SII-SWORD/CoKE huggingface dataset:
Pfam PF24061: Putative ionotropic receptor, ligand binding domain (domain)
This domain is found in a set of putative arthropod ionotropic receptors. It is predicted to adopt an alpha/beta structure with similarity to known ligand binding domains of ionotropic receptors such as [pfam:PF01094].
Pfam PF07001: BAT2 N-terminus (family)
This family represents the N-terminus (approximately 200 residues) of the proline-rich protein BAT2. BAT2 is similar to other proteins with large proline-rich domains, such as some nuclear proteins, collagens, elastin, and synapsin.
Pfam PF09079: CDC6, C terminal winged helix domain (domain)
The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity.
Wikipedia: Cdc6, or cell division cycle 6, is a protein in eukaryotic cells. It is mainly studied in the budding yeast Saccharomyces cerevisiae. It is an essential regulator of DNA replication and plays important roles in the activation and maintenance of the checkpoint mechanisms in the cell cycle that coordinate S phase and mitosis. It is part of the pre-replicative complex (pre-RC) and is required for loading minichromosome maintenance (MCM) proteins onto the DNA, an essential step in the initiation of DNA synthesis. In addition, it is a member of the family of AAA+ ATPases and highly related to ORC1; both are the same protein in archaea.
Pfam PF15560: Immunity protein 12 (family)
A predicted immunity protein with an alpha+beta fold and several conserved charged and hydrophobic residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-URI2 family. The protein is also found in heterogeneous poly-immunity loci.
Pfam PF17910: FeoB cytosolic helical domain (domain)
FeoB is a G-protein coupled membrane protein essential for Fe(II) uptake in prokaryotes. In the structures, a canonical G-protein domain (G domain) is followed by a helical bundle domain (S-domain) which is represented by this entry.
Pfam PF13117: Cag pathogenicity island protein Cag12 (family)
This is a Proteobacterial family of Cag pathogenicity island proteins.
Pfam PF01119: DNA mismatch repair protein, C-terminal domain (family)
This family represents the C-terminal domain of the mutL/hexB/PMS1 family.  This domain has a ribosomal S5  domain 2-like fold.
Wikipedia: DNA mismatch repair (MMR) is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage.
Pfam PF09691: Type II secretion system pilotin lipoprotein (PulS_OutS) (family)
This family comprises lipoproteins from four gamma proteobacterial species: PulS protein of Klebsiella pneumoniae (P20440), the OutS protein of Erwinia chrysanthemi (Q01567) and Pectobacterium chrysanthemi, and the functionally uncharacterized E. coli protein EtpO. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family. In the pilotin from this four-helix protein from enterohemorrhagic Escherichia coli, the straight helix alpha2, the curved helix alpha3 and the bent helix alpha4 surround the central N-terminal helix alpha1. These helices create a prominent groove, mainly formed by side chains of helices 1,2 and 3 suggesting this groove is important as a binding site.
Pfam PF07458: Sperm protein associated with nucleus, mapped to X chromosome (family)
This family contains human sperm proteins associated with the nucleus and mapped to the X chromosome (SPAN-X) (approximately 100 residues long). SPAN-X proteins are cancer-testis antigens (CTAs), and thus represent potential targets for cancer immunotherapy because they are widely distributed in tumours but not in normal tissues, except testes. They are highly insoluble, acidic, and polymorphic.
Pfam PF07444: Ycf66 protein N-terminus (family)
This family represents the N-terminus (approximately 80 residues) of Ycf66, a protein that seems to be restricted to eukaryotes that contain chloroplasts and to cyanobacteria.
Pfam PF14772: Sperm tail (family)
NYD-SP28 is expressed in a development-dependent manner, localised in spermatogenic cell cytoplams and human spermatozoa tail.  It is post-translationally modified during sperm capacitation and ultimately contributes to the success of fertilisation.
Pfam PF18354: CarS bacterial SH3 domain (domain)
This is an SH3 domain found in antirepressor proteins such as CarS from Myxococcus xanthus.  CarS antirepressor recognizes and neutralizes its cognate repressors to turn on a photo-inducible promoter. CarS physically interacts with the MerR-type winged-helix DNA-binding domain of these repressors leading to activation of carB operon. Structural studies of CarS from M. Xanthus reveals a beta-barrel fold akin to that in SH3 domains. However, it diverges from the typical SH3 domain fold in the lengths and conformations of the connecting loops. Functional analysis reveal that SH3 domain-like fold in the antirepressor CasS, mimics operator DNA in sequestering the repressor DNA recognition helix to activate transcription.
Pfam PF15485: Domain of unknown function (DUF4643) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 254 and 462 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 PF15290: Golgi-localised syntaxin-1-binding clamp (family)
Syntaphilin or Syntabulin is a family of eukaryotic proteins. Syntaphilin binds to syntaxin-1 thereby inhibiting SNARE complex formation by absorbing free syntaxin-1. So it is a syntaxin-1 clamp that controls SNARE assembly.
Pfam PF11777: Protein of unknown function (DUF3316) (family)
This family of bacterial proteins has no known function. Several members are, however, annotated as being putative acyl-CoA synthetase, but this could not be confirmed.
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 PF10503: Esterase PHB depolymerase (family)
This family of proteins include acetyl xylan esterases (AXE), feruloyl esterases (FAE), and poly(3-hydroxybutyrate) (PHB) depolymerases.
Pfam PF16527: Two-component sensor protein CpxA, periplasmic domain (domain)
CpxA_peri is the periplasmic domain-family of the Gram-negative Gammaproteobacteria two-component signalling system, Cpx. It represents the recognition-site for sensing specific envelope stress signals. The fold that the domain-core of CpxA_peri conforms to is a PAS fold. The domain senses the environmental change and triggers a signal transduction to the cytoplasmic domain. As well as the PAS-core, there is a C-terminal tail that is necessary for ligand-sensing and binding to CpxP, a CpxA-associated and a regulatory protein. This domain recognises KCl and RbCl (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF10433: RSE1/DDB1/CPSF1 first beta-propeller (repeat)
This entry represents the beta-propeller found towards the N-terminus of RSE1/SF3B3/DDB1/CPSF1/CFT1 proteins from eukaryotes, which share a domain architecture consisting of three beta-propeller. Members of the family have diverse functions, primarily related to RNA/DNA binding. Pre-mRNA-splicing factor RSE1 plays an important role in the spliceosome, a complex that removes introns from pre-mRNAs. Its orthologue, splicing factor 3B subunit 3 (SF3B3) also forms part of the U2 small nuclear ribonucleoprotein particle (snRNP) and has been identified as part of the SAGA transcriptional coactivator complex in Drosophila melanogaster. Also included in this entry is DNA damage -binding protein 1 (DDB1), which is both involved in the recognition and repair of UV-induced DNA damage, as part of the UV-DDB complex, and in protein ubiquitination, as part of the DCX (DDB1-CUL4-X-box) complex. Additionally, this family includes cleavage and polyadenylation specificity factor subunit 1 (CPSF1) and its orthologue protein CFT1, both involved in the cleavage and polyadenylation of pre-mRNAs.
Pfam PF10370: Rv2993c-like, N-terminal (domain)
This is the N-terminal 50 amino acids of a group of bacterial proteins annotated as fumarylacetoacetate hydrolase-containing enzymes, including Rv2993c from Mycobacterium tuberculosis. In most cases members are associated with FAA_hydrolase [pfam:PF01557] further towards the C-terminus.
Pfam PF24220: Family of unknown function (DUF7439) (family)
This entry represents a family of small putative transmembrane proteins found primarily in Streptomyces phages and some bacteria.  The family is characterized by a conserved transmembrane region typically located between residues 20-45 of the alignment. Many members of this family are around 70 amino acids in length. The function of this protein family is currently 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 PF20749: Domain of unknown function (DUF6833) (domain)
This presumed domain predominantly is found in sequences from tailed bacteriophages and proteobacterial prophages, including Pseudomonas phage LUZ7. Its function 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 PF17426: Putative Gamma DNA binding protein G5P (family)
This domain family is found in Gammaproteobacterial proteins. Members of the family are predicted to be G5P DNA binding proteins. Homologous proteins are found in [pfam:PF02303]
Pfam PF22765: Family of unknown function (DUF7010) (family)
This entry represents a family of uncharacterised bacterial proteins. They are predicted to adopt alpha-helical structure composed of six up-and-down helices. It is likely that these proteins are associated with the membrane.
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 PF09039: Mu DNA binding, I gamma subdomain (domain)
Members of this family are responsible for binding the DNA attachment sites at each end of the Mu genome. They adopt a secondary structure comprising a four helix bundle tightly packed around a hydrophobic core consisting of aliphatic and aromatic amino acid residues. Helices 1 and 2 are oriented antiparallel to each other. Helix 3 crosses helices 1 and 2 at angles of 60 and 120 degrees, respectively. Excluding the C-terminal helix 4, the fold of the I-gamma subdomain is remarkably similar to that of the homeodomain family of helix-turn-helix DNA-binding proteins, although their amino acid sequences are completely unrelated.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF04694: Coronavirus ORF3 protein (family)
This family represents the Coronavirus ORF3 protein, also known as the X2A protein.
Pfam PF21143: Intron-binding protein aquarius, beta-barrel (domain)
This entry represents the beta-barrel domain found at the N-terminal of intron-binding protein aquarius, a splicing factor which links excision of introns from pre-mRNA with snoRP assembly.
Pfam PF21396: AAA+ ATPase lid domain (domain)
This entry represents the AAA lid domain from the DNA polymerase III, gamma subunit-related protein from Thermotoga maritima.
Pfam PF19820: Family of unknown function (DUF6303) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis. This family appears to be predominantly found in 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 PF15881: Domain of unknown function (DUF4734) (family)
This domain family is found in species of Drosophila, and is approximately 90 amino acids in length. The family is found in association with [pfam:PF07707].
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 PF24386: Domain of unknown function (DUF7540) (domain)
This entry represents a small family of uncharacterised enterobacterial phage proteins. These proteins adopt a compact domain composed of a small three stranded beta sheet, with an alpha helix inserted between the first and second strand.
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 PF01673: Herpesvirus putative major envelope glycoprotein (family)
This family consists of probable major envelope glycoproteins from members of the herpesviridae including herpes simplex virus, human cytomegalovirus and varicella-zoster virus. Members of the herpesviridae have a dsDNA genome and do not have a RNA stage during there replication.
Pfam PF14093: Domain of unknown function (DUF4271) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 221 and 326 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 PF02773: S-adenosylmethionine synthetase, C-terminal domain (domain)
The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold.
Wikipedia: S-Adenosylmethionine synthetase, also known as methionine adenosyltransferase (MAT), is an enzyme that creates S-adenosylmethionine by reacting methionine and ATP.
Pfam PF13635: Domain of unknown function (DUF4143) (domain)
This domain is almost always found C-terminal to an ATPase core family.
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 PF14384: BrnA antitoxin of type II toxin-antitoxin system (domain)
BrnA is family of antitoxins that neutralises the toxin BrnT, [pfam:PF04365]. It consists of 3 alpha-helices and a C-terminal ribbon-helix-helix DNA binding domain. As in other toxin-antitoxin systems, BrnA negatively autoregulates the brnTA operon and has higher affinity for the DNA operator when complexed with BrnT. It dimerises with two molecules of its toxin BrnT.
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF15021: Shieldin complex subunit 1, C-terminal domain (domain)
SHLD1, also known as RINN3, is a component of the shieldin complex, a vertebrate-specific protein complex which functions as a downstream effector in the 53BP1 pathway, regulates NHEJ (non-homologous end joining). This entry represents a conserved helical domain found at the C-terminal of SHLD1.
Pfam PF16298: Domain of unknown function (DUF4940) (family)
This family consists of several uncharacterized proteins around 250 residues in length and is mainly found in various Thermotoga species. The function of this family is unknown.
Pfam PF15762: Domain of unknown function (DUF4691) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 317 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 PF13024: Protein of unknown function (DUF3884) (family)
This family of proteins is functionally uncharacterised. However several proteins are annotated as Tagatose 1,6-diphosphate aldolase, but evidence to support this could not be found. This family of proteins is found in bacteria. Proteins in this family are typically between 61 and 106 amino acids in length. There are two completely conserved residues (Y and F) that may be functionally important.
Pfam PF19917: MoxR-vWA-beta-propeller ternary system domain bpX1 (family)
Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems.
Pfam PF12250: Arabinofuranosyltransferase N terminal (family)
This domain family is found in bacteria, and is typically between 430 and 441 amino acids in length. This family is the N terminal region of AftA. The enzyme catalyses the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. The N terminal region has been predicted to span 11 transmembrane regions.
Pfam PF02330: Mitochondrial glycoprotein (domain)
This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q.  It is thought to be involved in mitochondrial oxidative phosphorylation and in nucleus-mitochondrion interactions.
Pfam PF11401: Tetrabrachion (family)
Tetrabrachion forms a parallel right-handed coiled coil structure with hydrophobic interactions and salt bridges forming a thermostable tetrameric structure. It contains large hydrophobic cavities. No function is known for this family of proteins.
Pfam PF00880: Nebulin repeat (repeat)
The nebulin-like motif or nebulin repeat is a tandemly repeated actin-binding module of about 35 amino acids. The repeat is named after the nebulin protein, which is a large protein specific for vertebrate skeletal muscle that may regulate the length of thin filaments. Nebulin contains about 185 copies of the repeat and those in the central part of nebulin are organised into seven-module super-repeats, which seems to reflect an interaction with tropomysin/troponin . Nebulin repeats occur in metazoan actin-binding proteins, most of which are specific for muscle tissues. Most nebulin repeat proteins contain a C-terminal SH3 domain and/or a N-terminal LIM zinc-binding domain. The repeats in nebulin and nebulette bind filamentous actin (F-actin) and may also associate with tropomyosin and troponin. The nebulin repeat has a predicted Î±-helical secondary structure and contains a central conserved SXXXY motif .
Pfam PF14075: Ubinuclein conserved middle domain (family)
Ubinuclein 1 and 2 (UBN1, UBN2) are members of a histone chaperone  complex involved in the formation of a certain type of facultative  heterochromatin, called senescence-associated heterochromatin foci  (SAHF). The domain described here is conserved in many  eukaryotes such as human, rat, drosophila, and zebra-fish and has been  targeted for protein structure determination by the Joint Center  for Structural Genomics.
Pfam PF14286: DHHW protein (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 366 and 404 amino acids in length. There is a conserved DHHW motif. There is some distant homology to the Lipase_GDSL_2 family.