F1 capsule antigen Caf1 synthesised by Yersinia bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the bacterium to sites of infection.
Wikipedia: In molecular biology, Caf1 capsule antigen proteins are a family of the F1 capsule antigens Caf1 synthesised by Yersinia bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the bacterium to sites of infection.
Pfam PF03517: Regulator of volume decrease after cellular swelling (domain)
ICln is a ubiquitously expressed multi-functional protein that plays a critical role in regulating volume decrease in cells after cellular swelling. In plants, ICln induces Cl- currents, thus regulating Cl- homoeostasis in eukaryotes. Structurally, the fold resembles a pleckstrin homology fold, on of whose roles is to recruit and tether their host protein to the cell membrane; and although the surface charges of the ICln fold are not equivalent to those of the PH domain, ICln can be phosphorylated in vitro and the PH-nature of the domain may be the part involving it in the transposition from cytosol to cell membrane during cytotonic swelling.
Pfam PF22438: Flagellar protein FlgA, HotDog domain-like (domain)
This domain is found in the flagellar protein FlgA from Thermotoga maritima ([swissprot:Q9X1M7]). Its structure has been characterised  (PDB:3frn).
Pfam PF03572: Peptidase family S41 (family)
This entry represents a domain found in the tail-specific proteases, such as retinol-binding protein 3 (also known as IRBP) from animals, C-terminal processing peptidases from algae and tricorn proteases from archaea. This domain share structural similarity with the crotonase fold that is formed from repeated Î²/Î²/Î± units, which comprises two perpendicular Î²-sheet surrounded by Î±-helices.
Pfam PF08782: c-SKI Smad4 binding domain (domain)
c-SKI is an oncoprotein that inhibits TGF-beta signaling through interaction with Smad proteins.  This domain binds to Smad4
Pfam PF01328: Peroxidase, family 2 (family)
The peroxidases in this family do not have similarity to other peroxidases.
Pfam PF14828: Amnionless (family)
The amnionless protein forms a complex with cubilin. This complex is necessary for vitamin B12 uptake.
Pfam PF15385: Specifically androgen-regulated gene protein (family)
This family of proteins is found in eukaryotes, the function of this protein is still unknown but it is thought to be an androgen receptor. Protein expression is up-regulated in the presence of androgens, but not in the presence of glucocorticoids. SARG tends to be highly expressed in prostate tissue. Proteins in this family are typically between 340 and 587 amino acids in length. There is a conserved EETI sequence motif.
Pfam PF03959: Serine hydrolase (FSH1) (domain)
This is a family of serine hydrolases.
Pfam PF05363: Herpesvirus US12 family (family)
US12 a key factor in the evasion of cellular immune response against HSV-infected cells. Specific inhibition of the transporter associated with antigen processing (TAP) by US12 prevents peptide transport into the endoplasmic reticulum and subsequent loading of major histocompatibility complex (MHC) class I molecules. US12 is comprised of three helices and is associated with cellular membranes.
Wikipedia: Infected cell protein 47 also ICP-47 or ICP47 is a protein encoded by the viruses such as Herpes simplex virus and Cytomegalovirus that allows them to evade the human immune system's CD8 T-cell response by interfering with an infected cell's ability to show viral epitopes to T cells. Its secondary structure shows three helices.
Pfam PF14404: Ribosomally synthesized peptide in Streptomyces species (family)
A ribosomally synthesized peptide related to microviridin and marinostatin, usually in the gene neighborhood of one or more RimK-like ATP-grasp. The gene-context suggests that it is further modified by the ATP-grasp. The peptide is predicted to function in a defensive or developmental role, or as an antibiotic.
Pfam PF12496: Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2 (family)
This domain family is found in eukaryotes, and is typically between 119 and 133 amino acids in length. There is a conserved HGGY sequence motif. This family is Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2. It interacts with pro- and anti- apoptotic molecules in the cell.
Pfam PF10190: Putative transmembrane protein 170 (family)
Tmem170 is a family of putative transmembrane proteins conserved from fungi to nematodes to humans. The protein is only of approximately 130 amino acids in length. The function is unknown.
Pfam PF20785: MACPF protein, D3 domain (family)
This domain is found in proteins of the membrane-attack complex/ perforin (MACPF) family from Bacteroidetes. These transmembrane pore- forming proteins are organized into three structured domains:  an MACPF domain ([pfam:PF01823]) and two C-terminal domains, D2 and D3. This entry represents the D3 domain, which adopts an alpha/beta fold and functions as a wedge between D2 and MACPF.
Pfam PF18225: Sensor histidine kinase (AbfS) sensor domain (domain)
This is the sensor domain of sensor histidine kinase (AbfS) present in Cellvibrio japonicus. AbfS forms part of the AbfR/S two-component system which is needed to to activate the expression of the suite of enzymes that remove the numerous side chains from xylan. The overall fold of the sensor domain is that of a classical Per Arndt Sim domain. This domain binds xylotriose and xylobiose (Matilla et.al, FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF20358: Family of unknown function (DUF6653) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 149 and 172 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 PF11869: Protein of unknown function (DUF3389) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 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 PF08129: Alpha/beta enterocin family (family)
This family consists of the alpha and beta enterocins and lactococcin G peptides. These peptides have some antimicrobial properties; they inhibit the growth of Enterococcus spp. and a few other gram-positive bacteria. These peptides act as pore- forming toxins that create cell membrane channels through a barrel-stave mechanism and thus produce an ionic imbalance in the cell. These family of antimicrobial peptides belong to the class II group of bacteriocin.
Wikipedia: Class II bacteriocins  are a class of small peptides that inhibit the growth of various bacteria.
Pfam PF01389: OmpA-like transmembrane domain (domain)
The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel. This family includes some other distantly related outer membrane proteins with low scores.
Wikipedia: OmpA-like transmembrane domain  is an evolutionarily conserved domain of bacterial outer membrane proteins. This domain consists of an eight-stranded beta barrel. OmpA is the predominant cell surface antigen in enterobacteria found in about 100,000 copies per cell. The expression of OmpA is tightly regulated by a variety of mechanisms. One mechanism by which OmpA expression is regulated in Vibrio species is by an antisense non-coding RNA called VrrA.
Pfam PF22049: PRRSV nonstructural protein 11 N-terminal domain (domain)
PRRSV nonstructural protein 11 (NSP11) consists of two domains. The N-terminal domain adopts an alpha/beta structure composed of a central antiparallel four-stranded beta-sheet packed with helices on both sides and capped with a beta-hairpin. This domain may be involved in oligomerisation.
Pfam PF19344: Tetracyclin repressor-like, C-terminal domain (domain)
This is the C-terminal domain found in putative transcriptional regulator, TetR family proteins.
Pfam PF14338: Mrr N-terminal domain (family)
This domain is found at the N-terminus of the Mrr restriction endonuclease catalytic domain, [pfam:PF04471]. Fold recognition analysis predicts that it is a diverged member of the winged helix variant of helix turn helix proteins. It may play a role in DNA sequence recognition.
Pfam PF19485: Family of unknown function (DUF6021) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000399) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This  family includes a protein from the orfamide A biosynthetic gene  cluster from Pseudomonas protegens Pf-5 and appears to be  predominantly found in Pseudomonadaceae.
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 PF16122: 40S ribosomal protein SA C-terminus (family)
This domain is found at the C-terminus of 40S ribosomal protein SA.
Pfam PF08662: Eukaryotic translation initiation factor eIF2A (repeat)
This is a family of eukaryotic translation initiation factors.
Pfam PF23920: Domain of unknown function (DUF7259) (domain)
This domain is found in uncharacterised proteins from proteobacteria. It is usually found C-terminal to [[pfam:PF22288]]. It is predicted to adopt a globular structure with a beta-barrel shape.
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 PF09155: Domain of unknown function (DUF1940) (domain)
Members of this family adopt a secondary structure consisting of six alpha helices, with four long helices (alpha1, alpha2, alpha5, alpha6) form a left-handed, antiparallel alpha helical bundle. The function of this family of Archaeal hypothetical proteins has not, as yet, been defined.
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 PF22768: Siphovirus-type tail component, C-terminal domain (domain)
This entry consists of several phage tail component proteins, including bacteriophage SPP1 distal tail protein Dit (also known as Gp19.1 or Gp19), as well as some bacterial proteins of unknown function. This entry represents the C-terminal domain.
Pfam PF24655: Domain of unknown function (DUF7645) (domain)
This domain is found in uncharacterised proteins mainly from plants. It is predicted to fold into a three helical bundle.
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 PF22212: CPV, RNA-directed RNA polymerase, central polymerase domain (domain)
This domain is found at the N-terminal of RNA-directed RNA polymerase (RdRP) from Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) and similar sequences from reovirus. This protein adopts a closed cage-like structure consisting of a central polymerase domain (this entry) sandwiched between N-terminal and C-terminal bracelet domains. This domain adopts the classical 'right-handed' polymerase architecture that includes fingers, palm, and thumb subdomains.
Pfam PF14642: FAM47 family (family)
The function of this Chordate family of proteins is not known.
Pfam PF18654: LegC3 N-terminal coiled-coil domain (coiled_coil)
LegC3 is an effector protein secreted by Legionella pneumophila which is believed to act by inhibiting vacuolar fusion. The N-terminal domain of LegC3 is composed of a long discontinuous coiled-coil capped by an antiparallel four-helix bundle that is rigidly connected to the coiled-coil segment. The features responsible for fusion inhibition are located mainly within the N-terminal domain, as this domain alone was sufficient to inhibit vacuole fusion, and that this domain remains associated with vacuoles.
Pfam PF00402: Calponin family repeat (repeat)
Calponin  is a thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin, troponin C and tropomyosin. The interaction of calponin with actin inhibits the actomyosin MgATPase activity. Calponin is a basic protein of approximately 34 Kd. Multiple isoforms are found in smooth muscles. Calponin contains three repeats of a well conserved 26 amino acid domain. Such a domain is also found in vertebrate smooth muscle protein (SM22 or transgelin), and a number of other proteins whose physiological role is not yet established, including Drosophila synchronous flight muscle protein SM20, Caenorhabditis elegans unc-87 protein , rat neuronal protein NP25 , and an Onchocerca volvulus antigen .
Wikipedia: In molecular biology, the calponin family repeat is a 26 amino acid protein domain. Calponin 1 (CNN1) contains three copies of this domain. This domain is also found in vertebrate smooth muscle protein, and a number of other proteins whose physiological role is not yet established, including Drosophila synchronous flight muscle protein SM20, Caenorhabditis elegans unc-87 protein, rat neuronal protein NP25, and an Onchocerca volvulus antigen.
Pfam PF19883: Family of unknown function (DUF6356) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 71 and 88 amino acids in length. There are two conserved sequence motifs: KTGS and RMV.
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 PF16450: Proteasomal ATPase OB C-terminal domain (domain)
This is the C-terminal interdomain (ID) or oligonucleotide binding (OB) domain of proteasomal ATPase
Pfam PF24219: Family of unknown function (DUF7438) (family)
This entry represents a family of uncharacterized proteins found in bacteriophages. The function of this protein family is currently unknown.  The family appears to be conserved across various phage species that infect Escherichia coli and related bacteria. The family includes members from Phage T2 and T6.Members of this family are typically short proteins of around 60-67 amino acids in length. The structure of these proteins is predicted to be composed of two alpha helices that pack together. Structure prediction suggests these proteins may homodimerise (iPTM=0.83).
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 PF14788: EF hand (domain)
This entry represents the EF-hand domain found in 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-3 (PLC-delta3).
PLC-delta-3 is essential for trophoblast and placental development . It locates at the cleavage furrow where it may participate in cytokinesis .
Wikipedia: The EF hand is a helix–loop–helix structural domain or motif found in a large family of calcium-binding proteins.
Pfam PF16347: N-sulphoglucosamine sulphohydrolase, C-terminal (family)
This domain is found at the C-terminal end of sulfatases and alkaline phosphatases from bacteria, eukaryotes and archaea, including N-sulphoglucosamine sulphohydrolase from humans (SGSH) and Bifunctional sulfatase/alpha-L-rhamnosidase from Formosa agariphila (P36_S1_25). It shows a four-stranded antiparallel beta-sheet, with four surrounding alpha-helices, followed by a C-terminal extension consisting of a small two-stranded antiparallel beta-sheet.