SII-SWORD/CoKE huggingface dataset:
Pfam PF21203: ER membrane protein complex subunit 10 (family)
EMC10 is a component of the endoplasmic reticulum (ER) membrane protein complex (EMC), a conserved co- and post-translational insertase which enables the energy-independent insertion into ER membranes of newly synthesized membrane proteins. It is involved in the co-translational insertion of multi-pass membrane proteins in which stop-transfer membrane-anchor sequences become ER membrane spanning helices. This complex controls the topology of multi-pass membrane proteins, such as G protein-coupled receptors.
Pfam PF24454: Family of unknown function (DUF7570) (family)
This entry represents a family of uncharacterised phage proteins. The proteins are composed of an N-terminal three helical bundle followed by an alpha helical region at the C-terminus.
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 PF03738: Glutathionylspermidine synthase preATP-grasp (domain)
This region contains the Glutathionylspermidine synthase enzymatic activity [ec:6.3.1.8]. This is the C-terminal region in bi-enzymes such as [swissprot:P43675]. Glutathionylspermidine (GSP) synthetases of Trypanosomatidae and Escherichia coli couple hydrolysis of ATP (to ADP and Pi) with formation of an amide bond between spermidine and the glycine carboxylate of glutathione (gamma-Glu-Cys-Gly). In the pathogenic trypanosomatids, this reaction is the penultimate step in the biosynthesis of the antioxidant metabolite, trypanothione (N1,N8-bis-(glutathionyl)spermidine), and is a target for drug design. This region, the pre-ATP grasp region, probably carries the substrate-binding site.
Pfam PF05975: Bacterial ABC transporter protein EcsB (family)
This family consists of several bacterial ABC transporter proteins which are homologous to the EcsB protein of Bacillus subtilis. EcsB is thought to encode a hydrophobic protein with six membrane-spanning helices in a pattern found in other hydrophobic components of ABC transporters.
Pfam PF12958: Protein of unknown function (DUF3847) (family)
A family of uncharacterized proteins found by clustering human gut metagenomic sequences.
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 PF08650: DASH complex subunit Dad4 (family)
The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.
Pfam PF10109: Phage tail assembly chaperone proteins, E, or 41 or 14 (family)
This is family of various Myoviridae bacteriophage tail assembly chaperone, or TAC, proteins.
Pfam PF01021: Ty transposon capsid protein (family)
Ty are yeast transposons.  A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB.  The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles.  This entry corresponds to the capsid protein from Ty1 and Ty2 transposons.
Pfam PF09066: Beta2-adaptin appendage, C-terminal sub-domain (domain)
Members of this family adopt a structure consisting of a 5 stranded beta-sheet, flanked by one alpha helix on the outer side, and by two alpha helices on the inner side. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15).
Wikipedia: The C-terminal domain of Beta2-adaptin is a protein domain is involved in cell trafficking by aiding import and export of substances in and out of the cell.
Pfam PF15451: Domain of unknown function (DUF4632) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 59 and 190 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 PF03627: PapG carbohydrate binding domain (domain)
PapG, the adhesin of the P-pili, is situated at the tip and is only a minor component of the whole pilus structure.  A two-domain structure has been postulated for PapG; a carbohydrate binding N-terminus (this domain) and chaperone binding C-terminus. The carbohydrate-binding domain interacts with the receptor glycan.
Pfam PF06766: Fungal hydrophobin (family)
This is a family of fungal hydrophobins that seems to be restricted to ascomycetes. These are small, moderately hydrophobic extracellular proteins that have eight cysteine residues arranged in a strictly conserved motif. Hydrophobins are generally found on the outer surface of conidia and of the hyphal wall, and may be involved in mediating contact and communication between the fungus and its environment. Note that some family members contain multiple copies.
Wikipedia: Hydrophobins are a group of small cysteine-rich proteins that were discovered in filamentous fungi that are lichenized or not. Later similar proteins were also found in Bacteria. Hydrophobins are known for their ability to form a hydrophobic (water-repellent) coating on the surface of an object. They were first discovered and separated in Schizophyllum commune in 1991. Based on differences in hydropathy patterns and biophysical properties, they can be divided into two categories: class I and class II. Hydrophobins can self-assemble into a monolayer on hydrophilic:hydrophobic interfaces such as a water:air interface. Class I monolayer contains the same core structure as amyloid fibrils, and is positive to Congo red and thioflavin T. The monolayer formed by class I hydrophobins has a highly ordered structure, and can only be dissociated by concentrated trifluoroacetate or formic acid. Monolayer assembly involves large structural rearrangements with respect to the monomer.
Pfam PF06152: Phage minor capsid protein 2 (family)
Family of related phage minor capsid proteins.
Pfam PF14891: Effector protein (family)
This family of proteins contains an HEXXH motif, typical of zinc metallopeptidases. The family includes the E. coli effector protein NleD, which cleaves and inactivates c-Jun N-terminal kinase (JNK).
Pfam PF12066: SERRATE/Ars2, N-terminal domain (domain)
This domain can be found in the N terminus of the SERRATE (SE) from plants and its homologue, Ars2, from animals. They play a role in nuclear RNA metabolism. They interact with the nuclear cap-binding complex (CBC) and mediates interactions with diverse RNA processing and transport machineries in a transcript-dependent manner. Interestingly, the plant SERRATE does not have the RNA recognition motif (RRM) domain found in metazoans and S. pombe. This domain has two completely conserved Y residues that may be functionally important.
Pfam PF17044: Borrelial persistence in ticks protein A (family)
BPTA is a family of proteins that are found in Borrelia species. The function is not known.
Pfam PF03520: KCNQ voltage-gated potassium channel (family)
This family matches to the C-terminal tail of KCNQ type potassium channels.
Wikipedia: Voltage-gated potassium channels (VGKCs) are transmembrane channels specific for potassium and sensitive to voltage changes in the cell's membrane potential. During action potentials, they play a crucial role in returning the depolarized cell to a resting state.
Pfam PF04485: Phycobilisome degradation protein nblA (family)
In the cyanobacterium Synechococcus PCC 7942 ([swissprot:P35087]) , nblA triggers degradation of light-harvesting phycobiliproteins in response to  deprivation nutrients including nitrogen, phosphorus and sulphur.  The  mechanism of nblA function is not known, but it has been hypothesised that nblA may act by disrupting phycobilisome structure, activating a protease or tagging phycobiliproteins for proteolysis. Members of this family have also been identified in the chloroplasts of some red algae.
Pfam PF08131: Defensin-like peptide family (domain)
This family consists of the defensin-like peptides (DLPs) isolated from platypus venom. These DLPs show similar three-dimensional fold to that of beta-defensin-12 and sodium-channel neurotoxin Shl. However the side chains known to be functionally important to beta-defensin-12 and Shl are not conserved in DLPs. This suggests a different biological function. Consistent with this contention, DLPs have been shown to possess no anti-microbial properties and have no observable activity on rat dorsal-root-ganglion sodium-channel currents.
Pfam PF19901: Family of unknown function (DUF6374) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002024) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the nargenicin biosynthetic gene cluster from Nocardia argentinensis.
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 PF19913: Wolframin C-terminal OB-fold domain (domain)
OB fold domain found at the C-terminus of the wolframin protein. Localizes to the ER lumen and lacks the conserved polar residues typical of OB-fold domain-mediated nucleic acid-binding. Predicted to mediate protein-protein interactions.
Pfam PF21793: Family of unknown function (DUF6877) (domain)
This entry represents a small family of short uncharacterised proteins. They are predicted to adopt a three helical structure.
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 PF13976: GAG-pre-integrase domain (domain)
This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.
Pfam PF23561: C2H2 zinc finger (domain)
This entry represents a set of C2H2 zinc fingers. This class is described approximately by the motif CXWXXCXnHXRXHTGEK.
Pfam PF07216: LcrG protein (family)
This family consists of several bacterial LcrG proteins. Yersiniae are equipped with the Yop virulon, an apparatus that allows extracellular bacteria to deliver toxic Yop proteins inside the host cell cytosol in order to sabotage the communication networks of the host cell or even to cause cell death. LcrG is a component of the Yop virulon involved in the regulation of secretion of the Yops.
Pfam PF18721: CxC6 like cysteine cluster associated with KDZ transposases (domain)
A predicted Zinc chelating domain inserted into the core of the KDZ transposase domain.
Pfam PF09032: Siah interacting protein, N terminal (domain)
The N terminal domain of Siah interacting protein (SIP) adopts a helical hairpin structure with a hydrophobic core stabilised by a classic knobs-and-holes arrangement of side chains contributed by the two amphipathic helices. Little is known about this domain's function, except that it is crucial for interactions with Siah. It has also been hypothesised that SIP can dimerise through this N terminal domain.
Wikipedia: In molecular biology the protein domain, Siah interacting protein N-terminal domain is found at the N-terminal of the protein, Siah interacting protein (SIP). It has a helical hairpin structure with a hydrophobic core which is further stabilised by an arrangement of side chains contributed by the two amphipathic helices. The function of this domain remains to be fully elucidated, but it is known to be vital for interactions with Siah. It has also been hypothesised that SIP can dimerise through this N-terminal domain.
Pfam PF00096: Zinc finger, C2H2 type (domain)
The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.
Wikipedia: A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells. Xenopus laevis TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein followed soon thereafter by the Krüppel factor in Drosophila. It often appears as a metal-binding domain in multi-domain proteins.
Pfam PF10429: Nuclear pore RNA shuttling protein Mtr2 (domain)
Mtr2 is a monomeric, dual-action, RNA-shuttle protein found in yeasts. Transport across the nuclear-cytoplasmic membrane is via the macro-molecular membrane-spanning nuclear pore complex, NPC. The pore is lined by a subset of NPC members called nucleoporins that present FG (Phe-Gly) receptors, characteristically GLFG and FXFG motifs, for shuttling RNAs and proteins. RNA cargo is bound to soluble transport proteins (nuclear export factors) such as Mex67 in yeasts, and TAP in metazoa, which pass along the pore by binding to successive FG receptors. Mtr2 when bound to Mex67 maximises this FG-binding. Mtr2 also acts independently of Mex67 in transporting the large ribosomal RNA subunit through the pore.
Pfam PF00654: Voltage gated chloride channel (family)
This family of ion channels contains 10 or 12 transmembrane helices. Each protein forms a single pore. It has been shown that some members of this family form homodimers. In terms of primary structure, they are unrelated to known cation channels or other types of anion channels. Three ClC subfamilies are found in animals. ClC-1 ([swissprot:P35523]) is involved in setting and restoring the resting membrane potential of skeletal muscle, while other channels play important parts in solute concentration mechanisms in the kidney. These proteins contain two [pfam:PF00571] domains.
Wikipedia: Chloride channels are a superfamily of poorly understood ion channels specific for chloride. These channels may conduct many different ions, but are named for chloride because its concentration in vivo is much higher than other anions. Several families of voltage-gated channels and ligand-gated channels have been characterized in humans.
Pfam PF08199: Bacteriophage E2-like protein (family)
Short conseved protein described in Lactococcus Bacteriophage c2 of 37 amino acids.
Pfam PF15930: Domain of unknown function (family)
YdiH is a family of proteins found in bacteria. Proteins in this family are typically between 62 and 80 amino acids in length. The function is not known.
Pfam PF13195: Protein of unknown function (DUF4011) (family)
This family of proteins is found in archaea and bacteria. Many members are annotated as being putative DNA helicase-related 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 PF17380: Family of unknown function (DUF5401) (family)
This is a family of unknown function found in Chromadorea.
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 PF23095: Transcription termination/antitermination protein NusA, KH domain (domain)
This domain is found at the C-terminal end of Transcription termination/antitermination protein NusA from a group of bacterial proteins. NusA contains two KH domains that associate with each other to produce a single continuous binding surface, which interacts with a short ribonucleotide recognition sequence. This entry represents the second KH domain.
Pfam PF10895: Domain of unknown function (DUF2715) (domain)
This family of proteins with unknown function appears to be largely found in spirochaete bacteria.  It is related to membrane beta barrel 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 PF06454: THH1/TOM1/TOM3 domain (domain)
This domain is found in plant proteins including THH1/TOM1/TOM3 from Arabidopsis. TOM1 and TOM3 are transmembrane proteins necessary for the efficient multiplication of tobamoviruses. THH1 supports tobamovirus multiplication, but to a lesser extent than TOM1 and TOM3. Members containing this domain are part of the GPCR superfamily and involved in stress tolerance.
Pfam PF19440: Tetratricopeptide repeat protein 7 N-terminal (repeat)
This is the N-terminal domain of TTC7, a protein that forms the regulatory subunit of the PI4KIIIalpha complex (also known as PI4KA). This complex is composed of PI4KIIIalpha, TTC7 and FAM126A and catalyses the first step in plasma membrane phosphoinositide synthesis. This TTC7 N-terminal domain contains basic residues suitable for interaction with the acidic inner leaflet of the plasma membrane and is required for localising the active site near its substrate. TTC7 acts as a bridge between PI4KA and EFR3B-FAM126A, via direct interactions. ERF3B is not part of the complex but contributes to its recruitment to the membrane.
Pfam PF09633: Protein of unknown function (DUF2023) (domain)
This protein of approx.120 residues consists of three beta strands and five alpha helices, thought to fold into a homo-dimer. It is expressed in bacteria.
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 PF01608: I/LWEQ domain (family)
I/LWEQ domains bind to actin. It has been shown that the I/LWEQ domains from mouse talin [swissprot:P26039] and yeast Sla2p [swissprot:P33338] interact with F-actin. I/LWEQ domains can be placed into four major groups based on sequence similarity: (1) Metazoan talin; (2) Dictyostelium TalA/TalB [swissprot:P54633] and SLA110; (3) metazoan Hip1p [swissprot:O00291]; and (4) yeast Sla2p [swissprot:P33338]. The domain has four conserved blocks, the name of the domain is derived from the initial conserved amino acid of each of the four blocks.
Pfam PF01113: Dihydrodipicolinate reductase, N-terminus (domain)
Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated  cyclic imine, dihydro-dipicolinate. This reaction is the  second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both  protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH.
Pfam PF12007: Protein of unknown function (DUF3501) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are about 200 amino acids in length. The structure of protein [swissprot:Q63J81] from B. pseudomallei has been solved. This protein contains two domains, domain I (1:31, 46:81) is a helical domain, domain II (32:45,82-193) is a mainly beta protein with a beta barrel. According to crystal contacts the proteins probably functions as a dimer. The gene neighbourhood analysis suggests that this protein may be functionally related to rubrerythrin and ferredoxin. The wedge surface between the two domains might be functionally important. The fold of this protein could best be described as a circularly permuted C2-like fold (details derived from TOPSAN).
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 PF16656: Purple acid Phosphatase, N-terminal domain (domain)
This domain is found at the N-terminus of Purple acid phosphatase proteins.
Pfam PF14957: Cdc42 effector (family)
The Cdc42 effector (CEP) or binder of Rho GTPases (BORG) proteins are involved in the organisation of the actin cytoskeleton. They may function as negative regulators of Rho GTPase signaling.
Pfam PF25158: ABC transporter A family member 11-like, C-terminal domain (domain)
This domain is found towards the C-terminal end of ABC transporter A family member 11 from Arabidopsis thaliana (ABCA11) and similar plant proteins. This domain is predicted to adopt a mainly beta structure.
Pfam PF22602: Nuclear RNA export factor, NTF2 domain (domain)
This entry represents the NTF2 domain of nuclear RNA export factors (NFX), proteins that are involved in the nuclear export of mRNAs.