SII-SWORD/CoKE huggingface dataset:
Pfam PF19066: Minor capsid protein P9 transmembrane helices (domain)
This entry represents the N-terminal transmembrane helices of the minor capsid protein P9 found in PBCV-1 and related viruses. These transmembrane helices are inserted in the bilayer membrane of the virus vesicle structure. P9 plays a role in the stabilisation of the capsomers.
Pfam PF04341: Protein of unknown function, DUF485 (family)
This family represents a putative component of ActP-like carboxylate transporters. Several members are cofit with adjacent ActP-like permeases, and the family appears to represent a membrane protein. It has been suggested to be involved in pyruvate utilisation.
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 PF17614: Viral CC-type chemokine (family)
Family members found in Fowlpox virus are CC chemokine-like proteins. Fpv060 contains the conserved pattern of four cysteine residues similar to the CC chemokine family. Fpv060 also contains more cysteines in the mature protein, than cellular chemokines and one predicted trans-membrane region. In vitro studies show N-terminal glycosylation and show that Fpv060 from Fowl pox virus is much larger and has many more cysteine residues than host chemokines and viral homologues.
Pfam PF01556: DnaJ C terminal domain (domain)
This family consists of the C terminal region of the DnaJ protein.  It is always found associated with [pfam:PF00226] and [pfam:PF00684].  DnaJ is a chaperone associated with the Hsp70 heat-shock system involved in protein folding and renaturation after stress. The two C-terminal domains CTDI and CTDII, both incorporated in this family are necessary for maintaining the J-domains in their specific relative positions. Structural analysis of PDB:1nlt shows that PF00684 is nested within this DnaJ C-terminal region.
Wikipedia: In molecular biology, chaperone DnaJ, also known as Hsp40, is a molecular chaperone protein. It is expressed in a wide variety of organisms from bacteria to humans.
Pfam PF22394: AfAlkA-like, TATA-box binding protein-like domain (domain)
This entry represents a TBP-like domain present in AfAlkA from Archaeoglobus fulgidus. AfAlkA is a glycosylase involved in base excision repair, capable of repairing mutagenic lesions such as N1-methyladenine (m1A) and N3-methylcytosine (m3C) found in DNA..
Pfam PF13534: 4Fe-4S dicluster domain (domain)
This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.
Pfam PF09587: Bacterial capsule synthesis protein PGA_cap (domain)
This protein is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein.
Pfam PF23255: Domain of unknown function (DUF7070) (domain)
This domain is found in a group of uncharacterised proteins mainly from actinopterygians that are distantly related and share overall similar domain organisation to the human NEDD4-binding protein 1 (N4BP1). This domain shares a weak sequence similarity to known UBA domains and it is predicted to fold into a typical three helical bundle.
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 PF08850: Domain of unknown function (DUF1820) (domain)
This family includes small functionally uncharacterised proteins around 100 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 PF21238: Pus10, C-terminal (domain)
This is the C-terminal catalytic domain of tRNA pseudouridine synthase Pus10, conserved in archaea and eukaryotes. In archaea it catalyses the formation of the pseudouridine at positions 54 and 55 in tRNA, while human Pus10 has different functions depending on its subcellular location: it is involved in miRNA processing in the nucleus and acts as a tRNA pseudouridylate synthase in the cytoplasm.
Pfam PF05277: Protein of unknown function (DUF726) (family)
This family consists of several uncharacterised eukaryotic 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 PF02172: KIX domain (domain)
CBP and P300 bind to the CREB via a domain known as KIX. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.
Wikipedia: In biochemistry, the KIX domain (kinase-inducible domain (KID) interacting domain) or CREB binding domain is a protein domain of the eukaryotic transcriptional coactivators CBP and P300. It serves as a docking site for the formation of heterodimers between the coactivator and specific transcription factors. Structurally, the KIX domain is a globular domain consisting of three α-helices and two short 310-helices.
Pfam PF11939: [NiFe]-hydrogenase assembly, chaperone, HybE (family)
Members of this family are chaperones for the assembly of [NiFe] hydrogenases, in the family of HybE, which is specific for hydrogenase-2 of Escherichia coli. Members often have an additional N-terminal rubredoxin domain.
Pfam PF12572: Protein of unknown function (DUF3752) (family)
This domain family is found in eukaryotes, and is typically between 140 and 163 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 PF22545: 2-Component system ADP-ribose glycohydrolase domain (domain)
This entry represents the 2CompARG domain, which coupled with its partner 2CompART, forms a two-domain T-A-like association in the duplex-forming systems likely functioning as the principal effector of these systems. One is likely to function as the antitoxin, regulating the toxin activity of the other.
Pfam PF08865: Domain of unknown function (DUF1830) (domain)
This family of short proteins is functionally uncharacterised.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF10994: Protein of unknown function (DUF2817) (family)
This family of proteins has no known function. They have similarity to catalytic domains of enzymes members of the Zn-dependent exopeptidases clan.
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 PF12387: Pestivirus NS2 peptidase (family)
The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the bovine viral diarrhea virus polyprotein, a cleavage that is correlated with cytopathogenicity. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv..
Pfam PF22384: Ca3427-like PBP (domain)
This entry represents domain II of CA3427 from Candida albicans which consists of a 5 stranded beta-sheet.
Pfam PF20777: SLS1 protein second KH domain (domain)
This entry represents the second KH-like domain in the SLS1 protein.
Pfam PF13249: Squalene-hopene cyclase N-terminal domain (repeat)
Squalene-hopene cyclase, [ec:5.4.99.17], catalyses the cyclisation of squalene into hopene in bacteria.  This reaction is part of a cationic cyclisation cascade, which is homologous to a key step in cholesterol biosynthesis. This family is the N-terminal domain.
Pfam PF20153: Family of unknown function (DUF6535) (family)
This entry represents an integral membrane region of a large family of fungal proteins. This region likely contains three transmembrane helices. Some proteins contain two copies of this region. The function of these proteins 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 PF19247: Family of unknown function (DUF5895) (family)
This is a family of uncharacterised proteins of unknown function found in viruses and 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 PF20654: Exocyst complex component Sec3, C-terminal (repeat)
Sec3 (also known as ExoC1) is a component of the exocyst complex, which mediates the tethering of post-Golgi secretory vesicles to the plasma membrane and promotes the assembly of the SNARE complex for membrane fusion. The exocyst is also involved in cell polarization, primary ciliogenesis, cytokinesis, pathogen invasion, tumourigenesis and metastasis. This complex has an elongated shape consisting of packed long rods, a a structure that is shared among the Complex Associated with Tethering Containing Helical Rods (CATCHRs) proteins from related complex such as Conserved Oligomeric Golgi complex (COG) and Golgi-Associated Retrograde Protein complex (GARP). Subunits of these complexes, apart of helical bundles, they usually have a coiled-coil (CC) region at the N-terminal. Sec3 is described as a membrane-anchoring component. This entry represents the C-terminal domain of Sec3 which interacts with small GTPases, which consists of the conserved alpha-helical bundle. Sec3 is recruited to the sites of polarised membrane growth through its interaction with the small GTP-binding protein Rho1p.
Pfam PF22534: Replication factor C subunit 3, C-terminal domain (domain)
This entry represents the C-terminal domain of Replication Factor C (RFC) subunit 3 and related proteins. RFC consists of five different AAA+ ATPase subunits and it functions as a structure-specific, DNA-dependent ATPase that is required for DNA replication.
Pfam PF06114: IrrE N-terminal-like domain (family)
This entry includes the catalytic domain of the protein ImmA, which is a metallopeptidase containing an HEXXH zinc-binding motif  from peptidase family M78. ImmA is encoded on a conjugative  transposon. Conjugating bacteria are able to transfer conjugative  transposons that can, for example, confer resistance to  antibiotics. The transposon is integrated into the chromosome, but  during conjugation excises itself and then moves to the recipient  bacterium and re-integrate into its chromosome. Typically a  conjugative tranposon encodes only the proteins required for this  activity and the proteins that regulate it. During exponential  growth, the ICEBs1 transposon of Bacillus subtilis is inactivated  by the immunity repressor protein ImmR, which is encoded by the  transposon and represses the genes for excision and transfer.  Cleavage of ImmR relaxes repression and allows transfer of the  transposon. ImmA has been shown to be essential for the cleavage  of ImmR. This domain is also found in in metalloprotease IrrE, a central  regulator of DNA damage repair in Deinococcaceae, HTH-type transcriptional regulators RamB and PrpC.
Pfam PF23547: FORGETTER1 first zinc ribbon domain (domain)
This domain is found in the Arabidopsis FORGETTER1 and related proteins (FGT1). FGT1 mediates stress-induced chromatin memory by modulating nucleosome occupancy. This protein interacts with chromatin remodelers of the SWI/SNF and ISWI families, which also display reduced heat stress memory. The domain represented by this entry is predicted to adopt a zinc ribbon fold and it is the first of the predicted pair of two.
Pfam PF03664: Glycosyl hydrolase family 62 (repeat)
Family of alpha -L-arabinofuranosidase (EC 3.2.1.55).  This enzyme hydrolysed aryl alpha-L-arabinofuranosides and  cleaves arabinosyl side chains from arabinoxylan and arabinan.
Wikipedia: In molecular biology, glycoside hydrolase family 62 is a family of glycoside hydrolases.
Pfam PF12460: RNAPII transcription regulator C-terminal (repeat)
MMS19 is required for both nucleotide excision repair (NER) and RNA polymerase II (RNAP II) transcription. This C-terminal domain, along with the N-terminal, MMS19_N, form part of a silencing complex in fission yeast that contains Dos2, Rik1, Mms19 and Cdc20 (the catalytic subunit of DNA polymerase-epsilon). This complex regulates RNA polymerase II (RNA Pol II) activity in heterochromatin and is required for DNA replication and heterochromatin assembly. This domain has a HEAT-like repeat structure.
Pfam PF05207: CSL zinc finger (domain)
This is a zinc binding motif which contains four cysteine residues which chelate zinc.  This domain is often found associated with a [pfam:PF00226] domain.  This domain is named after the conserved motif of the final cysteine.
Pfam PF00605: Interferon regulatory factor transcription factor (domain)
This family of transcription factors are important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. Three of the five conserved tryptophan residues bind to DNA.
Wikipedia: Interferon regulatory factors (IRF) are proteins which regulate transcription of interferons. Interferon regulatory factors contain a conserved N-terminal region of about 120 amino acids, which folds into a structure that binds specifically to the IRF-element (IRF-E) motifs, which is located upstream of the interferon genes. Some viruses have evolved defense mechanisms that regulate and interfere with IRF functions to escape the host immune system. For instance, the remaining parts of the interferon regulatory factor sequence vary depending on the precise function of the protein. The Kaposi sarcoma herpesvirus, KSHV, is a cancer virus that encodes four different IRF-like genes; including vIRF1, which is a transforming oncoprotein that inhibits type 1 interferon activity. In addition, the expression of IRF genes is under epigenetic regulation by promoter DNA methylation.
Pfam PF14420: Clr5 domain (domain)
This domain is found at the N-terminus of the Clr5 protein which has been shown to be involved in silencing in fission yeast. This domain has been found to often be associated with proteins that contain ankyrin repeats and large regions of disordered sequence.
Pfam PF08706: D5 N terminal like (domain)
This domain is found in D5 proteins of DNA viruses and bacteriophage P4 DNA primases phages.
Pfam PF20883: KNL (Kinetochore null) Binding Protein 5 (family)
This family represents KNL (Kinetochore null) Binding Protein 5 (Kbp-5) from C. elegans which interacts with KNL-1 and it is thought to be homologous to human Zwint and yeast Kre28. Proteins in this family are part of the kinetochore network involved in chromosome segregation. Unlike its homologue Kre28, Kbp-5 has not essential mitotic function.
Pfam PF09260: Alpha-amylase, domain C (domain)
This domain is found at the C-terminal of various fungal alpha-amylase proteins. It has been identified as a secondary binding site, which might be part of a starch interaction site. It has a beta- sandwich fold comprising an antiparallel beta-sheet with eight strands.
Pfam PF03502: Nucleoside-specific channel-forming protein, Tsx (family)
The tsx gene of Escherichia coli encodes an outer membrane protein, Tsx, which constitutes the receptor for colicin K and Bacteriophage T6, and functions as a substrate-specific channel for nucleosides and deoxy-nucleosides . The protein contains 294 amino acids, the first 22 of which are characteristic of a bacterial signal sequence peptide. The putative mature form of Tsx contains 272 residues with a calculated Mr of 31418. The Tsx sequence shows an even distribution of charged residues and lacks extensive hydrophobic stretches . Tsx shows no significant similarities to the channel-forming proteins OmpC, OmpF, PhoE and LamB from the E. coli outer membrane.

This entry also contains related proteins of unknown function.
Wikipedia: Nucleoside-specific porin is an outer membrane protein, Tsx, which constitutes the receptor for colicin K and Bacteriophage T6, and functions as a substrate-specific channel for nucleosides and deoxy-nucleosides. The protein contains 294 amino acids, the first 22 of which are characteristic of a bacterial signal sequence peptide. Tsx shows no significant similarities to general bacterial porins.
Pfam PF01261: Xylose isomerase-like TIM barrel (domain)
This TIM alpha/beta barrel structure is found in xylose isomerase ([swissprot:P19148]) and in endonuclease IV ([swissprot:P12638], [ec:3.1.21.2]).  This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae.
Pfam PF16065: Domain of unknown function (DUF4807) (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 171 and 270 amino acids in length. There is a conserved STLGG sequence motif.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12558: ATP-binding cassette cobalt transporter (family)
This domain family is found in bacteria, and is approximately 70 amino acids in length. The family is found in association with [pfam:PF00005].  There is a conserved REP sequence motif. There is a single completely conserved residue P that may be functionally important. The proteins in this family are frequently annotated as ABC Cobalt transporters however there is little accompanying literature to confirm this.
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 PF02990: Endomembrane protein 70 (family)
The transmembrane 9 superfamily protein (TM9SF) may function as a channel or small molecule transporter. Proteins in this group are endosomal integral membrane proteins.
Pfam PF20683: Domain of unknown function (DUF6819) (domain)
This domain of unknown function is found at the C-terminal of [pfam:PF16413] and it may have an alpha-helical 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 PF16296: N-terminal of TM subunit in PBP-dependent ABC transporters (family)
This family mainly consists of Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs, such as Binding-protein-dependent transport systems inner membrane component and Maltose transport permease MalF. It is around 580 residues in length and is mainly found in various species, such as Thermotoga, Dictyoglomus, Thermosipho, Fervidobacterium, Mesotoga and so on. The function of this family is unknown.
Pfam PF14761: Hermansky-Pudlak syndrome 3 protein, N-terminal (repeat)
This domain is at the N-terminus of these vertebrate proteins. This region carries the clathrin-binding motif LLDFE at residues 172-176 in SwissProt:Q969F9. There is also reference to a human Mendelian disease at MIM:614072. Mutations in the gene that encode this protein causes Hermansky-Pudlak syndrome 3 (HPS3), a genetically heterogeneous autosomal recessive disorder characterised by oculocutaneous albinism, a bleeding diathesis due to the absence of platelet dense granules and lysosomal storage defects.
Pfam PF19024: Family of unknown function (DUF5750) (family)
The function of this family of proteins 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.