SII-SWORD/CoKE huggingface dataset:
Pfam PF08993: T4 gene Gp59 loader of gp41 DNA helicase (domain)
Bacteriophage T4 gene-59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene-59 helicase assembly protein accelerates the loading of the T4 gene-41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene-59 helicase assembly protein binds to both T4 gene-41 helicase and T4 gene-32 single-stranded DNA binding protein, and to single and double-stranded DNA. The structure of T4 gene-59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size, this being the N-terminal domain that consists of six alpha-helices linked by loop segments and short turns. The surface of the domain contains large regions of exposed hydrophobic residues and clusters of acidic and basic residues. This domain has structural similarity to members of the high-mobility-group (HMG) family of DNA minor groove binding proteins including rat HMG1A and lymphoid enhancer-binding factor, and is required for binding of the helicase to the DNA minor groove.
Pfam PF23369: Capsid protein Vp25 (family)
This entry represents the capsid Vp24 protein from apple-latent spherical virus (ALSV) and related picorna-like plant viruses. This protein is encoded in a polyprotein that is cleaved into three capsid proteins, Vp25, Vp20 and Vp24, which all have jellyroll folds and form one protomer; 60 copies of this unit compose one virion. Vp25, Vp20 and Vp24 contribute to capsid stabilization.  Vp25 has two extra beta-sheets (beta1 and beta2) comparing to Vp20 and Vp24. Vp25 and Vp20 form more extensive interactions with their neighbours and likely form a rigid capsid frame that supports the looser Vp24 protrusions.
Pfam PF08151: FerI (NUC094) domain (domain)
This domain is present in proteins of the Ferlin family.  It is often located between two C2 domains.
Pfam PF17038: Cellulose biosynthesis protein BcsN (family)
This is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria. (Roemling U. and Galperin M.Y. "Bacterial cellulose biosynthesis. Diversity of operons and subunits" (manuscript in preparation)).
Pfam PF11464: Rabenosyn Rab binding domain (domain)
Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively. Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking.
Pfam PF13464: RodZ C-terminal domain (domain)
This short domain is often found at the C-terminus of RodZ cytoskeletal proteins. These proteins usually contain a helix-turn-helix domain.
Pfam PF03338: Poxvirus J1 protein (family)
This family includes proteins from Poxvirus, such as Protein J1 (also known as Virion assembly protein OPG100), a late protein which is a part of a large complex required for early virion morphogenesis. This complex participates in the formation of virosomes and the incorporation of virosomal contents into nascent immature virions. J1 protein is important for DNA packaging during immature virions (IV) formation .
Pfam PF03463: eRF1 domain 1 (domain)
The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown.  Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.
Pfam PF17349: Family of unknown function (DUF5378) (family)
This is a family of unknown function which is found in Mycoplasmataceae.Family members are predicted to contain 7 trans-membrane regions
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 PF08492: SRP72 RNA-binding domain (domain)
This region has been identified as the binding site of the SRP72 protein to SRP RNA.
Pfam PF09164: Vitamin D binding protein, domain III (domain)
Members of this family are predominantly found in Vitamin D binding protein, and adopt a multi-helical structure. They are required for formation of an actin 'clamp', allowing the protein to bind to actin.
Wikipedia: In molecular biology, Vitamin D binding protein domain III protein domain is predominantly found in Vitamin D binding proteins (DBP). Vitamin D-binding protein (DBP)(also referred to as Gc-globulin) is synthesized primarily in the liver. This entry outlines the domain III of DBP. Domain III is G-actin binding region located in the C-terminal. Domain. This protein is found ubiquitously in vivo in significant quantities and can be detected in all fluid compartments. During acute phase inflammatory response, DBP levels tend to increase.
Pfam PF01534: Frizzled/Smoothened family membrane region (family)
This family contains the membrane spanning region of frizzled and smoothened receptors.  This membrane region is predicted to contain seven transmembrane alpha helices.  Proteins related to Drosophila frizzled ([swissprot:P18537]) are receptors for Wnt (mediating the beta-catenin signalling pathway), but also the planar cell polarity (PCP) pathway and the Wnt/calcium pathway. The predominantly alpha-helical Cys-rich ligand-binding region (CRD) of Frizzled is both necessary and sufficient for Wnt binding.  The smoothened receptor mediates hedgehog signalling.
Wikipedia: Frizzled is a family of atypical G protein-coupled receptors that serve as receptors in the Wnt signaling pathway and other signaling pathways. When activated, Frizzled leads to activation of Dishevelled in the cytosol.
Pfam PF22944: Diacylglycerol kinase delta, helical domain (domain)
This domain is found in metazoan homologues of Diacylglycerol kinase delta (DGKD). This enzyme plays important roles in lipid signaling by converting diacylglycerol to phosphatidic acid. DGKD is a multidomain protein composed of seven globular domains. The domain represented by this entry locates toward the C terminus and precedes the C-terminal SAM domain ([pfam:PF07647]). It is predicted to adopt an alpha-helical structure arranged in a four helical bundle.
Pfam PF19469: Family of unknown function (DUF6006) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001016) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from then microcystin  biosynthetic gene cluster from Anabaena sp. 90.
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 PF00887: Acyl CoA binding protein (domain)
Acyl-CoA-binding protein (ACBP) is a small (10 Kd) protein that binds medium-and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters . ACBP is also known as diazepam binding inhibitor (DBI) or endozepine (EP) because of its ability to displace diazepam from the benzodiazepine (BZD) recognition site located on the GABA type A receptor. It is therefore possible that this protein also acts as a neuropeptide to modulate the action of the GABA receptor .

ACBP is a highly conserved protein of about 90 residues that is found in all four eukaryotic kingdoms, Animalia, Plantae, Fungi and Protista, and in some eubacterial species .

Although ACBP occurs as a completely independent protein, intact ACB domains have been identified in a number of large, multifunctional proteins in a variety of eukaryotic species. These include large membrane-associated proteins with N-terminal ACB domains, multifunctional enzymes with both ACB and peroxisomal enoyl-CoA Delta(3), Delta(2)-enoyl-CoA isomerase domains, and proteins with both an ACB domain and ankyrin repeats (IPR002110) .

The ACB domain consists of four Î±-helices arranged in a bowl shape with a highly exposed acyl-CoA-binding site. The ligand is bound through specific interactions with residues on the protein, most notably several conserved positive charges that interact with the phosphate group on the adenosine-3'phosphate moiety, and the acyl chain is sandwiched between the hydrophobic surfaces of CoA and the protein .

Other proteins containing an ACB domain include:


 * Endozepine-like peptide (ELP) (gene DBIL5) from mouse . ELP is a testis-specific ACBP homologue that may be involved in the energy metabolism of the mature sperm.
 * MA-DBI, a transmembrane protein of unknown function which has been found in mammals. MA-DBI contains a N-terminal ACB domain.
 * DRS-1 , a human protein of unknown function that contains a N-terminal ACB domain and a C-terminal enoyl-CoA isomerase/hydratase domain.
Wikipedia: In molecular biology, the acyl-CoA-binding protein (ACBP) is a small protein that binds medium- and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters. ACBP is also known as diazepam binding inhibitor (DBI) or endozepine (EP) because of its ability to displace diazepam from the benzodiazepine (BZD) recognition site located on the GABA type A receptor. It is therefore possible that this protein also acts as a neuropeptide to modulate the action of the GABA receptor.
Pfam PF14072: DNA-sulfur modification-associated (family)
This is family of bacterial proteins likely to be necessary for binding to DNA and recognising the modification sites.  Members are found in bacteria, archaea and on viral plasmids, and are typically between 354 and 474 amino acids in length. There is a conserved DGQHR sequence motif.
Pfam PF24894: GlmU-like, C-terminal hexapeptide (repeat)
This domain is found at the C-terminal end of Bifunctional protein GlmU from Streptococcus pneumoniae and similar sequences. This domain is responsible for the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P). This domain consists of hexapeptide repeats that form a left-handed beta-helix.
Pfam PF20249: VasX toxin N-terminal region (family)
This entry represents the N-terminal region of the VasX toxin [swissprot:Q9KNE5] from Vibrio cholerae.
Pfam PF12530: Focadhesin/RST1, DUF3730 (repeat)
This domain of unknown function is found in Focadhesin from animals and RST1 (RESURRECTION 1) from plants. Focadhesin (FOCAD) is a focal adhesion protein with potential tumour suppressor function in gliomas. RST1 was originally identified in a genetic screen for factors involved in the biosynthesis of epicuticular waxes. Later, RST1 and RST1 INTERACTING PROTEIN (RIPR) have been shown to act as cofactors of the cytoplasmic exosome and the Ski complex in plants. It is involved in the suppression of siRNA-mediated silencing of transgenes and certain endogenous transcripts. Structure predictions suggest that this is an alpha-helical domain with and armadillo-like fold.
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 PF10075: CSN8/PSMD8/EIF3K family (family)
This domain is conserved from plants to humans. It is a signature protein motif found in components of CSN (COP9 signalosome) where it functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development. It is found in Eukaryotic translation initiation factor 3 subunit K, a component of the eukaryotic translation initiation factor 3 (eIF-3) complex required for the initiation of protein synthesis. It is also found in 26S proteasome non-ATPase regulatory subunit 8 (PSMD8), a regulatory subunit of the 26S proteasome.
Pfam PF06573: Churchill protein (family)
This family includes animal Churchill proteins and similar sequences. Churchill shows a a highly unusual solvent -exposed five-stranded beta-sheet, stabilised by the coordination of three zinc ions, including a zinc binuclear cluster.
Pfam PF11647: Membrane Localization Domain (domain)
This is a membrane localization domain found in multiple families of bacterial toxins including all of the clostridial glucosyltransferase toxins and various MARTX toxins (multifunctional-autoprocessing RTX toxins). In the Pasteurella multocida toxin (PMT) C-terminal fragment, structural analysis have indicated that the C1 domain possesses a signal that leads the toxin to the cell membrane. Furthermore, the C1 domain was found to structurally resemble the phospholipid-binding domain of C. difficile toxin B. Functional studies in Vibrio cholera indicate that the subdomain at the N terminus of RID (Rho-inactivation domain), homologous to the membrane targeting C1 domain of Pasteurella multocida toxin, is a conserved membrane localization domain essential for proper localization. The Rho-inactivation domain (RID) of MARTX (Multifunctional Autoprocessing RTX toxin) is responsible for inactivating the Rho-family of small GTPases in Vibrio cholerae. It is a bacterial toxin that self-process by a cysteine peptidase mechanism. The Vibrio cholerae RTX toxin is an autoprocessing cysteine protease whose activity is stimulated by the intracellular environment. This cysteine peptidase belongs to MEROPS peptidase family G6.
Pfam PF05701: Weak chloroplast movement under blue light (coiled_coil)
WEMBL consists of several plant proteins required for the chloroplast avoidance response under high intensity blue light. This avoidance response consists in the relocation of chloroplasts on the anticlinal side of exposed cells. Acts in association with PMI2 to maintain the velocity of chloroplast photo-relocation movement via the regulation of cp-actin filaments.  Thus several member-sequences are described as "myosin heavy chain-like".
Pfam PF16217: Peptidase M64 N-terminus (domain)
This domain is found at the N-terminus of IgA Peptidase M64. Its function is unknown.
Pfam PF20544: Family of unknown function (DUF6758) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 215 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 PF01773: Na+ dependent nucleoside transporter N-terminus (family)
This family consists of nucleoside transport proteins. [swissprot:Q62773] is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. [swissprot:Q62674] is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the N terminus of this family
Pfam PF19466: Family of unknown function (DUF6003) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000100) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a  protein from monensin biosynthetic gene cluster from Streptomyces  cinnamonensis.
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 PF04921: XAP5, circadian clock regulator C-terminal domain (domain)
This protein is found in a wide range of eukaryotes. It is a nuclear protein previously suggested to be DNA binding but recent studies suggest that they play a role in the spliceosome complex.  In plants, this family is essential for correct circadian clock functioning by acting as a light-quality regulator coordinating the activities of blue and red light signalling pathways during plant growth - inhibiting growth in red light but promoting growth in blue light. The AlphaFold model of this domain shows structural similarity to the RA domain [pfam:PF00788].
Pfam PF09200: Monellin (domain)
Monellin, a protein produced by the West African plant Dioscoreophyllum cumminsii, is approximately 70,000 times sweeter than sucrose on a molar basis. The protein adopts an alpha-beta structure, with a cystatin-like fold, where each helix packs against a coiled antiparallel beta-sheet.
Pfam PF07261: Replication initiation and membrane attachment (family)
This family consists of several bacterial replication initiation and membrane attachment (DnaB) proteins, as well as DnaD which is a component of the PriA primosome.  The PriA primosome functions to recruit the replication fork helicase onto the DNA. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication. DnaD has been merged into this family. This family also includes Ftn6, a cyanobacterial-specific divisome component possibly playing a role at the interface between DNA replication and cell division. Ftn6 possesses a conserved domain localised within the N-terminus of the proteins. This domain, named FND, exhibits sequence and structure similarities with the DnaD-like domains [pfam:PF04271] now merged into [pfam:PF07261].
Pfam PF15615: TerB-C domain (domain)
TerB-C occurs C-terminal of TerB in TerB-N containing proteins. This domain displays multiple conserved acidic residues (TerBC). The presence of conserved acidic residues in both TerB-N and TerB-C suggests that they, like the TerB domain, might also chelate metals.  These two domains may also occur together in the same protein independently of TerB.
Pfam PF08986: Domain of unknown function (DUF1889) (domain)
This domain is found in a set of hypothetical bacterial proteins. They are probably cytoplasmic 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 PF20738: Cellophane-induced 1 (cin1) repeat (repeat)
Venturia inaequalis is a hemi-biotrophic fungus that causes scab disease of apple. A recently-identified gene from this fungus, cin1 (cellophane-induced 1), is up-regulated over 1000-fold in planta and considerably on cellophane membranes, and encodes a cysteine-rich secreted protein of 523 residues with eight imperfect tandem repeats of ~60 amino acids.
Pfam PF15092: Uncharacterised protein family UPF0728 (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in metazoa. There is a conserved GPY sequence motif.
Pfam PF13561: Enoyl-(Acyl carrier protein) reductase (domain)
This domain is found in Enoyl-(Acyl carrier protein) reductases.
Pfam PF24187: Domain of unknown function (DUF7415) (domain)
This entry represents a family of uncharacterised phage domains. This domain is found in one to two copies per proteins. It seems likely that the proteins with a single copy of the domain form homodimers.
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 PF07319: Primosomal protein DnaI N-terminus (family)
This family represents the N-terminus (approximately 120 residues) of bacterial primosomal DnaI proteins, although one family member appears to be of viral origin. DnaI is one of the components of the Bacillus subtilis replication restart primosome, and is required for the DnaB75-dependent loading of the DnaC helicase.
Pfam PF09769: Apolipoprotein O (family)
Members of this family promote cholesterol efflux from macrophage cells. They are present in various lipoprotein complexes, including HDL, LDL and VLDL. The apoprotein is secreted by a microsomal triglyceride transfer protein (MTTP)-dependent mechanism, probably as a VLDL-associated protein that is subsequently transferred to HDL.
Wikipedia: Apolipoprotein O also known as protein FAM121B is a protein that in humans is encoded by the APOO gene. APOO is a member of the apolipoprotein family.
Pfam PF13990: YjcZ-like protein (family)
This family of proteins is functionally uncharacterised. The family includes the YjcZ protein from E. coli [swissprot:P39267]. This family of proteins is found in enteric bacteria. Proteins in this family are approximately 300 amino acids in length. There are two conserved sequence motifs: FGD and MPR.
Pfam PF14624: VWA / Hh protein intein-like (domain)
VWA-Hint proteins carry this conserved domain of around 300 residues, now named the Vwaint domain. Such proteins do not seem to have a signal peptide for secretion. Generally, this domain lies between the N-terminal VWA domain and the more C-terminal 'Vint'-type Hint domain. The exact function of this domain is not known.
Pfam PF16330: MukB hinge domain (domain)
The hinge domain of chromosome partition protein MukB is responsible for dimerisation and is also involved in protein-DNA interactions and conformational flexibility.
Pfam PF06240: Carbon monoxide dehydrogenase subunit G (CoxG) (family)
The CO dehydrogenase structural genes coxMSL are flanked by nine accessory genes arranged as the cox gene cluster. The cox genes are specifically and coordinately transcribed under chemolithoautotrophic conditions in the presence of CO as carbon and energy source.