SII-SWORD/CoKE huggingface dataset:
Pfam PF10972: Peptidoglycan-binding protein, CsiV (family)
CsiV, a small periplasmic protein (cell-shape integrity in Vibrio), is essential for growth of Vibrio cholerae in the presence of DAA, non-canonical amino-acids, the typical components of peptidoglycan side-chains in Vibrio cholerae. CsiV interacts with LpoA, the lipoprotein activator of penicillin-binding-protein1A that is necessary for mediating the assembly of peptidoglycan.  CsiV acts through LpoA to promote peptidoglycan biogenesis in V. cholerae and other vibrio species as well as in the other genera where this protein is found.
Pfam PF15276: Protein phosphatase 1 binding (family)
This domain contains a protein phosphatase 1 (PP1) binding site.
Pfam PF09999: Uncharacterized protein conserved in archaea (DUF2240) (family)
This domain, found in various hypothetical archaeal 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 PF17586: Family of unknown function (DUF5485) (family)
This is a family of unknown function found in Alphabaculovirus.
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 PF19687: MARF1 LOTUS domain (domain)
This is the LOTUS domain which is repeated in the C-terminal of of Meiosis regulator and mRNA stability factor 1 (MARF1) protein, an essential regulator of oogenesis required for completion of meiosis and retrotransposon silencing, key to maintain germline integrity. This domain provides RNA-binding properties to this protein, acting as an adapter to recruit targets for the effector domain NYN ([pfam:PF01936]) at the N-terminal (RNase activity).
Pfam PF17223: Cuticle protein CPCFC (family)
This entry contains cuticle proteins with a CX(5)C motif, although some members have a CX(7)C motif. In Anopheles gambiae, mRNA for  this protein is most abundant immediately following  ecdysis in larvae, pupae and adults, and is localised primarily in epidermis that secretes hard cuticle,  sclerites, setae, head capsules, appendages and  spermatheca. EM immunolocalisation studies  have shown that the protein is present in the  endocuticle of legs and antennae. CPCFC is found throughout the Hexapoda and in several classes  of Crustacea.
Pfam PF21457: RNA-binding, Nab2-type zinc finger (domain)
This domain is found in nuclear polyadenylated RNA-binding 2 protein NAB2 from Saccharomyces cerevisiae (also known as Nab2p). Nab2p is a major family of Poly A-binding proteins whose interactions are thought to be crucial for the control of poly(A) tail length. This domain is the second of seven CCCH zinc fingers which are responsible for polyadenosine. The first four zinc fingers together may bind RNA in the 3' to 5' direction.
Pfam PF11208: Protein of unknown function (DUF2992) (family)
This bacterial family of proteins has no known function. However, the cis-regulatory yjdF motif, just upstream from the gene encoding the proteins for this family, is a small non-coding RNA, Rfam:RF01764. The yjdF motif is found in many Firmicutes, including Bacillus subtilis. In most cases, it resides in potential 5' UTRs of homologues of the yjdF gene whose function is unknown. However, in Streptococcus thermophilus, a yjdF RNA motif is associated with an operon whose protein products synthesise nicotinamide adenine dinucleotide (NAD+). Also, the S. thermophilus yjdF RNA lacks typical yjdF motif consensus features downstream of and including the P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the S. thermophilus RNAs might sense a distinct compound that structurally resembles the ligand bound by other yjdF RNAs. On the ohter hand, perhaps these RNAs have an alternative solution forming a similar binding site, as is observed with some SAM riboswitches.
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 PF21066: Reovirus core-spike protein lambda-2 (L2), methyltransferase-2 (domain)
Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the second methyltransferase domain (MT2), which catalyses the last reaction, 2'O-methylation.
Pfam PF13583: Metallo-peptidase family M12B Reprolysin-like (domain)
This zinc-binding metallo-peptidase has the characteristic binding motif HExGHxxGxxH of Reprolysin-like peptidases of family M12B.
Pfam PF21052: EFR3, armadillo repeat (repeat)
EFR3 protein form a complex with Ypp1/TTC7 which is required to localise phosphatidylinositol 4-kinase (PI4K) to the plasma membrane. EFR3 acts as a regulator of the Stt4p phosphatidylinositol 4-kinase at contact sites between the endoplasmic reticulum and the plasma membrane. EFR3 consists of armadillo repeats at its N-terminal, which act as a scaffold and a basic patch binds acidic phospholipids that anchors the complex to the plasma membrane.
Pfam PF14808: TMEM164 family (domain)
This entry represents a family of integral membrane proteins. In eukaryotes this protein is known as TMEM164, but it is also widely distributed in bacteria. Proteins in this family are typically between 200 to 300 amino acids in length. The protein contains several conserved cysteine and histidine residues that are likely to be functionally important. Proteins in this family appear to have seven transmembrane helices.
Pfam PF22180: RH3 domain (domain)
This domain family includes ORF E73 from Sulfolobus virus. This domain, called RH3 domain, show great similarity to domains found in proteins involved in transcriptional regulation, but with an additional third helix.
Pfam PF04304: Protein of unknown function (DUF454) (family)
Predicted membrane protein.
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 PF04552: Sigma-54, DNA binding domain (domain)
This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex.  Furthermore this region contains a putative helix-turn-helix motif.  At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.
Pfam PF04117: Mpv17 / PMP22 family (family)
The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis.  More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH).  MDDS is a clinically heterogeneous group of disorders characterised by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues.  Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids.  NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America.  The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance.
Pfam PF24175: SU10 adaptor protein (family)
This entry represents adaptor proteins found in SU10-like bacteriophages and prophages. The dodecamer of SU10 adaptor proteins forms the interface between the dodecamer of portal proteins and hexamer of nozzle proteins. The adaptor complex provides six attachment sites for long tail fibers, each of which is formed by a trimer of long tail fiber proximal proteins and a trimer of long tail fiber distal proteins. The adaptor protein of SU10 has the same domain organization as those of phages T7 and KP32. Its structure consists of an alpha-helical bundle domain composed of intertwined N- and C-terminal helices; and a beta-sandwich long tail fiber dock domain.
Pfam PF17293: Arm DNA-binding domain (domain)
This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases.
Pfam PF15822: MAPK-interacting and spindle-stabilising protein-like (disordered)
MISS is a family of eukaryotic MAPK-interacting and spindle-stabilising protein-like proteins.  MISS is rich in prolines and has four potential MAPK-phosphorylation sites, a MAPK-docking site, a PEST sequence (PEST motif) and a bipartite nuclear localisation signal. The endogenous protein accumulates during mouse meiotic maturation and is found as discrete dots on the MII spindle. MISS is the first example of a physiological MAPK-substrate that is stabilised in MII that specifically regulates MII spindle integrity during the CSF arrest.
Pfam PF11343: Protein of unknown function (DUF3145) (family)
This family of proteins with unknown function appear to be restricted to 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 PF02157: Mannose-6-phosphate receptor (family)
This family includes both Cation-dependent and cation independent mannose-6-phosphate receptors.
Pfam PF17556: MIT-like atracotoxin family (family)
This family includes peptides such as the Atracotoxin-Hvf17 [swissprot:P81803]. It is a a non-toxic peptide isolated from the venom of Blue Mountains funnel-web spider Hadronyche versuta. It does not function like classical funnel-web spider atracotoxins to modulate mammalian or insect voltage-gated ion channel function since it lacks insecticidal activity and fails to affect vas deferens smooth muscle or skeletal muscle contractility. This peptide has ten conserved cysteine residues similar to AVIT family members such as MIT1. Due to the lack of the AVIT N-terminal four residues and lack of functional similarity to the AVIT family, the Atracotoxin-Hvf17 is classified as MIT-like atracotoxin.
Pfam PF10714: Late embryogenesis abundant protein 18 (family)
This is a family of late embryogenesis-abundant proteins There is high accumulation of this protein in dry seeds, and in the roots of full-grown plants in response to dehydration and ABA (abscisic acid application) treatments. This LEA protein disappears after germination. It accumulates in growing regions of well irrigated hypocotyls and meristems suggesting a role in seedling growth resumption on rehydration. As a group the LEA proteins are highly hydrophilic, contain a high percentage of glycine residues, lack Cys and Trp residues and do not coagulate upon exposure to high temperature, and for these reasons are considered to be members of a group of proteins called hydrophilins. Expression of the protein is negatively regulated during etiolating growth, particularly in roots, in contrast to its expression patterns during normal growth.
Pfam PF11626: TRF2-interacting telomeric protein/Rap1 - C terminal domain (family)
This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C terminal domain.  Rap1 is otherwise known as TRF2-interacting protein, as it is one of the six subunit components of the Shelterin complex. Shelterin protects telomere ends from attack by DNA-repair mechanisms. Model doesn't capture Sch. pombe as it cuts this sequence into two.
Pfam PF18507: WW domain (domain)
This is a WW domain found in histone-lysine N-methyltransferase, H3 lysine-36 specific ([ec:2.1.1.43]) in Saccharomyces cerevisiae. The WW domain is the simplest natural beta-sheet structure. It is a 35-residue protein module found in signaling and regulatory proteins with two highly conserved tryptophans and a strictly conserved proline.
Wikipedia: The WW domain is a modular protein domain that mediates specific interactions with protein ligands. This domain is found in a number of unrelated signaling and structural proteins and may be repeated up to four times in some proteins. Apart from binding preferentially to proteins that are proline-rich, with particular proline-motifs, [AP]-P-P-[AP]-Y, some WW domains bind to phosphoserine- and phosphothreonine-containing motifs.
Pfam PF02109: DAD family (family)
Members of this family are thought to be integral membrane proteins.  Some members of this family have been shown to cause apoptosis if mutated, these proteins are known as DAD for defender against death.  The family also includes the epsilon subunit of the oligosaccharyltransferase that is involved in N-linked glycosylation.
Pfam PF04623: Adenovirus E1B protein N-terminus (family)
This family constitutes the amino termini of E1B 55 kDa ([pfam:PF01696]). E1B 55K binds p53 the tumour suppressor protein converting it from a transcriptional activator which responds to damaged DNA in to an unregulated repressor of genes with a p53 binding site. This protects the virus against p53 induced host antiviral responses and prevents apoptosis as induced by the by the adenovirus E1A protein. The role of the N terminus in the function of E1B is not known.
Pfam PF18273: Type III R-M EcoP15I C-terminal domain (domain)
This domain is found in the Type III restriction-modification EcoP15I complex, present in E. coli. The Mod subunits function as a dimer with ModA recognizing the DNA and ModB methylating the target adenine base. This domain is found in the C-terminal of the ModB subunit.
Pfam PF21044: CIP2A, N-terminal (repeat)
Cancerous inhibitor of PP2A (CIP2A) functions via protein binding through interactions with many other proteins including MYC, polo like kinase (PLK1) and NIMA protein. t is an inhibitor of PP2A, a tumour suppressor. CIP2A binds to PP2A and inhibits its phosphatase functions resulting in tumourigenesis transformation of cells. This is the N-terminal HEAT repeats domain, which can be subdivided into tip, stem and C-dimerisation subdomains; the latter is responsible for CIP2A dimerisation.
Pfam PF21118: DosC CZB-like middle domain (domain)
This entry represents the middle (Mid) domain of DosC proteins an oxygen-regulated diguanylate cyclase.
Pfam PF15265: FAM196 family (family)
This protein family is a domain of unknown function.  This family of proteins is found in eukaryotes and are typically between 441 and 534 amino acids in length.
Pfam PF03770: Inositol polyphosphate kinase (family)
ArgRIII has has been demonstrated to be an inositol polyphosphate kinase.
Pfam PF14282: FlxA-like protein (coiled_coil)
This family includes FlxA from E. coli, [swissprot:P77609]. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation.
Pfam PF22184: Carbohydrate binding module family 56 (domain)
CBM56 is a carbohydrate-binding module found in beta-1,3-glucanase, that binds to soluble beta-1,3-glucan laminarin and it is proposed to bind to quaternary polysaccharide structures, most likely to triple helix formed by polymerised beta-1,3-glucans. This domain adopts a typical Ig-like beta-sandwich.
Pfam PF14833: NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase (domain)
3-Hydroxyisobutyrate is a central metabolite in the valine catabolic pathway, and is reversibly oxidised to methylmalonate semi-aldehyde by a specific dehydrogenase belonging to the 3-hydroxyacid dehydrogenase family. The reaction is NADP-dependent and this region of the enzyme binds NAD. The NAD-binding domain of 6-phosphogluconate dehydrogenase adopts an alpha helical structure.
Pfam PF20193: Family of unknown function (DUF6556) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Firmicutes. Proteins in this family are typically between 130 and 155 amino acids in length. Some members are predicted histone acetyltransferases.
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 PF00834: Ribulose-phosphate 3 epimerase family (domain)
This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.
Wikipedia: Phosphopentose epimerase encoded in humans by the RPE gene is a metalloprotein that catalyzes the interconversion between D-ribulose 5-phosphate and D-xylulose 5-phosphate.D-ribulose 5-phosphate  D-xylulose 5-phosphate
Pfam PF00994: Probable molybdopterin binding domain (domain)
This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation.
Pfam PF04170: NlpE N-terminal domain (domain)
This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. In Escherichia coli and Salmonella typhi, NlpE is also known to confer copper tolerance in copper-sensitive strains of Escherichia coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes.
Pfam PF07193: Protein of unknown function (DUF1408) (family)
This family consists of several hypothetical Lactococcus lactis and related phage proteins of around 75 residues in length. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF05064: Nsp1-like C-terminal region (family)
This family probably forms a coiled-coil.  This important region of Nsp1 is involved in binding Nup82.
Pfam PF19992: Family of unknown function (DUF6427) (family)
This entry represents a set of uncharacterised bacterial proteins that are likely 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 PF21323: Lysine-specific demethylase 5, C-terminal helical domain (domain)
This is the C-terminal helical domain from Lysine-specific demethylase 5 subfamily (KDM5), which is localised between the Jumonji C (JmjC) domain and the C5HC2 zinc finger motif ([pfam:PF02928]).
Pfam PF10226: CCDC85 family (family)
This entry includes human CCDC85A/B/C and C. elegans  Picc-1 protein. Picc-1 serves as  a linker protein which helps  to recruit the Rho GTPase-activating protein, pac-1, to  adherens junctions. Human CCDC85B suppresses the  beta-catenin activity in a p53-dependent manner.
Pfam PF18546: Methanogen output domain 1 (domain)
MetOD1 (Methanogen output domain 1) is a protein domain that is found in euryarchaeal classes Methanobacteria and Methanomicrobia, either in stand-alone form or in combination with the Response_reg [pfam:PF00072] domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems). This domain is distantly related to the HNOB and V4R domains.
Pfam PF06526: Protein of unknown function (DUF1107) (family)
This family consists of several short, hypothetical bacterial proteins of unknown 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 PF07542: ATP12 chaperone protein (family)
Mitochondrial F1-ATPase is an oligomeric enzyme composed of five distinct subunit polypeptides. The alpha and beta subunits make up the bulk of protein mass of F1. In Saccharomyces cerevisiae both subunits are synthesised as precursors with amino-terminal targeting signals that are removed upon translocation of the proteins to the matrix compartment.  These proteins include examples from eukaryotes and bacteria and may have chaperone activity, being involved in F1 ATPase complex assembly.