SII-SWORD/CoKE huggingface dataset:
Pfam PF20844: Pre-mRNA cleavage complex 2 protein Pcf11, RFEGP repeat (repeat)
This repeat is found in Pre-mRNA cleavage complex 2 protein Pcf11 from human ([swissprot:O94913]) and similar proteins from vertebrates. This repeat is about thirteen amino acids with a high content of proline and glycine residues, however, it varies in length among the sequences included in this entry. These repeats contain the highly conserved RFE/DG motif, conserved in PCF11 orthologues in vertebrates but not in Drosophila, C. elegans, or yeast. It has been described that human PCF11 has 30 repeats of the RFE/DG motif (referred as FEGP in) which are necessary for pre-mRNA cleavage complex II (CFII) activity. PCF11 is a subunit and an essential component of CFII (the orthologue of cleavage and polyadenylation factor IA (CFIA) from yeast) which is involved in pre-mRNA 3' end processing and in transcription termination. PCF11 is thought to be one of the scaffold proteins of the processing complex. PCF11-mediated termination is essential for vertebrate development.
Pfam PF19414: Astrovirus p19 protein (family)
This entry represents the p19 protein found in human astrovirus.
Pfam PF11187: Mbeg1-like (family)
This family includes a group of uncharacterised proteins from bacteria. Recently, a member from Gemella sanguinis M325, Mbeg1 (for "microbiome bacteria effector gene") has been identified as the first example of this protein family being associated with a potential effector function in the human microbiome.
Pfam PF11479: RNA silencing suppressor P21 C-terminal domain (domain)
P21 is produced by Beet yellows virus to suppress the antiviral silencing response mounted by the host. P21 acts by binding directly to siRNA which is a mediator in the process. P21 has an octameric ring structure with a large central cavity. This is the C-terminal domain. The N-terminal domain is [pfam:PF11757].
Pfam PF19167: Family of unknown function (DUF5849) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in viruses.
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 PF19449: Family of unknown function (DUF5987) (family)
This family of uncharacterised proteins is found in actinobacteria. Proteins in this family are approximately 190 amino acids in length. Many protein in this family are annotated as regulator, but the source of this annotation is uncertain.
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 PF19666: Family of unknown function (DUF6169) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 137 and 167 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 PF15649: Restriction endonuclease fold toxin 7 (family)
A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, or type 7 secretion system.
Pfam PF10178: Proteasome assembly chaperone 3 (family)
PAC3 is a family of eukaryotic proteasome assembly chaperone 3 proteins conserved from fungi to plants to humans. PAC3 plays a crucial part in the assembly of the 20S core proteasome unit, in conjunction with PAC4.
Pfam PF00989: PAS fold (domain)
The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+.
Wikipedia: A Per-Arnt-Sim (PAS) domain is a protein domain found in all kingdoms of life. Generally, the PAS domain acts as a molecular sensor, whereby small molecules and other proteins associate via binding of the PAS domain. Due to this sensing capability, the PAS domain has been shown as the key structural motif involved in protein-protein interactions of the circadian clock, and it is also a common motif found in signaling proteins, where it functions as a signaling sensor.
Pfam PF15932: Domain of unknown function (DUF4748) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 114 and 139 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 PF24560: Ubiquitin thioesterase OTU1, C-terminal C2H2-type zinc finger (domain)
This C2H2-type zinc finger is found at the C-terminal end of human Ubiquitin thioesterase OTU1 and similar animal proteins. OTU1 is a hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal proteins.
Pfam PF15324: Hedgehog signalling target (family)
TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.
Pfam PF17451: Glycosyl hydrolase 101 beta sandwich domain (domain)
Virulence of pathogenic organisms such as the Gram-positive Streptococcus pneumoniae is largely determined by the ability to degrade host glycoproteins and to metabolise the resultant carbohydrates. This family is the enzymatic region, [ec:3.2.1.97], of the cell surface proteins that specifically cleave Gal-beta-1,3-GalNAc-alpha-Ser/Thr (T-antigen, galacto-N-biose), the core 1 type O-linked glycan common to mucin glycoproteins. This reaction is exemplified by the S. pneumoniae protein [swissprot:B2DRU5], where Asp764 is the catalytic nucleophile-base and Glu796 the catalytic proton donor. This domain represents C-terminal the beta sandwich domain.
Wikipedia: In molecular biology, glycoside hydrolase family 101 is a family of glycoside hydrolases.
Pfam PF22071: FAP42 domain B2 (domain)
FAP42 is a large protein that forms the peripheral 'beam' of the C1b projection of the ciliary central apparatus (CA). This protein forms a complex with FAP413 and FAP246, which is essential for a stable assembly of the C1b, C1f and C2b projections, and loss of these proteins leads to ciliary motility defects. FAP42 structure has been determined along with other components of the Chlamydomonas reinhardtii ciliary central apparatus. FAP42 contains cysteine peptidase domain, adenylate kinase domain, five guanylate kinase domains and three beta-sandwich domains. The latter adopt a jelly-roll topology and have a significant sequence and structural similarity to domain III in calpains and the predicted beta-sandwich domains in androglobin. This entry represents the second FAP42 beta-sandwich domain B2.
Pfam PF12230: Pre-mRNA splicing factor PRP21 like protein (family)
This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with [pfam:PF01805]. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form.
Pfam PF20762: Domain of unknown function (DUF6836) (domain)
This domain is predominantly found in proteins from bacteria, including CLOLEP_02462 from Clostridium leptum. The function of this protein 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 PF00974: Rhabdovirus spike glycoprotein fusion domain (domain)
This entry includes the glycoprotein G from Rhabdoviruses, such as rabies virus (RABV), Mokola virus (MOKV) and European bat lyssavirus 1 (EBLV), which attaches the virus to host cellular receptor, and induces endocytosis of the virion. It forms the glycoprotein spike that is made up of a trimer of G proteins. Each protomer of the trimer is composed of three domains: a membrane-distal pleckstrin homology domain (PH),  a membrane-proximal fusion domain (FD) and a laterally positioned central domain (CD). This entry represents the elongated FD (also known as domain IV).
Pfam PF20542: Family of unknown function (DUF6757) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are approximately 50 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 PF07996: Type IV secretion system proteins (family)
Members of this family  are components of the type IV  secretion system.  They mediate intracellular transfer of macromolecules via a mechanism ancestrally related to that of bacterial conjugation  machineries.
Wikipedia: Secretion is the movement of material from one point to another, such as a secreted chemical substance from a cell or gland. In contrast, excretion is the removal of certain substances or waste products from a cell or organism. The classical mechanism of cell secretion is via secretory portals at the plasma membrane called porosomes. Porosomes are permanent cup-shaped lipoprotein structures embedded in the cell membrane, where secretory vesicles transiently dock and fuse to release intra-vesicular contents from the cell.
Pfam PF07870: Protein of unknown function (DUF1657) (family)
This domain appears to be restricted to the Bacillales.
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 PF11542: Mitochondrial division protein 1 (family)
Mdv1 is a component of the mitochondrial fission machinery in Saccharomyces cerevisiae. The protein is also involved in peroxisome proliferation. Mdv1 along with Fis1 is also involved in controlling Dnm-1 dependant devision, a GTPase involved in the mediation of mitochondrial division. In this role, Mdv1 is the linker between Fis1 and Dnm1. Mdv1 plays a key role in the regulation of Dnm1 self-assembly.
Pfam PF16202: N-terminal region of Bloom syndrome protein (family)
BLM_N is the very N-terminal region of chordate Bloom syndrome proteins. The exact function is not known.
Pfam PF06070: Herpesvirus large structural phosphoprotein UL32 (family)
The large phosphorylated protein (UL32-like) of herpes viruses is the polypeptide most frequently reactive in immuno-blotting analyses with antisera when compared with other viral proteins.
Pfam PF24244: INO80 complex subunit 3-like, middle region (domain)
This entry represents the central region of a group of fungal sequences that are homologues of the INO80 complex subunit 3 (Iec3) from S.pombe. They differ in this region that is absent on the S.pombe homologue which only consists on a helix. According to structure predictions, this section may adopt an arrangement of short helices connected by loops. The C-terminal region is disordered.
Pfam PF04764: Protein of unknown function (DUF613) (family)
Family of chloroplast proteins of unknown function.  Some members have two copies of the conserved region.
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 PF19221: MELT motif (conserved_site)
The outer kinetochore protein scaffold KNL1 is essential for error-free chromosome segregation during mitosis and meiosis. A critical feature of KNL1 is an array of repeats containing MELT-like motifs. When phosphorylated, these motifs form docking sites for the BUB1-BUB3 dimer that regulates chromosome biorientation and the spindle assembly checkpoint. This entry mainly represents vertebrate proteins although MELT motifs are found much more widely.
Pfam PF04566: RNA polymerase Rpb2, domain 4 (domain)
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.
Pfam PF14365: Neprosin activation peptide (family)
Pitcher plants are insectivorous and secrete a digestive fluid into the pitcher. This fluid contains a mixture of enzymes including peptidases. One of these is neprosin, characterized from the pitcher plant Nepenthes ventrata. This peptidase is of unknown catalytic type and is unaffected by standard peptidase inhibitors. Unusually, activity is directed towards prolyl bonds, but unlike most peptidase that cleave after proline, there is no restriction on sequence length or position of the proline residue. The peptidase is secreted and is presumed to possess an N-terminal activation peptide. This domain corresponds to the presumed activation peptide.
Pfam PF05980: Toxin 7 (family)
This family consists of several short spider neurotoxin proteins including many from the Funnel-web spider.
Pfam PF10691: Protein of unknown function (DUF2497) (family)
Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
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 PF07524: Bromodomain associated (domain)
This domain is predicted to bind DNA and is often found associated with [pfam:PF00439] and in transcription factors. It has a histone-like fold.
Pfam PF20990: Predicted membrane protein (DUF2207) C-terminal domain (family)
This domain, found in various hypothetical bacterial proteins, has 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 PF11101: Protein of unknown function (DUF2884) (family)
Some members in this bacterial family of proteins are annotated as YggN which currently has 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 PF15800: Clock interacting protein circadian (family)
CiPC is a family of proteins found in eukaryotes. The protein was identified in sheep as a gene-orthologue involved in regulation of the circadian clock. Proteins in this family are typically between 220 and 400 amino acids in length.
Pfam PF05361: PKC-activated protein phosphatase-1 inhibitor (family)
Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction.
Pfam PF08821: CGGC domain (domain)
This putative domain contains a quite highly conserved sequence of CGGC in its central region.  The domain has many conserved cysteines and histidines suggestive of a zinc binding function.
Pfam PF13100: OstA-like protein (family)
This is a family of OstA-like proteins that are related to [pfam:PF03968].
Pfam PF14672: Late cornified envelope (family)
This is a family of late cornified envelope proteins that are expressed in skin.
Pfam PF18943: Family of unknown function (DUF5690) (family)
This is a family of unknown function mostly found 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 PF20202: Domain of unknown function (DUF6564) (domain)
This domain is functionally uncharacterised and is found in proteins from bacteria and archaea. This domain is found in Protein LicC (swiss:P14183), a CTP:phosphocholine cytidylyltransferase involved in LPS biosynthesis. Members containing this domain are annotated as nucleotidyltransferases. It is probable that this domain has a Rossmann like fold.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15929: Myofilin (family)
Myofilin is an insect muscle protein found in thick muscle filaments.
Pfam PF19959: Effector-associated domain 4 (domain)
Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements.
Pfam PF16730: DnaG-primase C-terminal, helicase-binding domain (domain)
DnaG-primase_C is the C-terminal of a set of eubacterial DnaG primases that are a single-stranded DNA (ssDNA)-dependent RNA polymerase responsible for the synthesis of oligonucleotide primers needed for the replication of DNA. It interacts with helicase at the replication fork.
Pfam PF01351: Ribonuclease HII (family)
The entry represents the Rnase H type-II domain.
Ribonuclease H (RNase H) (3.1.26.4) is a member of the ribonuclease family, which recognises and cleaves the RNA strand of RNA-DNA heteroduplexes. The enzyme is widely present in all three kingdoms of living organisms, including bacteria, archaea, and eukaryotes, and their counterpart domains are also found in reverse transcriptases (RTs) from retroviruses and retroelements . RNases H are classified into two evolutionarily unrelated families, type-I and type-II RNase H, with common structural features of the catalytic domain but different range of substrates for enzymatic cleavage. There appears to be three evolutionarily distinct lineages of cellular Rnase H enzymes . Type-I or RNase HI domains have been found in all Eukarya, one Archaea, many Eubacteria, a few non-LTR retroposons and all LTR retrotransposons. Type II enzymes consist of RNase HII (rnhB) and HIII (rnhC), which are homologous enzymes. RNase HII can be found in Archaea, Eubacteria and all Eukarya, while RNase HIII appears only in some Eubacteria. In eukaryotes and all Archaea, RNase HII enzymes may constitute the bulk of all Rnase H activity, while the reverse is true in Eubacteria like E. coli where RNase HI is the major source of RNH activity . All LTR retrotransposons acquired an enzymatically weak RNase H domain that is missing an important catalytic residue found in all other RNase H enzymes. Vertebrate retroviruses appear to have reacquired their RNase H domains, which are catalytically more active, but their ancestral RNase H domains (found in other LTR retrotransposons) have degenerated to give rise to the tether domain unique to vertebrate retrovirus . Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Retroviral RNase H is synthesised as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins.
Wikipedia: Ribonuclease H is a family of non-sequence-specific endonuclease enzymes that catalyze the cleavage of RNA in an RNA/DNA substrate via a hydrolytic mechanism. Members of the RNase H family can be found in nearly all organisms, from bacteria to archaea to eukaryotes.