SII-SWORD/CoKE huggingface dataset:
Pfam PF21745: PMI1/PMIR1-2, C-terminal domain (domain)
This entry represents a presumed domain found towards the C-terminal of plant proteins, such as PMI1 (PLASTID MOVEMENT IMPAIRED 1 and PMIR1/2 (PMI1 related 1 and 2) from Arabidopsis. PMI1 and PMIR1 are required for efficient chloroplast photorelocation movement, while PMIR2 seems not necessary for this. PMI1 is a mobile signal that initiates coordinated changes in protein-protein and protein-plasma membrane interactions for chloroplast movement in response to light, which determines where in the cell chloroplasts are able to anchor o the plasma membrane. PMI1 has been found to mediate ABA sensitivity during germination.
Pfam PF04391: Protein of unknown function (DUF533) (family)
Some family members may be secreted or integral membrane 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 PF13576: Pentapeptide repeats (9 copies) (repeat)
These repeats were first identified in many cyanobacterial proteins but they are also found in bacterial as well as in plant proteins . The repeats were first identified in hglK . Pentapeptide repeat proteins (PRPs) are characterised by the repetition of the pentapeptide repeat motif , which allows it to adopt a right-handed Î²-helical structure conformation . The functions of these repeats is unknown but it has been shown that members of this family share the ability to interact with DNA-binding proteins, such as DNA gyrase. For example, McbG (from Escherichia coli) protects the DNA gyrase from microcin B17 toxicity, MfpAMt (from Mycobacterium tuberculosis) and Qnr (from Klebsiella pneumoniae and other enterobacteria) are involved in resistance to fluoroquinolones .
Wikipedia: Pentapeptide repeats are a family of sequence motifs found in multiple tandem copies in protein molecules. Pentapeptide repeat proteins are found in all species, but they are found in many copies in cyanobacterial genomes. The repeats were first identified by Black and colleagues in the hglK protein. The later Bateman et al. showed that a large family of related pentapeptide repeat proteins existed. The function of these repeats is uncertain in most proteins. However, in the MfpA protein a DNA gyrase inhibitor it has been suggested that the pentapeptide repeat structure mimics the structure of DNA. The repeats form a regular right handed four sided beta helix structure known as the Rfr-fold.
Pfam PF21966: AppA, sensor containing heme instead of cobalamin (domain)
This domain is found at the C-terminal end of AppA protein from Rhodobacter sphaeroides and similar sequences from alphaproteobacteria. AppA is a light-sensing antirepressor involved in oxygen and light control of photosynthesis-gene expression. This protein senses blue-light via its N-terminal blue-light using FAD (BLUF) domain ([pfam:PF04940]) and oxygen via its sensor containing heme instead of cobalamin (SCHIC) domain (this entry). This domain has a flavodoxin-like fold.
Pfam PF09184: PPP4R2 (family)
PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex.  It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes.
Pfam PF08399: VWA N-terminal (family)
This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, [pfam:PF00092]) and Cache ([pfam:PF02743]) domains.  It has been found in vertebrates, Drosophila and C. elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits.
Pfam PF11775: Cobalamin biosynthesis protein CobT VWA domain (domain)
This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid.
Pfam PF10393: Trimeric coiled-coil oligomerisation domain of matrilin (coiled_coil)
This short domain is a coiled coil structure and has a single cysteine residue at the start which is likely to form a di-sulfide bridge with a corresponding cysteine in an upstream EGF ([pfam:PF00008]) domain thereby spanning a VWA ([pfam:PF00092]) domain. All three domains can be associated together as in the cartilage matrix protein matrilin, where this domain is likely to be responsible for oligomerisation.
Pfam PF09786: Cytochrome B561, N terminal (family)
Members of this family are found in the N terminal region of cytochrome B561, as well as in various other putative uncharacterised proteins.
Pfam PF21867: Virion DNA-directed RNA polymerase domain (domain)
This domain is found in Virion DNA-directed RNA polymerase from Bacteriophage N4 (vRNAP), which is injected into the host upon infection and transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure. This entry represents a region located C-terminal to the mini-vRNAP, which possesses all RNAP functions.
Pfam PF21750: Probable sensor domain DACNH (domain)
This entry represents a potential sensor domain found at the N-terminal of bacterial diadenylate cyclases which is typically followed by the DAC ([pfam:PF02457]) domain. This domain may consist of two alpha-helices and seven beta-strands. In deltaproteobacteria members this domain is preceded by the DACND domain ([pfam:PF21749]).
Pfam PF22816: Alpha-1,3-glucanase catalytic domain D2 (repeat)
This entry represents a domain found in the homologues of Alpha-1,3-glucanase. This domain is found C-terminal in the catalytic domain (CatAgl-FH1). It folds into a right-handed beta-helix fold.
Pfam PF14021: Tuberculosis necrotizing toxin (domain)
This is the C-terminal domain secreted by Mycobacterium tuberculosis (Mtb). It induces necrosis of infected cells to evade immune responses. Mtb utilizes the protein CpnT to kill human macrophages by secreting its C-terminal domain (CTD), named tuberculosis necrotizing toxin (TNT) that induces necrosis. It acts as a NAD+ glycohydrolase which hydrolyzes the essential cellular coenzyme NAD+ in the cytosol of infected macrophages resulting in necrotic cell death. CpnT transports its toxic CTD from the cell surface of M. tuberculosis by proteolytic cleavage, where the toxin is cleaved to induce host cell death. Structural analysis determined that the TNT core contains only six beta-strands as opposed to seven found in all known NAD+-utilizing toxins, and is significantly smaller, with only two short alpha-helices and two 3/10 helices. Furthermore, the putative NAD+ binding pocket identified Q822, Y765 and R757 as residues possibly involved in NAD+-binding and hydrolysis based on similar positions of catalytic amino acids of ADP-ribosylating toxins. While glutamine 822 residue was detected to be highly conserved among TNT homologs.
Pfam PF01329: Pterin 4 alpha carbinolamine dehydratase (domain)
Pterin 4 alpha carbinolamine dehydratase is also known as DCoH (dimerisation cofactor of hepatocyte nuclear factor 1-alpha).
Pfam PF06458: MucBP domain (domain)
The MucBP (MUCin-Binding Protein) domain is found in a wide variety of bacterial proteins, in several repeats. The domain is found in bacterial peptidoglycan bound proteins and is often found in conjunction with [pfam:PF00746] and [pfam:PF00560].
Pfam PF06834: TraU protein (family)
This family consists of several bacterial TraU proteins. TraU appears to be more essential to conjugal DNA transfer than to assembly of pilus filaments.
Pfam PF09225: Restriction endonuclease PvuII (domain)
Members of this family are predominantly found in prokaryotic restriction endonuclease PvuII. They recognise the double-stranded DNA sequence 5'-CAGCTG-3' and cleave after G-3, resulting in specific double-stranded fragments with terminal 5'-phosphates.
Pfam PF19198: RsaA N-terminal domain (domain)
This entry represents the N-terminal domain of the RsaA S-layer protein from Caulobacter crescentus. This domain binds to lipopolysaccharide.
Pfam PF10817: Protein of unknown function (DUF2563) (family)
This family of proteins with unknown function appears to be restricted to Mycobacterium.
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 PF20341: Family of unknown function (DUF6636) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 136 and 200 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 PF18836: YdcK Beta solenoid repeat (repeat)
The crystal structure of YdcK from Salmonella cholerae includes a  beta-solenoid repeat. This Pfam entry includes a single repeat unit  of YDCK repeat.
Pfam PF01756: Acyl-CoA oxidase (family)
This is a family of Acyl-CoA oxidases [ec:1.3.3.6]. Acyl-coA oxidase converts acyl-CoA into trans-2- enoyl-CoA.
Pfam PF13103: TonB C terminal (family)
This family contains TonB members that are not captured by [pfam:PF03544].
Pfam PF19155: Family of unknown function (DUF5837) (family)
This family of unknown function is associated with the tenuecyclamide A biosynthetic gene cluster.
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 PF00410: Ribosomal protein S8 (domain)
This entry includes small ribosomal subunit protein uS8 from bacteria, archaea and eukaryotes (in yeast, these proteins are also known as S22 and in vertebrates S15A) . In Escherichia coli, uS8 is known to bind directly to 16S ribosomal RNA.
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 PF00094: von Willebrand factor type D domain (domain)
[swissprot:P17554] contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods. This domain is structurally homologous to the C-terminal domain of repulsive guidance molecules (RGM) despite low sequence identity.
Wikipedia: Von Willebrand factor type D domain (vWD) is an evolutionarily-conserved protein domain found in, among others, the von Willebrand factor (vWF). vWF is a large multimeric glycoprotein and it is synthesized by a type of bone marrow cell called megakaryocytes. The vWD domain allows vWF to perform its blood-clotting function by carrying factor VIII around.
Pfam PF07482: Domain of Unknown Function (DUF1522) (family)
The function of these proteins is unknown. All are from Bradyrhizobium japonicum.
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 PF05944: Phage small terminase subunit (family)
This family consists of several phage small terminase subunit proteins as well as some related bacterial sequences.
Pfam PF23739: HTH 3-helical bundle (domain)
This domain is found C-terminal in uncharacterised proteins mainly from Caenorhabditis. It shares sequence similarity to the HTH 3-helical bundle domains and it is predicted to adopt similar structure.
Pfam PF01198: Ribosomal protein L31e (family)
A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 87 to 128 amino-acid residues. This family consists of:


 * Yeast eL31A (also known as L34)
 * Archaeal L31 
 * Plants L31
 * Mammalian L31 


Ribosomal protein eL31, which is present in archaea and eukaryotes, binds the 23S rRNA and is one of six protein components encircling the polypeptide exit tunnel. It is a component of the eukaryotic 60S (large) ribosomal subunit, and the archaeal 50S (large) ribosomal subunit .
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 PF07879: PHB/PHA accumulation regulator DNA-binding domain (domain)
This domain is found at the N-terminus of the Polyhydroxyalkanoate (PHA) synthesis regulators. These regulators have been shown to directly bind DNA and PHA (). The invariant nature of this domain compared to the C-terminal [pfam:PF05233] domain(s) suggests that it contains the DNA-binding function.
Pfam PF02482: Sigma 54 modulation protein / S30EA ribosomal protein (family)
This Pfam family contains the sigma-54 modulation protein family and the S30AE family of ribosomal proteins which includes the light- repressed protein (lrtA) ([swissprot:P47908]).
Pfam PF24869: Domain of unknown function (DUF7734) (domain)
This domain is found in uncharacterised proteins. It is predicted to adopt globular structure consisting of a curved beta-sheet and alpha-helices packed on one side of it. It contains a semi-conserved FKGFSS sequence motif.
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 PF08687: Apx/Shroom domain ASD2 (family)
This region is found in the actin binding protein Shroom which mediates apical contriction in epithelial cells and is required for neural tube closure.
Wikipedia: In molecular biology, the Shroom protein family is a small group of related proteins that are defined by sequence similarity and in most cases by some link to the actin cytoskeleton. The Shroom (Shrm) protein family is found only in animals. Proteins of this family are predicted to be utilised in multiple morphogenic and developmental processes across animal phyla to regulate cells shape or intracellular architecture in an actin and myosin-dependent manner. While the founding member of the Shrm family is Shrm1, it appears that this protein is found only in Xenopus. In mice and humans, the Shrm family of proteins consists of:Shrm2, a protein involved in the morphogenesis, maintenance, and/or function of vascular endothelial cells.
Shrm3, a protein necessary for neural tube closure in vertebrate development as deficiency in Shrm results in spina bifida. Shrm3 is also conserved in some invertebrates, as orthologues can be found in sea urchins.
Shrm4, a regulator of cyto-skeletal architecture that may play an important role in vertebrate development. It is implicated in X-linked intellectual disability in humans.
Pfam PF17524: Anti-sigma factor CnrY (family)
This family is found in alpha and beta proteobacteria. Family members include anti-sigma factor CnrY from Cupriavidus metallidurans. Sigma factors are multi-domain sub-units of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. They also control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants.  CnrH, controls cobalt and nickel resistance in Cupriavidus metallidurans. CnrH is regulated by a complex of two transmembrane proteins: the periplasmic sensor CnrX and the anti-sigma CnrY. At rest, CnrH is sequestered by CnrY whose 45-residue-long cytosolic domain is one of the shortest anti-sigma domains. Upon Ni(II) or Co(II) ions detection by CnrX in the periplasm, CnrH is released between CnrH and the cytosolic domain of CnrY (CnrYc). The CnrH/CnrYC complex displays an unexpected structural similarity to the anti-sigma NepR in complex with its antagonist PhyR, whereas NepR shares no sequence similarity with CnrY. Crystal structure of CnrH/CnrY shows that CnrYC residues 3-19 are folded as a well-defined alpha-helix. The peptide further extends along the hydrophobic groove of sigma 2 with no canonical structure except for a short helical turn spanning residues 24-28. CnrY has a hydrophobic knob made of V4, W7 and L8 side chains protruding into sigma 4 hydrophobic pocket and contributing to the interface. In vivo investigation of CnrY function pinpoints part of the hydrophobic knob as a hotspot in CnrH inhibitory binding.
Pfam PF21644: Histone H3 binding protein ORF158L-like (domain)
This domain family is found in [swissprot:Q5YFA7] from Singapore grouper iridovirus (ORF158L) and similar viral proteins. ORF158L interacts with the histone H3/H4 complex and H3. It may play a key role in histone H3 modulation and function as a histone H3 chaperon. It folds into two beta-sheets that form an elongated beta-sandwich domain, and two short alpha-helices on one surface of the molecule with several loops between the secondary structures. The beta-sheets consist of four antiparallel beta-strands and five antiparallel beta-strands, respectively.
Pfam PF19438: LIN9 C-terminal (domain)
MuvB transcriptional regulatory complex interacts with B-Myb to form the MMB complex during S-phase of the cell cycle to activate genes required for the G2 and M phases. This is a domain found at the C-terminal of LIN9, one of the core members of the MuvB complex that functions as a scaffold protein and forms a subcomplex with the C-terminal of LIN152. This subcomplex forms a binding interface that recruits B-Myb to the MuvB complex which is arranged as a three-stranded antiparallel coiled-coil as the core of the structure. LIN9 contributes two helices (alpha1 and alpha2) that run antiparallel and are connected through a short linker.
Pfam PF11157: Protein of unknown function (DUF2937) (family)
This family of proteins with unknown function appears to be restricted to Proteobacteria.
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.