SII-SWORD/CoKE huggingface dataset:
Pfam PF22605: IBR domain (domain)
This entry represents an IBR domain which is found to occur between pairs of ring fingers.
Pfam PF04244: Deoxyribodipyrimidine photo-lyase-related protein (family)
This family appears to be related to [pfam:PF00875].
Wikipedia: DNA photolyase, N-terminal is an evolutionary conserved protein domain. This domain binds a light harvesting chromophore that enhanced the spectrum of photolyase or cryptochrome light absorption, i.e. an antenna. It adopts the Rossmann fold.
Pfam PF09393: Phage tail tube protein (domain)
This is a family of phage tail tube proteins including protein XkdM from phage-like element PBSX protein ([swissprot:P54332]) whose structure adopts a beta barrel flanked with alpha helical regions.
Pfam PF21649: APMV, Putative poly(A) polymerase, catalytic subunit, C-terminal (domain)
This domain is found at the C-terminal end of Putative poly(A) polymerase catalytic subunit from Acanthamoeba polyphaga mimivirus (APMV). This entry comprises domains D3 and D4. D3 is very similar to the D2 domain (part of [pfam:PF19244]) and shows the typical topology of a nucleotidyltransferase (NT) domain made of a mixed five-stranded beta-sheet and two connecting helices. D4 is an extension that the entrance of the central tunnel at the interface of the dimer.
Pfam PF08684: DNA mimic ocr (family)
The structure of an ocr protein from bacteriophage T7 has shown that this protein mimics the size and shape of a bent DNA molecule. ocr has also been shown to be an inhibitor of the complex type I DNA restriction enzymes.
Pfam PF17749: Microtubule-binding protein MIP-T3 C-terminal region (coiled_coil)
This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3.  The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved.
Pfam PF22277: EncFtn-like (family)
This protein family includes Encapsulated ferritin-like protein from Rhodospirillum rubrum (EncFtn) and similar prokaryotic sequences. This encapsulated ferritin that acts as a ferroxidase adopts an open decameric structure. Each monomer has an N-terminal 3-10-helix, two long antiparallel alpha-helices and a shorter helix at the end.
Pfam PF24300: Kiwellin-1 (domain)
This entry represents Kiwellin-1 (KWL1) which specifically blocks the catalytic activity of the chorismate mutase Cmu1. KWL1 binds in proximity to the Cmu1 active site and thus likely blocking the substrate access. It adopts a double psi beta-barrel fold and shares a significant sequence similarity to members of this clan.
Pfam PF06453: Type II heat-labile enterotoxin , B subunit (LT-IIB) (domain)
Family of B subunits from the type II heat-labile enterotoxin. The B subunits form a pentameric ring, which interacts with one A subunit.  Thus, the structural arrangement of type I and type II heat-labile enterotoxins are very similar.
Wikipedia: In molecular biology, the heat-labile enterotoxin family includes Escherichia coli heat-labile enterotoxin and cholera toxin (Ctx) secreted by Vibrio cholerae.
Pfam PF08238: Sel1 repeat (repeat)
This short repeat is found in the Sel1 protein.  It is related to TPR repeats.
Wikipedia: The enzyme cytochrome c oxidase or Complex IV is a large transmembrane protein complex found in bacteria, archaea, and the mitochondria of eukaryotes.
Pfam PF12699: phiKZ-like phage internal head proteins (family)
Phage internal head proteins (IP) are proteins that are encoded by a bacteriophage and assembled into the mature virion inside the capsid head.  The most analogous characterised IP proteins are those of bacteriophage T4, which are known to be proteolytically processed during phage maturation, and then subsequently injected into the host cell during infection. The phiKZ_IP family consists of internal head proteins encoded by phiKZ-like phages.  Each phage encodes three to six members of this family.  Members of the family reside in the head and are cleaved during phage maturation to separate an N-terminal propeptide from a C-terminal domain.  The C-terminal domain remains in the mature capsid.  The N-terminal propeptide domain is either mostly or completely removed from the mature capsid. In one case, an unrelated polypeptide is embedded in the propeptide and also remains in the mature capsid.  The phiKZ-like IP proteins are not discernibly homologous to the T4 IP proteins, and it is not known if the phiKZ-like IP proteins are injected into the host cell, or have some other function within the head. The alignment and HMM model exclude most of the propeptide region, but include the cleavage sites.  The first 100 residues, including the cleavage sites, constitute the most conservative part of the seed alignment.
Pfam PF11935: Symplekin/PTA1 N-terminal (repeat)
This is the N-terminal domain found in the symplekin protein from animals and PTA1 protein from budding yeasts and is typically between 239 to 261 amino acids in length. Symplekin is a scaffold protein that functions as a component of a multimolecular complex involved in histone mRNA 3'-end processing. PTA1 is involved in pre-tRNA processing. PTA1 is a subunit of the cleavage and polyadenylation factor (CPF), which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. This domain has the ARM or HEAT fold, with seven pairs of antiparallel alpha-helices arranged in the shape of an arc. It is important for interaction with Ssu72 and stimulates Ssu72 C-terminal domain phosphatase activity in vitro.
Pfam PF05553: Cotton fibre expressed protein (family)
This family consists of several plant proteins of unknown function. Three of the sequences (from Gossypium hirsutum) in this family are described as cotton fibre expressed proteins. The remaining sequences, found in Arabidopsis thaliana, are 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 PF19703: Family of unknown function (DUF6201) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001133) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It  includes a member from the taxlllaid A biosynthetic gene cluster  from Xenorhabdus bovienii SS-2004. This family appears to be predominantly found in Proteobacteria.
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 PF05465: Halobacterial gas vesicle protein C (GVPC) repeat (repeat)
This family consists of Halobacterium gas vesicle protein C sequences which are thought to confer stability to the gas vesicle membranes.
Pfam PF07139: Spermatogenesis-associated serine-rich protein 2-like (family)
This family includes spermatogenesis-associated serine-rich protein 2 (SPATS2) and SPATS2-like proteins from mammals. SPATS2 is involved in  spermatogenesis and likely to be a cytoplasmic RNA-binding protein.  SPATS2 is highly expressed in hepatocellular carcinoma (HCC) and may function as an oncogene. It constitutes a novel diagnostic prognostic  marker in liver cancer and a potential therapeutic target for the treatment of HCC.
Pfam PF07887: Calmodulin binding protein-like N-terminal domain (domain)
The members of this family are putative or actual calmodulin binding proteins expressed by various plant  species. Some members (for example, [swissprot:Q8H6T7]), are known to be involved in the induction of plant defence responses. However, their precise function in this regards is as yet unknown.
Pfam PF04707: PRELI-like family (family)
This family includes a conserved region found in the PRELI protein and yeast YLR168C gene MSF1 product. The function of this protein is unknown, though it is thought to be involved in intra-mitochondrial protein sorting. This region is also found in a number of other eukaryotic proteins.
Pfam PF22663: Picornavirus coat protein (domain)
This domain is found in capsid proteins from picornavirus, such as enterovirus, rhinovirus and foot-and-mouth disease virus.
Pfam PF08452: DNA polymerase family B exonuclease domain, N-terminal (family)
This domain is found in viral DNA polymerases to the N-terminus of DNA polymerase family B exonuclease domains ([pfam:PF03104]).
Pfam PF06733: DEAD_2 (family)
This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast.
Pfam PF12342: Protein of unknown function (DUF3640) (family)
This family of proteins is found in viruses. Proteins in this family are typically between 25 and 211 amino acids in length.
Pfam PF00541: Adenoviral fibre protein (knob domain) (domain)
Specific  attachment of adenovirus is achieved through interactions  between host-cell receptors and the adenovirus fibre protein and is  mediated by the globular carboxy-terminal domain of the adenovirus fibre protein, termed the carboxy-terminal knob domain.
Pfam PF22437: BRCT domain (domain)
This entry represents the BRCT domain found in Dbf4 protein. Dbf4 is a conserved eukaryotic protein that functions as the regulatory subunit of the Dbf4-dependent kinase (DDK) complex. DDK plays essential roles in DNA replication initiation and checkpoint activation. During the replication checkpoint, Saccharomyces cerevisiae Dbf4 is phosphorylated in a Rad53-dependent manner, and this, in turn, inhibits initiation of replication at late origins. This entry represents the minimal region of Dbf4 required for the interaction with the checkpoint kinase Rad53.
Pfam PF19009: Family of unknown function (DUF5738) (family)
A highly conserved domain of unknown function found in various Platyhelminthes.
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 PF11656: YjbD family (DUF3811) (family)
This is a family of proteobacteria proteins of unknown function. This family is unrelated to [pfam:PF03960] which contains a set of transcription factors that are also named YjbD.
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 PF22088: HIT-related (domain)
These are uncharacterised proteins that are related to proteins which are members of the HIT-like superfamily.
Pfam PF24445: Family of unknown function (DUF7564) (family)
This entry represents a small family of uncharacterised proteins found in Haloferacales. They contain two pairs of conserved cysteines that are likely involved in metal coordination. These proteins are predicted to structurally resemble treble-clef zinc fingers.
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 PF04129: Vps52/Sac2 family, coiled-coil (repeat)
Vps52 complexes with Vps53 and Vps54 to form a multi-subunit complex, the Golgi-associated retrograde protein (GARP) complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network, regulating membrane trafficking events. It is also part of the EARP (Endosome-Associated Recycling Protein) complex, involved in endocytic recycling. GARP complex is part of the family of evolutionarily related complexes associated with tethering containing helical rods (CATCHR), which includes the conserved oligomeric Golgi (COG), Dsl1 and exocyst complexes. They share structural features consisting of an alpha-helical bundle at the C-terminal and usually a coiled-coil (CC) region at the N-terminal. This entry represents the CC region found at the N-terminal of Vps52.
Pfam PF05344: Domain of Unknown Function (DUF746) (family)
This is a short conserved region found in some transposons. Structural modelling suggests this domain may bind nucleic acids.
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 PF24320: Domain of unknown function (DUF7492) (domain)
This entry represents a domain of unknown function found in fungal sequences. It may adopt a Ig-like fold similar to that in Auxiliary Activity family 9 (AA9), [pfam:PF03443].
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 PF18914: Domain of unknown function (DUF5666) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 60 amino acids in length.  This domain is likely to adopt an OB-fold based on similarity to other families.
Pfam PF01110: Ciliary neurotrophic factor (domain)
Ciliary neurotrophic factor (CNTF) is a member of the gp130 family of cytokines. CNTF is a survival factor for various neuronal cell types and seems to prevent the degeneration of motor axons after axotomy suggesting it may be a potential therapeutic for treating neurodegeneration and nerve injury. CNTF acts on oligodendrocytes by favoring their final maturation, and this effect is mediated through the 130kDa glycoprotein receptor common to the CNTF family and transduced through the Janus kinase pathway. The functional receptor complex of CNTF is composed of the CNTF receptor alpha (CNTFR), gp130 and the leukemia inhibitory factor receptor (LIFR).
Pfam PF24752: Family of unknown function (DUF7697) (family)
This entry represents a small family of uncharacterised proteins. Although apparently having a bacterial origin these proteins appear in genomic contexts suggesting they are part of an integrated phage genome. Structurally these proteins are composed of a beta hairpin followed by a pair of alpha helices.
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 PF04995: Heme exporter protein D (CcmD) (family)
The CcmD protein is part of a C-type cytochrome biogenesis operon.  The exact function of this protein is uncertain. It has been proposed that CcmC, CcmD and CcmE interact directly with each other, establishing a cytoplasm to periplasm haem delivery pathway for cytochrome c maturation. This protein is found fused to CcmE in [swissprot:P52224]. These proteins contain a predicted transmembrane helix.
Pfam PF19582: Solute-binding protein AdeT 1/2 (family)
This entry represents the Probable solute-binding protein AdeT1/2 from Acinetobacter baumannii. These proteins are involved in resistance to antibiotics by active efflux.
Pfam PF15223: Elongin BC and Polycomb repressive complex 2-associated protein (family)
This family of proteins is found in eukaryotes. Family members are approximately 835 amino acids in length and include the polycomb repressive complex 2-associated factor EPOP (Elongin BC and Polycomb Repressive Complex 2 (PRC2) Associated Protein, also termed C17orf96, esPRC2p48, E130012A19Rik), a scaffold protein expressed in the inner cell mass of the mouse blastocyst serving as a bridging partner between the PRC2/EED-EZH2 complex and the elongin BC complex, and fine-tuning the transcriptional status of Polycomb group (PcG) target genes in embryonic stem cells. Both EPOP and Elongin BC are required to maintain low levels of expression at PRC2 genomic targets. EPOP interacts with the H2B deubiquitinase USP7 to modulate transcriptional processes in mESCs similar to MYC. Functional studies found that the C-terminal region of EPOP directly interacts with PRC2 and that this region associates with the VEFS-box of the PRC2 core member SUZ12. Thus, suggesting that EPOP may directly affect PRC2 chromatin binding by altering the functionality of Suz12. This region is proposed to have evolved in early vertebrates and is also present in the paralog SKIDA1 (C10orf140) another novel PRC2-interacting protein, supporting the idea that proteins possessing this sequence are PRC2 regulators in the entire vertebrate branch. The family is found in association with [pfam:PF02437].
Pfam PF08560: Protein of unknown function (DUF1757) (family)
This family of proteins are about 150 amino acids in length and 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 PF19946: Family of unknown function (DUF6408) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000106) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the naphthomycin A biosynthetic gene cluster from Streptomyces sp. CS.
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 PF13845: Septum formation (family)
This domain is found in a protein which is predicted to play a role in septum formation during cell division.
Pfam PF07814: Wings apart-like protein regulation of heterochromatin (family)
This family contains sequences expressed in eukaryotic organisms bearing high similarity to the WAPL conserved region of D. melanogaster wings apart-like protein. This protein is involved in the regulation of heterochromatin structure. hWAPL ([swissprot:Q7Z5K2]), the human homologue, is found to play a role in the development of cervical carcinogenesis, and is thought to have similar functions to Drosophila wapl protein. Malfunction of the hWAPL pathway is thought to activate an apoptotic pathway that consequently leads to cell death.
Pfam PF12537: The Golgi pH Regulator (GPHR) Family N-terminal (family)
GPHR_N is the N-terminal 5TM region of the Golgi pH regulator proteins in eukaryotes. It plays vital roles in the transport of newly synthesized proteins from the Golgi to the plasma membrane, in the glycosylation of proteins along the exocytic pathway and the structural organisation of the Golgi apparatus.
Pfam PF16245: Domain of unknown function (DUF4902) (family)
This family of proteins mainly found in Proteobacteria includes RsaM from Burkholderia cenocepacia. RsaM is a transcriptional regulator involved in quorum sensing (QS). This protein folds into a unique domain with a five-stranded antiparallel beta-sheet that wraps around two alpha-helices.
Pfam PF14774: FAM177 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 134 and 205 amino acids in length.
Pfam PF15373: Stabilizer of axonemal microtubules 5 (family)
This family (previously DUF4601) represents the homologues of Stabilizer of axonemal microtubules 5 (SAXO5, also known as C19orf45, TEX45). SAXO5 is a filamentous SAXO protein that binds along protofilament A04 with 96-nm periodicity. A typical feature of SAXO proteins is the presence of Mn motif which forms a 5- to 6-residue helix flanked by a Tyr/Phe residue on one end and by a Ser/Thr on the other that binds the shoulder of the alpha-tubulin S9/S10 loop. SAXO5 contains 11 Mn motifs and therefore has 96-nm periodicity, matching the external periodicity of the axoneme.
Pfam PF18254: HMW1 domain 2 (domain)
This domain is found in Actinobacillus pleuropneumoniae HMW1C (ApHMW1C). HMW1 adhesin is an N-linked glycoprotein that mediates adherence to respiratory epithelium through N-glycosylation of protein acceptor sites and O-glycosylation of sugar acceptor sites.  This domain forms an all alpha domain (AAD) when combined with the N-terminal domain. The AAD interacts extensively with the C-terminal GT-B fold in order to create a unique groove with the potential to accommodate the acceptor protein.
Pfam PF17862: AAA+ lid domain (domain)
This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.
Pfam PF23960: Family of unknown function (DUF7289) (family)
This entry represents a group of uncharacterised archaeal proteins. They genes occur in pilB/pilC operons.
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.