SII-SWORD/CoKE huggingface dataset:
Pfam PF15467: Secretogranin-3 (family)
Secretogranin_3 is a family of vertebrate proteins that is one of the granin family. Granins are rich in acidic amino acids, exhibit aggregation at low pH, and possess a high capacity for calcium binding. Because granins are restricted in their localisation to secretory granules of neuroendocrine cells, two interesting characteristics of their sorting mechanisms have been observed.  These are, first, that they aggregate on low pH/high calcium concentrations and second that two of them carry an N-terminal disulfide loop, mutations in which lead to mis-sorting. Thus, granins are thought to be essential for the sorting of secretory proteins at the trans-Golgi network. Chromogranin A (CgA) binds to SGIII in secretory granules of endocrine cells. SGIII directly binds to cholesterol components of the secretory granule membrane and targets CgA to secretory granules in pituitary and pancreatic endocrine cells. Mutations in the SGIII gene may influence the risk of obesity through possible regulation of hypothalamic neuropeptide secretion.
Pfam PF05785: Rho-activating domain of cytotoxic necrotizing factor (domain)
This family consists of several bacterial cytotoxic necrotizing factor proteins as well as related dermonecrotic toxin (DNT) from Bordetella species. Cytotoxic necrotizing factor 1 (CNF1) causes necrosis of rabbit skin and re-organisation of the actin cytoskeleton in cultured cells. Bordetella dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin which is composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain.
Wikipedia: In molecular biology, the cytotoxic necrotising factor family of proteins includes bacterial cytotoxic necrotising factor proteins and the related dermonecrotic toxin (DNT) from Bordetella species. Cytotoxic necrotizing factor 1 (CNF1) is a toxin whose structure from Escherichia coli revealed a 4-layer alpha/beta/beta/alpha structure containing mixed beta-sheets. CNF1 is expressed in strains of E. coli causing uropathogenic and neonatal meningitis. CNF1 alters host cell actin cytoskeleton and promotes bacterial invasion of the blood–brain barrier endothelial cells. CNF1 belongs to a unique group of large cytotoxins that cause constitutive activation of Rho guanosine triphosphatases (GTPases), which are key regulators of the actin cytoskeleton.
Pfam PF07888: Calcium binding and coiled-coil domain (CALCOCO1) like (coiled_coil)
Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1, [swissprot:Q8CGU1]). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 ([swissprot:Q61026]), and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.
Pfam PF07357: Dinitrogenase reductase ADP-ribosyltransferase (DRAT) (family)
This family consists of several bacterial dinitrogenase reductase ADP-ribosyltransferase (DRAT) proteins. Members of this family seem to be specific to Rhodospirillum, Rhodobacter and Azospirillum species. Dinitrogenase reductase ADP-ribosyl transferase (DRAT) carries out the transfer of the ADP-ribose from NAD to the Arg-101 residue of one subunit of the dinitrogenase reductase homodimer, resulting in inactivation of that enzyme. Dinitrogenase reductase-activating glycohydrolase (DRAG) removes the ADP-ribose group attached to dinitrogenase reductase, thus restoring nitrogenase activity. The DRAT-DRAG system negatively regulates nitrogenase activity in response to exogenous NH4+ or energy limitation in the form of a shift to darkness or to anaerobic conditions.
Pfam PF19527: Family of unknown function (DUF6055) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and fungi. Proteins in this family are typically between 431 and 744 amino acids in length.  Protein in this family often contain a C-terminal [pfam:PF16151] domain. These proteins are likely to be cell surface 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 PF24980: Response to Low Sulfur (LSU) family (coiled_coil)
The Response to Low Sulfur (LSU) protein family is involved in various physiological processes in Arabidopsis thaliana. Members of this family play roles in flower development under short-day conditions and may participate in defense response monitoring. Additionally, they are likely implicated in osmotic stress signaling. These functions suggest that the LSU protein family is crucial for plant adaptation to environmental stressors and developmental cues related to sulfur availability. Structure prediction shows that this protein adopts a long alpha helical structure. Structure prediction also suggests that this protein may form a homotrimeric coiled-coil ([swissprot:Q9SCK1] iPTM 0.72 pTM 0.74).
Pfam PF18463: Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain (domain)
This entry represents a subdomain found in the C-terminal cysteine/histidine-rich domain (CRD) of PCSK9 (also known as neural apoptosis-regulated convertase, NARC-1). PCSK9 has been shown to regulate circulating LDL-R levels by controlling LDL-R degradation. Furthermore, numerous mutations in the PCSK9 gene have been identified and associated with hypercholesterolemia (gain of function) or hypocholesterolemia (loss of function). The fully folded CRD, shows structural similarity to the resistin homotrimer, a small cytokine associated with obesity and diabetes. The C-terminal domain from PCSK9 consists of three, three-stranded beta-subdomains arranged in a pseudothreefold, and each of the subdomains in the CRD of PCSK9 consists of three structurally conserved disulfide bonds.
Pfam PF13789: Domain of unknown function (DUF4181) (family)
This protein family is functionally uncharacterised.
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 PF13054: Protein of unknown function (DUF3915) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length.
Pfam PF20779: MACPF protein, D2 domain (domain)
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 D2 domain, which adopts an alpha/beta fold.
Pfam PF20934: Bacillus phage phi29, Tail knob protein gp9, C-terminal domain (domain)
This domain is found at the C-terminal end of Tail knob protein gp9 from Bacillus phage phi29 and similar proteins from tailed bacteriophages. This protein blocks the end of the tube before DNA ejection while forming a channel perforating the host membrane in the process by adopting a hexameric tube structure with six flexible hydrophobic loops. This entry represents the region of the protein that forms the central part of the tube. It is organised into an alpha/beta subdomain, a long loop that protrudes from the inner wall covering about two-thirds of the tube, and a beta-domain in which the beta-strands are almost parallel with the tube axis.
Pfam PF17164: Domain of unknown function (DUF5122) beta-propeller (repeat)
This repeat often occurs in tandem, up to as many as 13 times, in proteins from Bdellovibrio bacteriovorus, Azotobacter vinelandii, Geobacter sulfurreducens, Pirellula sp. 1, Myxococcus xanthus, amongst others, many of which are Deltaproteobacteria. The length of the repeat ranges from about 57 to 61 amino acids -this entry represents a core region of approximately 54 amino acids.
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 PF00658: MLLE domain (domain)
The MLLE domain, also known as the PABC or CTC domain, is found at the C-terminus of cytoplasmic poly(A)-binding proteins (PABPs). It consists of a bundle of 4-5 alpha helices and contains a conserved KITGMLLE signature motif. The MLLE domain functions as a peptide-binding domain that interacts with PAM2 (PABP-interacting motif 2) sequences found in various PABP regulatory proteins involved in translation and mRNA decay.  Key conserved residues in the MLLE domain form binding pockets that accommodate an invariant phenylalanine and other residues in the PAM2 motif. Besides PABPs, the MLLE domain is also found in the E3 ubiquitin ligase UBR5 where it serves as a protein interaction module. In some fungi, Rrm4 RNA-binding proteins contain a binding platform of 2-3 divergent MLLE domains that interact with PAM2-like motifs in the Upa1 protein to mediate attachment of mRNA-protein particles to endosomes for transport and localized translation.
Pfam PF02746: Mandelate racemase / muconate lactonizing enzyme, N-terminal domain (domain)
SCOP reports fold similarity with enolase N-terminal domain.
Pfam PF12191: Tumour necrosis factor receptor stn_TNFRSF12A_TNFR domain (domain)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 129 and 184 amino acids in length. This is the stn_TNFRSF12A_TNFR domain from the tumour necrosis factor receptor. The function of this domain is unknown.
Pfam PF10124: Mu-like prophage major head subunit gpT (family)
Members of this family of proteins comprise various caudoviral prophage proteins, including the Mu-like prophage major head subunit gpT.
Pfam PF02264: LamB porin (domain)
Maltoporin (LamB protein) forms a trimeric structure which facilitates the diffusion of maltodextrins across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an antiparallel  beta-barrel.
Wikipedia: Maltoporins are bacterial outer membrane proteins of the porin family. Maltoporin forms a trimeric structure which facilitates the diffusion of maltodextrins across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an antiparallel beta-barrel.
Pfam PF17802: Prealbumin-like fold domain (domain)
This entry contains a prealbumin-like domain from a wide variety of bacterial surface proteins. This entry corresponds to domain 1 and domain 3 of SpaA from Corynebacterium diphtheriae. Some members of this family contain an isopeptide bond.ED A0A1Y3W7T5.1/11-86;
Pfam PF00179: Ubiquitin-conjugating enzyme (domain)
Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine.
Wikipedia: Ubiquitin-conjugating enzymes, also known as E2 enzymes and more rarely as ubiquitin-carrier enzymes, perform the second step in the ubiquitination reaction that targets a protein for degradation via the proteasome. The ubiquitination process covalently attaches ubiquitin, a short protein of 76 amino acids, to a lysine residue on the target protein. Once a protein has been tagged with one ubiquitin molecule, additional rounds of ubiquitination form a polyubiquitin chain that is recognized by the proteasome's 19S regulatory particle, triggering the ATP-dependent unfolding of the target protein that allows passage into the proteasome's 20S core particle, where proteases degrade the target into short peptide fragments for recycling by the cell.
Pfam PF13799: Domain of unknown function (DUF4183) (family)
This domain of unknown function contains a highly conserved ING 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 PF09583: Phage shock protein G (Phageshock_PspG) (family)
This protein was previously designated as YjbO in Escherichia coli. It is found only in genomes that have the phage shock operon (psp), but it is only rarely encoded near other psp genes. The psp regulon is upregulated in response to a number of stress conditions, including ethanol, expression of the filamentous phage secretin protein IV and other secretins and heat shock.
Pfam PF12522: Cytomegalovirus glycoprotein N terminal (family)
This domain family is found in viruses, and is approximately 30 amino acids in length. The family is found in association with [pfam:PF03554]. This family is an envelope glycoprotein of human cytomegalovirus (HCMV).
Pfam PF01516: Orbivirus helicase VP6 (family)
The VP6 protein a minor protein in the core of the virion is probably the viral helicase.
Pfam PF24262: Family of unknown function (DUF7463) (family)
This entry represents a small family of uncharacterised mycobacterial phage proteins. The family includes gene 82 from mycobacterial phage Bxb1.
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 PF11205: Protein of unknown function (DUF2987) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF04841: Vps16, N-terminal region (repeat)
This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole.  It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport.  The role of VPS16 in this complex is not known.
Pfam PF08346: AntA/AntB antirepressor (family)
In E. coli the two proteins AntA and AntB have 62% amino acid identities near their N termini. AntA appears to be encoded by a truncated and divergent copy of AntB.  The two proteins are homologous to putative antirepressors found in numerous bacteriophages, such as the hypothetical antirepressor protein encoded by the gene LO142 of the bacteriophage 933W.
Pfam PF19336: Domain of unknown function (DUF5921) (domain)
This family represents a domain of unknown function located between the Transcription factor IIIC subunit delta N-term ([pfam:PF12657]) and the Putative zinc-finger of transcription factor IIIC complex ([pfam:PF12660]) within the transcription Factor IIIC 90 kDa subunit (TFIIIC-delta/TFIIIC90, also known as general transcription factor 3C polypeptide 4). TFIIIC is a multisubunit complex that directly recognises promoter elements and recruits TFIIIB and RNA polymerase III, being absolutely required for RNA polymerase III transcription. TFIIIC90 has an intrinsic histone acetyltransferase activity with a substrate specificity for histone H3. This domain is likely to be involved in the interaction with other components of the TFIIIC complex.
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 PF00613: Phosphoinositide 3-kinase family, accessory domain (PIK domain) (repeat)
PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation.
Pfam PF10609: NUBPL iron-transfer P-loop NTPase (family)
This family contains ATPases involved in plasmid partitioning.  It also contains the cytosolic Fe-S cluster assembling factor NBP35 which is required for biogenesis and export of both ribosomal subunits.
Wikipedia: Nucleotide-binding protein 2 also known as cytosolic Fe-S cluster assembly factor NUBP2 is a protein that in humans is encoded by the NUBP2 gene.
Pfam PF21818: Family of unknown function (DUF6884) (domain)
This is a domain of unknown function that is found either as a standalone protein or in combination with other domains. Members of this family possess a highly conserved LSAXXG motif that may constitute an active site. This domain may be distantly related to oxidative stress response YaaA 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 PF15262: Domain of unknown function (DUF4592) (family)
This protein family is a domain of unknown function, which lies to the N-terminus of the protein. This domain family is found in eukaryotes, and is typically between 114 and 130 amino acids in length. There are two completely conserved residues (L and A) that may be functionally important. In humans, the gene that encodes this protein lies in the position, chromosome 2 open reading frame 55.
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 PF14734: Domain of unknown function (DUF4469) with IG-like fold (domain)
A C-terminal domain in a large family of (predicted) secreted proteins with uknown functions from human gut bacteroides
Pfam PF12928: tRNA-splicing endonuclease subunit sen54 N-term (domain)
This is an N-terminal family of archaeal and metazoan sen54 proteins that forms one of the tRNA-splicing endonuclease subunits.
Pfam PF01798: snoRNA binding domain, fibrillarin (family)
This family consists of various Pre RNA processing ribonucleoproteins. The function of the aligned region is unknown however it may be a common RNA or snoRNA or Nop1p binding domain. Nop5p (Nop58p) [swissprot:Q12499] from yeast is the protein component of a ribonucleoprotein required for pre-18s rRNA processing and is suggested to function with Nop1p in a snoRNA complex. Nop56p [swissprot:O00567] and Nop5p interact with Nop1p and are required for ribosome biogenesis. Prp31p Swiss:p49704 is required for pre-mRNA splicing in S. cerevisiae. Fibrillarin, or Nop, is the catalytic subunit responsible for the methyl transfer reaction of the site-specific 2'-O-methylation of ribosomal and spliceosomal RNA.
Pfam PF23762: SHCBP N-terminal domain (domain)
This entry represents the N-terminal domain of SHC SH2 domain-binding protein 1 (SHCBP) and related sequences such as SHCBA-B, SHP1L and NESD, from animals. SHCBP is involved in the regulation of multiple signalling pathways, such as FGF, NF-kB, MAPK/ERK, PI3K/AKT, TGF-beta/Smad and beta-catenin signalling. SHCBP participates in T-cell development, the regulation of downstream signal transduction pathways, and cytokinesis during mitosis and meiosis. SHCBP has been demonstrated to correlate with different forms of cancer and other diseases, and may play an important role in tumourigenesis and progression. The N-terminal domain of SHCBP was shown to be pivotal for its binding with RACGAP1, a component of the central spindlin complex in the nucleus with a significant role in oncogenic development and tumour recurrence. This domain might be found in association with a C-terminal beta-helix.
Pfam PF04811: Sec23/Sec24 trunk domain (domain)
COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface.
Pfam PF15221: Lens epithelial cell protein LEP503 (family)
This protein may be involved in lens epithelial cell differentiation.
Pfam PF15067: FAM124 domain (domain)
The FAM124 domain belongs to the Vicinial Oxygen Chelatase (VOC) superfamily of proteins and is comprised of two tandem alpha/beta domains. Residue conservation suggests that it might be enzymatic. Certain FAM124 domains fused to the TRADD-N domain are predicted to have secondarily lost their enzymatic activity and might be involved in protein-protein interactions.
Pfam PF15190: Transmembrane protein 251 (family)
This family of proteins, also known as UPF0694, is found in eukaryotes. Proteins in this family are around 135 amino acids in length. In humans, it is found on the chromosomal position, C14orf109.
Pfam PF03323: Bacillus/Clostridium GerA spore germination protein (family)
Dormant Bacillus subtilis spores germinate in the presence of particular nutrients called germinants. The spores are thought to recognise germinants through receptor proteins encoded by the gerA family of operons, which includes gerA, gerB, and gerK . The GerA proteins are predicted to be membrane associated.
Pfam PF09689: Plasmodium yoelii repeat (PY_rept_46) (disordered)
This repeat is found in the products of only 2 genes in Plasmodium species. It is found in no other organisms.
Pfam PF12671: Putative amidase domain (domain)
This entry represents a putative amidase domain.
Pfam PF17079: Male-specific protein scotti (family)
Soti is a post-meiotically transcribed gene that is required in late spermiogenesis for normal spermatid individualisation. Besides, it is expressed in primary spermatocytes and round spermatids.