SII-SWORD/CoKE huggingface dataset:
Pfam PF21735: C-terminal repeat from RTX toxins (repeat)
This entry represents a short repeat found near the C-terminus of some RTX toxins such as [swissprot:Q9KS12]. AlphaFold models suggest this repeat forms a beta solenoid structure. These repeats contain a GXGXD motif in each repeat which is similar to that found in the RTX calcium-binding nonapeptide repeat [pfam:PF00353]. This suggests that these repeats may also be needed for translocation via the type I secretion system.
Pfam PF19222: Nodavirus Vmethyltransferase (family)
This entry represents a family of nodavirus proteins that is homologous to [pfam:PF01660]. These proteins are likely methytransferases involved in mRNA capping.
Pfam PF12517: Protein of unknown function (DUF3720) (family)
This domain family is found in eukaryotes, and is approximately 100 amino acids in length. There are two completely conserved A residues that may be functionally important.
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 PF15461: Beta-carotene 15,15'-dioxygenase (family)
This is a family of bacterial and archaeal proteins that catalyses or regulates the conversion of beta-carotene to retinal. Characterisation of BCD proteins shows them to cleave beta-carotene at its central double bond (15,15') to yield two molecules of all-trans-retinal. However, the oxygen atom of retinal originated not from water but from molecular oxygen, suggesting that the enzyme was a beta-carotene 15,15'-dioxygenase, rather than a mono-oxygenase that catalyses the same biochemical reaction.
Pfam PF00108: Thiolase, N-terminal domain (domain)
Thiolase is reported to be structurally related to beta-ketoacyl synthase ([pfam:PF00109]), and also chalcone synthase.
Wikipedia: Thiolases, also known as acetyl-coenzyme A acetyltransferases (ACAT), are enzymes which convert two units of acetyl-CoA to acetoacetyl CoA in the mevalonate pathway.
Pfam PF05182: Fip1 motif (conserved_site)
This short motif is about 40 amino acids in length.  In the Fip1 protein that is a component of a yeast pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase. This region of Fip1 is needed for the interaction with the Th1 subunit of the complex and for specific polyadenylation of the cleaved mRNA precursor.
Pfam PF14047: Dppa2/4 conserved region (family)
This domain has been characterized in the finding of a developmental pluripotency associated gene (Dppa) in the lower vertebrate Xenopus laevis. Previous to this discovery, Dppa genes were known only in higher vertebrates. The domain is subject to structure determination by the Joint Center of Structural Genomics.
Pfam PF21705: p55, C-terminal domain (domain)
This entry corresponds to the C-terminal domain (CTD) of the p55 protein of emaraviruses (plant-infecting bunyaviruses), a highly conserved domain found in all p55 proteins. The function of these proteins is unknown, but in Rose rosette virus, p55 proteins were dispensable for transcription of a minireplicon. Structure prediction using AlphaFold colab tool, suggests that this domain may have three alpha-helices.
Pfam PF06202: Amylo-alpha-1,6-glucosidase (repeat)
This family includes human glycogen branching enzyme [swissprot:P35573]. This enzyme contains a number of distinct catalytic activities. It has been shown for the yeast homologue [swissprot:O93808] that mutations in this region disrupt the enzymes Amylo-alpha-1,6-glucosidase ([ec:3.2.1.33]).
Pfam PF16648: Unstructured region on Calpain-3 (disordered)
Calpain_u2 is a region of natively unstructured sequence that lies between the Calpain_III, [pfam:PF01067] and the first EF-hand, Pfam;PF13833, domains on higher eukaryote calpain-3 proteins.  The function is not known.
Pfam PF03793: PASTA domain (domain)
This domain is found at the C termini of several Penicillin-binding proteins and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.
Wikipedia: The PASTA domain is a small protein domain that can bind to the beta-lactam ring portion of various β-lactam antibiotics. The domain was initially discovered in 2002 by Yeats and colleagues as a region of sequence similarity found in penicillin binding proteins and PknB-like kinases found in some bacteria. The name is an acronym derived from PBP and Serine/Threonine kinase Associated domain.
Pfam PF08133: Anticodon nuclease activator family (family)
This family consists of the anticodon nuclease activator proteins.  Pre-existing host tRNAs are reprocessed during bacteriophage T4 infection of certain Escherichia coli strains. In this pathway, tRNA(Lys) is cleaved 5' by the anticodon nuclease to the wobble base and is later restored in polynucleotide kinase and RNA ligase reactions.
Pfam PF12765: HEAT repeat associated with sister chromatid cohesion (repeat)
This HEAT repeat is found most frequently in sister chromatid cohesion proteins such as Nipped-B. HEAT repeats are found tandemly repeated in many proteins, and they appear to serve as flexible scaffolding on which other components can assemble.
Pfam PF19108: Family of unknown function (DUF5795) (family)
Family of unknown function predominantly found in Halobacteria.
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 PF20436: Archaeal LonB, AAA+ ATPase LID domain (domain)
The species-specific Lon-insertion domain (LID) is characteristic of Lon proteases (also known as endopeptidase La) and is fused to the AAA+ module. Bacterial and eukaryotic Lons (LonA) have a LID at the N-terminal of AAA+ module; in archaeal Lons (LonB) the LID, represented in this entry, is inserted within the AAA+ module in a series of transmembrane segments known as the membrane-anchoring region (MA). In the Lon-like protease LonC, which does not have ATPase activity, the LID is also within the AAA-like module similar to LonBs; in this case, it is predicted to contain coiled-coil regions rather than transmembrane segments.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF07306: Protein of unknown function (DUF1455) (family)
This family consists of several hypothetical putative outer membrane proteins which appear to be specific to Anaplasma marginale and Anaplasma ovis.
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 PF17721: POU domain class 2-associating factor 2 (family)
POU domain class 2-associating factor 2 (also known as Protein OCA-T1) is a transcriptional coactivator that specifically associates with POU2F3, forming a complex that drives the development of tuft cells, a rare chemosensory cells that coordinate immune and neural functions within mucosal epithelial tissues.
Pfam PF16643: Unstructured region on cNMP-binding protein (disordered)
cNMPbd_u2 is a natively unstructured region on a set of higher eukaryote cyclic nucleotide-binding domain-containing proteins. It lies between the second cNMP_binding, [pfam:PF00027], and the F-box, [pfam:PF00646], domains. The function is not known but there is a highly conserved DPDPFL sequence motif.
Pfam PF02320: Ubiquinol-cytochrome C reductase hinge protein (domain)
The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 'hinge' protein of the complex which is thought to mediate formation of the cytochrome c1 and cytochrome c complex.
Pfam PF04700: Structural glycoprotein p40/gp41 conserved region (family)
Family of viral structural glycoproteins.
Pfam PF07502: MANEC domain (domain)
This region of similarity, comprising 8 conserved cysteines, is found in the N-terminal region of several membrane-associated and extracellular proteins.  Although formerly called MANSC (for motif at N terminus with seven cysteines) it has now been renamed by MANEC (motif at N terminus with eight cysteines) by Richard Mitter and Stephen Fitzgerald after the discovery of an eighth conserved cysteine. It is postulated that this domain may play a role in the formation of protein complexes involving various protease activators and inhibitors.
Pfam PF14094: Domain of unknown function (DUF4272) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 221 and 399 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 PF15358: Testis-specific serine kinase substrate (family)
TSKS, testis-specific serine kinase substrate, is expressed in the testis and is downregulated in cancerous testicular tissue, in comparison with adjacent normal tissue. TSKS expression is very low to undetectable in seminoma, teratocarcinoma, embryonal, and Leydig cell tumours, while high in testicular tissue adjacent to tumours which contain pre-malignant carcinoma in situ. Recently it has been shown in human testis to be localised to the equatorial segment of ejaculated human sperm. The finding of a TSKS family member in mature sperm suggests that this family of kinases might play a role in sperm function. TSKS is localised during spermiogenesis to the centrioles of post-meiotic spermatids, where it reaches its greatest concentration during the period of flagellogenesis.
Pfam PF16815: Protein HRI1 (domain)
This fungal protein interacts with Sec72 and Hrr25, it's function is not yet known.
Pfam PF08918: PhoQ Sensor (domain)
The PhoQ Sensor is required for the virulence of various Gram-negative bacteria by allowing interaction of PhoPQ with the intracellular membrane, resulting in remodelling of the bacterial cell surface and subsequent bacterial resistance to host antimicrobial peptides. The domain contains a major flat acidic surface, which binds to at least 3 calcium ions, neutralising the domain's negative charge and allowing interaction with the negatively charged membrane. This domain recognises divalent metal cations, and antimicrobial cationic peptides (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF09153: Methylated DNA-protein cysteine methyltransferase, N-terminal (domain)
This domain is found in the archaeal protein O6-alkylguanine-DNA alkyltransferase (also known as Methylated DNA-protein cysteine methyltransferase MGMT), adopt a secondary structure consisting of a three stranded antiparallel beta-sheet and three alpha helices. This entry represents the N-terminal ribonuclease H-like domain, associated with 6-O-methylguanine DNA methyltransferase activity. The exact function has not, as yet, been defined, though it has been postulated that they confer thermostability to the archaeal protein.
Pfam PF12180: TSG101 and ALIX binding domain of CEP55 (domain)
This domain family is found in eukaryotes, and is approximately 40 amino acids in length. This domain is the active domain of CEP55. CEP55 is a protein involved in cytokinesis, specifically in abscission of the plasma membrane at the midbody. To perform this function, CEP55 complexes with ESCRT-I (by a Proline rich sequence in its TSG101 domain) and ALIX. This is the domain on CEP55 which binds to both TSG101 and ALIX. It also acts as a hinge between the N and C termini. This domain is called EABR.
Pfam PF04939: Ribosome biogenesis regulatory protein (RRS1) (family)
This family consists of several eukaryotic ribosome biogenesis regulatory (RRS1) proteins. RRS1 is a nuclear protein that is essential for the maturation of 25 S rRNA and the 60 S ribosomal subunit assembly in Saccharomyces cerevisiae.
Pfam PF04146: YT521-B-like domain (domain)
A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells.  It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing.  The rat protein [swissprot:Q9QY02] YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. The YTH domain has been identified as part of the PUA superfamily.
Wikipedia: In molecular biology, the protein domain YTH refers to a member of the YTH family that has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. They also play a role in the epitranscriptome as reader proteins for m6A.
Pfam PF02370: M protein repeat (repeat)
This short repeat is found in multiple copies in bacterial M proteins. The M proteins bind to IgA and are closely associated with virulence. The M protein has been postulated to be a major group A Streptococcal (GAS) virulence factor because of its contribution to the bacterial resistance to opsonophagocytosis.
Pfam PF15141: Ubiquinol-cytochrome-c reductase complex assembly factor 3 (family)
Complex III (cytochrome bc1) is a protein complex of the mitochondrial inner membrane that transfers electrons from ubiquinol to cytochrome c. UQCC3 functions in complex III assembly. The human UQCC3 is the ortholog of the fungal complex III assembly factor CBP4. It is also a potent antiviral protein independent of interferon production.
Pfam PF24122: Type I-B CRISPR Cas8b C-terminal domain (domain)
This entry represents the C-terminal domain of Type I-B CRISPR Synechocystis Cas8b and related proteins. Type I CRISPR-Cas systems employ multi-subunit effector Cascade and helicase-nuclease Cas3 to target and degrade foreign nucleic acids, representing the most abundant RNA-guided adaptive immune systems in prokaryotes. Cas8b subunit displays very low sequence similarity with the large subunits of any other known type I CRISPR systems. Cas8b N-terminal domain is involved in PAM recognition. The C-terminal domain of Cas8b and three Cas11b small subunits together form the inner 'belly' of the cascade integral complex. They provide support for the non-target strand within the full R-loop state structure.
Pfam PF02782: FGGY family of carbohydrate kinases, C-terminal domain (domain)
This domain adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain.
Wikipedia: In molecular biology the FGGY carbohydrate kinase family is a family of evolutionarily related carbohydrate kinase enzymes. These enzymes include L-fuculokinase EC 2.7.1.51 ; gluconokinase EC 2.7.1.12 ; glycerol kinase EC 2.7.1.30 ; xylulokinase EC 2.7.1.17 ; D-ribulose kinase EC 2.7.1.47 ; and L-xylulose kinase EC 2.7.1.53. These enzymes are proteins of from 480 to 520 amino acid residues.
Pfam PF19755: Domain of unknown function (DUF6242) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 290 amino acids in length. It contains a BNR/Asp box motif at the C-terminal, which contains the characteristic sequence motif SxDxGxT/xW of the BNR family, present as repeats in sialidases and others glycosyl hydrolases.
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 PF10084: Uncharacterized protein conserved in bacteria (DUF2322) (family)
Members of this family of hypothetical bacterial proteins have 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 PF20724: Domain of unknown function (DUF6831) (domain)
This domain s is functionally uncharacterised. It is predominantly found in eukaryotic sequences mostly from Alveolata. There are several highly conserved motifs, including YxKHxR and WPPE at the C terminus. The domain is predicted to adopt an alpha-beta  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 PF04654: Protein of unknown function, DUF599 (family)
This family includes several uncharacterised 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 PF20478: P2X purinoreceptor 7 intracellular domain (domain)
This entry represents the intracellular domain found at the the C-terminus of P2X purinoreceptor 7 protein.
Pfam PF20265: ATPase, RavA, LARA domain (domain)
This is the LARA (LdcI Associating domain of RavA) domain of bacterial regulatory ATPase RavA (Regulatory ATPase variant A). It adopts an unique fold which consists of a compact antiparallel beta-barrel- like structure formed by six beta-strands and one alpha-helix. This domain mediates the interaction between RavA and LdcI (inducible lysine decarboxylase) which form a cage-like complex proposed to assist assembly of specific respiratory complexes in E. coli.
Pfam PF14137: Domain of unknown function (DUF4304) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 154 and 223 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 PF22676: Alpha-galactosidase, N-terminal (domain)
This domain is found at the N-terminal end of Alpha-galactosidase from Thermotoga maritima (GalA), which hydrolyses the short-chain alpha-galactosaccharides raffinose, melibiose and stachyose. This GH36 enzyme is organised into three domains: an N-terminal beta -sandwich fold domain (this entry), a canonical (beta/alpha)8-fold domain housing the active site ([pfam:PF02065]), and a C-terminal beta-sandwich domain with a Greek-key motif.
Pfam PF15863: Extended EGL-27 and MTA1 homology domain (domain)
EELM2, the extended EGL-27 and MTA1 homology domain is a protein domain that occurs in proteins from apicomplexan parasites. Part of the EELM2 domain is homologous to the ELM2 domain, but is 'extended' in that its boundaries (the region of conservation) are longer than in the ELM2 domain. Currently (as of 2012), little is known about the function of this domain. However, some proteins that contain an EELM2 domain also contain a PHD finger domain, which is thought to be involved in chromatin remodelling. This suggests an associated role for the EELM2 domain.
Wikipedia: The extended EGL-27 and MTA1 homology domain, or EELM2 domain, is a protein domain that occurs in proteins from apicomplexan parasites.
Pfam PF01384: Phosphate transporter family (family)
This family includes PHO-4 from Neurospora crassa which is a is a Na(+)-phosphate symporter. This family also contains the leukaemia virus receptor [swissprot:Q08344].
Pfam PF22427: Maltogenic amylase, C-terminal domain (domain)
This entry represents the C-terminal GHD-like domain present in Staphylothermus marinus maltogenic amylase (SMMA). SMMA is a extreme thermophile maltogenic amylase with an optimal temperature of 100 C, which hydrolyzes alpha(1-4)glycosyl linkages in cyclodextrins and in linear malto-oligosaccharides.
Pfam PF22904: BOS complex subunit NOMO1-like, second beta sandwich domain (domain)
This domain is found at the N-terminal end of human BOS complex subunit NOMO1 and similar sequences mainly from animals and plants. NOMO1 is a component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes. This domain is predicted to adopt a seven stranded beta sandwich fold.
Pfam PF12284: Hox protein A13 N terminal (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 149 and 306 amino acids in length. The family is found in association with [pfam:PF00046]. This family is the N terminal of the Hox gene protein involved in formation of the digital arch of the hands and feet as well as in correct genital formation. Mutation of the protein is associated with hand-foot-genital syndrome.
Pfam PF08308: PEGA domain (domain)
This domain is found in both archaea and bacteria and has similarity to S-layer (surface layer) proteins.  It is named after the characteristic PEGA sequence motif found in this domain. The secondary structure of this domain is predicted to be beta-strands [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16].