SII-SWORD/CoKE huggingface dataset:
Pfam PF17441: Family of unknown function (DUF5419) (family)
This is a family of unknown function found in Mycobacterium phages 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 PF22302: Domain of unknown function (DUF6968) (domain)
This domain is found in uncharacterised bacterial proteins either standalone or C-terminal to HTH winged helix domains. It has a partial sequence similarity to ribosome associated factors that are members of [pfam:PF02482].
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 PF21905: Nsp1alpha N-terminal zinc finger (domain)
Porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV), a positive-strand RNA virus that belongs to the Arteriviridae family of Nidovirales, has been identified as the causative agent of PRRS. Nsp1alpha is the amino (N)-terminal protein in a polyprotein encoded by the PRRSV genome and is reported to be crucial for subgenomic mRNA synthesis, presumably by serving as a transcription factor. Before functioning in transcription, nsp1alpha proteolytically releases itself from nsp1beta. Nsp1alpha contains a ZF domain (this entry), a papain-like cysteine protease (PCP) domain with a zinc ion unexpectedly bound at the active site (which is essential for proteolytic self-release of nsp1alpha), and a carboxyl-terminal extension (which occupies the substrate binding site of the PCP domain).
Pfam PF18612: Bacterial Alpha amylase C-terminal domain (domain)
This is a bacterial alpha amaylase C-terminal domain found mostly in bacilli.
Pfam PF14462: Prokaryotic E2 family E (family)
A member of the E2/UBC superfamily of proteins found in diverse bacteria. Analysis of the active site residues suggest that members of this family are inactive as they lack the characteristic catalytic residues of the E2 enzymes. They are usually fused  to or in the neighborhood of a multi/poly ubiquitin domain protein. Other proteins of the ubiquitin modification pathway such as  the E1 and JAB proteins are also found in its gene neighborhood along with a distinct predicted metal-binding protein.
Pfam PF04541: Herpesvirus virion protein U34 (family)
The virion proteins in this family include membrane phosphoprotein-like proteins such as UL34, Epstein-Barr and R50, from dsDNA viruses, no RNA stage, Herpesvirales. The family Herpes_BFRF1, [pfam:PF05900], has been merged in.
Pfam PF13563: 2'-5' RNA ligase superfamily (family)
This family contains proteins related to [pfam:PF02834]. These proteins are likely to be enzymes, but they may not share the RNA ligase activity.
Pfam PF04461: Protein of unknown function (DUF520) (family)
The structure of the DUF520 family of uncharacterised proteins shows that it has composed of two domains each of which has the same topology.
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 PF00836: Stathmin family (family)
The Stathmin family of proteins play an important role in the regulation of the microtubule cytoskeleton.  They regulate microtubule dynamics by promoting depolymerization of microtubules and/or preventing polymerisation of tubulin heterodimers.
Wikipedia: Stathmin, also known as metablastin and oncoprotein 18 is a protein that in humans is encoded by the STMN1 gene.
Pfam PF12362: DNA polymerase III gamma and tau subunits C terminal (family)
This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with [pfam:PF00004]. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
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 PF05228: CHASE4 domain (domain)
CHASE4. This is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in prokaryotes. Specifically, CHASE4 domains are found in histidine kinases in Archaea and in predicted diguanylate cyclases/phosphodiesterases in Bacteria. Environmental factors that are recognised by CHASE4 domains are not known at this time.
Pfam PF05595: Domain of unknown function (DUF771) (family)
Family of uncharacterised ORFs found in  Bacteriophage and Lactococcus lactis.
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 PF21107: STPRs (score and three amino acid peptide repeats) (repeat)
The silkgland-specific transcription factor FMBP-1 from the silkworm Bombyx mori contains a unique DNA-binding domain of four tandem STPRs, namely the score and three amino acid peptide repeats. In the presence of target DNA, STPRs adopts a zig-zag structure of three or four tandem alpha-helices that run along the major groove of DNA.
Pfam PF24622: Tape measure protein domain (domain)
This domain is found in Tape measure protein from Pseudomonas phage PAJU2 (TMP), which serves as a ruler that controls the length of tail by stopping the tail tube polymerisation and is probably released from the tail shaft during infection to facilitate DNA translocation into the host cell. The specific function of this domain is unknown.
Pfam PF01687: Riboflavin kinase (domain)
This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein known as RibC in Bacillus subtilis.  The RibC protein from Bacillus subtilis has both flavokinase and flavin adenine dinucleotide synthetase (FAD-synthetase) activities. RibC plays an essential role in the flavin metabolism.  This domain is thought to have kinase activity.
Wikipedia: In enzymology, a riboflavin kinase is an enzyme that catalyzes the chemical reactionATP + riboflavin  ADP + FMN
Pfam PF20175: Tra1 HEAT repeat central region (repeat)
This entry represents part of the Tra1 protein composed of alpha solenoid repeats that forms the central region. This is named as central due to its position relative to the ring region.
Pfam PF06743: FAST kinase-like protein, subdomain 1 (family)
This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases ([ec:2.7.1.-]) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This region is often found immediately N-terminal to the FAST kinase-like protein, subdomain 2.
Pfam PF06480: FtsH Extracellular (family)
This domain is found in the FtsH family of proteins. FtsH is the only membrane-bound ATP-dependent protease universally conserved in prokaryotes (). It only efficiently degrades proteins that have a low thermodynamic stability - e.g. it lacks robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In Oenococcus oeni FtsH is involved in protection against environmental stress (), and shows increased expression under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded (personal obs: Yeats C). The precise function of this N-terminal region is unclear.
Pfam PF09548: Stage III sporulation protein AB (spore_III_AB) (family)
SpoIIIAB represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Pfam PF01741: Large-conductance mechanosensitive channel, MscL (domain)
Mechanosensitive ion channels (MscL) play a critical role in transducing physical stresses at the cell membrane into an electrochemical response. MscL is a protein which forms a channel organised as a homopentamer, with each subunit containing two transmembrane regions . Prokaryotes harbor a large-conductance mechanosensitive channel (gene mscL) that opens in response to stretch forces in the membrane lipid bilayer and participate in the regulation of osmotic pressure changes within the cell . MscL has a conserved domain architecture which comprises an amphipathic Î±-helix (S1) that lies along the cytoplasmic membrane, a highly conserved first transmembrane domain (TM1) that forms the pore constriction, a periplasmic loop, a second transmembrane domain (TM2) that faces the lipid membrane, and a linker that leads to a cytoplasmic Î±-helical bundle .
This family also includes anditomin synthesis protein L (AndL), which is part of the gene cluster that mediates the biosynthesis of anditomin. Its role of in this pathway is not known .
Wikipedia: Large conductance mechanosensitive ion channels (MscLs) (TC# 1.A.22) are a family of pore-forming membrane proteins that are responsible for translating stresses at the cell membrane into an electrophysiological response. MscL has a relatively large conductance, 3 nS, making it permeable to ions, water, and small proteins when opened. MscL acts as stretch-activated osmotic release valve in response to osmotic shock.
Pfam PF24910: Integrin beta-like protein A-E, third Ig-like domain (domain)
This entry represents the third Ig-like domain (according to structure predictions) of Integrin beta-like proteins A-E (SIBA-E) from Dictyostelium discoideum and similar sequences. These proteins may be implicated in cellular adhesion to substrate or phagocytic particles.
Pfam PF10377: Autophagy-related protein 11 (family)
The function of this family is conflicting. In the fission yeast, Schizosaccharomyces pombe, this protein has been shown to interact with the telomere cap complex and it is also required for dimerisation and kinase activation of Atg1. However, in budding yeast, Saccharomyces cerevisiae, this protein is called ATG11 and is shown to be involved in autophagy.
Pfam PF00869: Flavivirus glycoprotein, central and dimerisation domains (domain)
Flaviviruses and alphaviruses are arthropod-borne, enveloped RNA viruses that cause infections in vertebrate hosts . These viruses have two envelope glycoproteins (also known as 'spike' glycoproteins), one that undergoes proteolytic cleavage to prime the virus (glycoproteins M and P62 in flaviviruses and alphaviruses, respectively), and the other to mediate receptor binding and fusion (glycoproteins E and E1 in flaviviruses and alphaviruses, respectively). Glycoprotein E/E1 is comprised of three domains: domain I (dimerisation domain) is a Î²-barrel, domain II (central domain) is an elongated Î²-stranded and Î±-helical domain, and domain III (immunoglobulin-like domain) is an IgC-like Î²-sandwich. This entry represents the intertwined central and dimerisation domains found in flaviviral glycoprotein E .
Pfam PF05302: Protein of unknown function (DUF720) (family)
This family consists of several uncharacterised Chlamydia proteins of unknown 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 PF06972: GBF-interacting protein 1 N-terminal (domain)
This entry represents the N-terminal domain of GBF1-interacting protein 1 (GIP1, AT3G13222) from Arabidopsis. GIP1 may act as a coactivator that regulates transcription factors involved in lateral organ development of plants, such as bZIP transcription factors and LBD18.
Pfam PF10138: vWA found in TerF C terminus (domain)
vWA domain fused to TerD domain typified by the TerF protein. Some times found as solos.
Pfam PF20820: Fibroin heavy chain, N-terminal domain (domain)
This domain is found at the N-terminal end of Fibroin heavy chain (Fib-H) from Bombyx mori and similar proteins mainly from arthropods and bacteria. This hydrophilic region plays an important role in the assembly of silk by changing its conformation in response to pH decreases: it transitions from random coil to beta sheets and form micelle-like oligomers at around pH 6.0.
Pfam PF24621: 3-dehydroquinate synthase C-terminal (domain)
This entry represents the C-terminal domain of 3-dehydroquinate synthase (DHQS) and related proteins. DHQS catalyses the formation of  dehydroquinate (DHQ) and orthophosphate from 3-deoxy-D-arabino heptulosonic 7 phosphate. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. DHQS consists of an N-terminal Rossmann fold domain and a C-terminal alpha-helical domain. The active site is located in a cleft between the two somains. This domain contains most of the residues involved in catalysis and in substrate and Zn2+ binding. This domain is also found in AROM proteins which are pentafunctional enzymes that catalyse 5 consecutive enzymatic reactions in prechorismate polyaromatic amino acid biosynthesis.
Pfam PF16741: mRNA-decapping enzyme C-terminus (domain)
The C-terminal domain of mRNA-decapping enzyme in Metazoa is responsible for trimerisation.
Pfam PF23996: Domain of unknown function (DUF7314) (domain)
This domain is found in uncharacterised archaeal proteins. It is predicted to fold into an alpha-helical hairpin and it is likely associated with the membrane.
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 PF13607: Succinyl-CoA ligase like flavodoxin domain (domain)
This domain contains the catalytic domain from Succinyl-CoA ligase alpha subunit and other related enzymes. A conserved histidine is involved in phosphoryl transfer.
Pfam PF15347: Phosphoprotein associated with glycosphingolipid-enriched (family)
PAG, or Cbp/PAG (Csk binding protein/phospho-protein associated with glycosphingolipid-enriched microdomains) is a transmembrane family that has a negative regulatory role in T-cell activation through being an adapter for C-terminal Src kinase, Csk. This family of proteins is found in eukaryotes.
Pfam PF01940: Integral membrane protein DUF92 (family)
Members of this family have several predicted transmembrane helices.  One member of the family has been characterised as protein PGR (AtPGR). PGR is suggested to be a potential glucose-responsive regulator in carbohydrate metabolism in plants. This entry also includes protein VTE6, which is a Pphytyl-phosphate kinase catalysing the conversion of phytyl-monophosphate to phytyl-diphosphate.
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 PF17499: Ant venom peptides (family)
Members of this family are found in Myrmecia pilosula and represent a group of peptides that display cytotoxic, hypotensive, histamine-releasing and antimicrobial activities. Pilosulins constitute the major allergens of the venom of Myrmecia pilosula (Myrmeciinae). Pilosulin 1 is a long linear peptide (57 amino acids) and displays haemolytic and cytolytic activities. Pilosulins 3, 4, and 5 are a group of homo- and heterodimeric peptides. Pilosulin 1 [swissprot:Q07932] is expressed in the venom sac of ants in the form of a propeptide (112 kDa) which undergoes extensive post-translational modification. It is proposed to give rise to a family of six homologous C-terminal peptide sub-sequences containing between 27 and 56 amino acid residues in the final venom. Furthermore, it is found to form random coils and have minimal secondary structure. However, in increasingly hydrophobic conditions, approximately one-third of the peptide forms alpha-helix secondary structures. Studies on human erythrocytes and lymphocytes, show that Pilosulin 1 is highly lytic towards leukocytes and that the NH2-terminus (20 N-terminal residues) of Pilosulin 1 is critical for its cytotoxic activity and antimicrobial activities. Another family member Pilosulin 3 [swissprot:Q68Y23], is a heterodimer of Pilosulin 3a and Pilosulin 3b linked in anti-parallel fashion through 2 disulfide bridges. This peptide is the most abundant peptide found in native venom.
Pfam PF05155: Replication-associated protein G2P C-terminal (domain)
This entry represents the C-terminal domain found in gene II protein (G2P) from bacteriophage. A much shorter protein of unknown function, translated from a conserved in-frame alternative initiator, is designated gene X protein (G10P), such as [swissprot:A7BJW3] or [swissprot:J7I4I2].
Pfam PF02741: FTR, proximal lobe (domain)
The FTR (Formylmethanofuran--tetrahydromethanopterin formyltransferase) enzyme [ec:2.3.1.101] is involved in archaebacteria in the formation of methane from carbon dioxide. C-terminal proximal lobe of alpha+beta ferredoxin-like fold. SCOP reports fold duplication with N-terminal distal lobe.
Wikipedia: In enzymology, a formylmethanofuran-tetrahydromethanopterin N-formyltransferase is an enzyme that catalyzes the chemical reactionformylmethanofuran + 5,6,7,8-tetrahydromethanopterin  methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin
Pfam PF17743: Family of unknown function (DUF5580) N-terminal domain (domain)
This is a family of unknown function found in metazoa. This entry represents the N-terminal calmodulin-like domain.
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 PF07837: Formiminotransferase domain, N-terminal subdomain (domain)
The formiminotransferase (FT) domain of formiminotransferase- cyclodeaminase (FTCD) forms a homodimer, and each protomer comprises two subdomains. The N-terminal subdomain is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This,  in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a  short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to  form a number of contacts with residues found in both the N-terminal and C-terminal subdomains.
Wikipedia: Glutamate formimidoyltransferase is a methyltransferase enzyme which uses tetrahydrofolate as part of histidine catabolism. It catalyses two reactions:5-formimidoyltetrahydrofolate + L-glutamate &lt;=&gt; tetrahydrofolate + N-formimidoyl-L-glutamate
5-formyltetrahydrofolate + L-glutamate &lt;=&gt; tetrahydrofolate + N-formyl-L-glutamate
Pfam PF08980: Domain of unknown function (DUF1883) (domain)
Predicted ligand-binding domain of the PPC-like beta-sandwich fold. Observed in conserved gene neighbourhoods with diverse nucleotide-activated effector and related conflict systems, potentially recognises invasive molecules and initiates system responses or directly triggers directly-associated effector domains.
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 PF20830: Reovirus turret protein, bridge domain (domain)
Cytoplasmic polyhedrosis virus (CPV) has a turreted single-layer capsid consisting of 12 pentameric turrets on the five-fold vertices. Each turret has one Turret protein (TP), also known as VP3, which shows a polyhedrin-binding domain (PBD), a guanylyltransferase (GTase) domain ([pfam:PF20790]), two methylase domains and a bridge domain (this entry), which has two discontinuous regions.
Pfam PF18762: Serine/Threonine/Tyrosine Kinase found in polyvalent proteins (family)
A family of protein kinases found in polyvalent proteins of phages and prophages that although preserving their active site residues for ATP-binding and phosphotransfer appear to have lost the C-terminal subdomain characteristic of this superfamily.
Pfam PF03531: Structure-specific recognition protein (SSRP1) (domain)
SSRP1 has been implicated in transcriptional initiation and elongation and in DNA replication and repair. This domain belongs to the Pleckstrin homology fold superfamily.
Pfam PF11393: Type-IV b secretion system, inner-membrane complex component (family)
IcmL contains two amphipathic beta-sheet regions, required for the pore-forming ability which may be related to the transfer of this protein into a host cell membrane. The icmL gene shows significant similarity to plasmid genes involved in conjugation however IcmL is thought to be required for macrophage killing. It is unknown whether conjugation plays a role in macrophage killing. This is a family of DotI/IcmL proteins of type IVb secretion systems, that reside in the inner-membrane. It carries a single transmembrane helix in the N-terminal conserved region, has an extra-periplasmic domain, and is conserved in all T4BSSs including I-type conjugation systems (TraM). DotI/IcmL (and DotJ) may form an inner membrane complex that associates with the core complex.