SII-SWORD/CoKE huggingface dataset:
Pfam PF10466: Saccharopepsin inhibitor I34 (family)
The saccharopepsin inhibitor is highly specific for the aspartic peptidase saccharopepsin.                  It is largely unstructured in the absence of saccharopepsin, but in the presence, the inhibitor undergoes a conformation change forming an almost perfect alpha-helix from Asn2 to Met32 in the active site cleft of the peptidase.
Wikipedia: In biology and biochemistry, protease inhibitors, or antiproteases, are molecules that inhibit the function of proteases. Many naturally occurring protease inhibitors are proteins.
Pfam PF01847: VHL beta domain (domain)
VHL forms a ternary complex with the elonginB  [swissprot:O44226] and elonginC [swissprot:O13292] proteins. This complex binds Cul2, which then is involved in regulation of vascular endothelial growth factor [swissprot:P15692] mRNA.
Pfam PF00814: tRNA N6-adenosine threonylcarbamoyltransferase (family)
This domain can be found in Kae1/Qri7/YgjD, products of COG0533 that belong to a small group of 60 proteins that are present in all three domains of life. COG0533 proteins are suggest to play a role in a post translational modification of certain tRNAs. For example, YgjD along with YeaZ, YjeE, and YrdC have been deemed necessary and sufficient for the tRNA modification. This modification involves the formation of N6-threonyl carbamoyl adenosine (t6A) at position 37 in the anti-codon stem loop which is critical for translational speed and accuracy. Structural analysis indicate that YeaZ lacks resemblance to any known protease active site. Together with the absence of a putative zinc-binding motif. Thus the likelyhood of it being a protease, as previously thought, has been negated. [ec:2.3.1.234]
Pfam PF00929: Exonuclease (domain)
This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;
Wikipedia: Ribonuclease T is a ribonuclease enzyme involved in the maturation of transfer RNA and ribosomal RNA in bacteria, as well as in DNA repair pathways. It is a member of the DnaQ family of exonucleases and non-processively acts on the 3' end of single-stranded nucleic acids. RNase T is capable of cleaving both DNA and RNA, with extreme sequence specificity discriminating against cytosine at the 3' end of the substrate.
Pfam PF13104: Protein of unknown function (DUF3956) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length.
Pfam PF24337: Domain of unknown function (DUF7505) (domain)
This domain is found in a group of uncharacterised proteins from nematodes. These proteins contain a semi-conserved PPChHPGQ motif (where h is a hydrophobic residue) and are predicted to fold into a incomplete beta-sandwich.
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 PF08983: Vasopressin V1 receptor, C-terminal (domain)
This is the conserved C-terminal domain of Vasopressin V1a/b receptors (V1R), which is involved in receptor trafficking and facilitates the interaction between the intracellular loops of the receptor, the G proteins and coupling to phospholipase C. This domain is unstructured and may reflect its conformational plasticity that may be necessary for proper function of V1R.
Pfam PF01835: MG2 domain (domain)
This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin in eukaryotes. Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. This domain is found in eukaryotic and bacterial proteins. In human A2Ms, this domain is termed macroglobulin-like (MG) domain 2 and in Salmonella enterica ser A2Ms, this is domain 4.
Wikipedia: α2-Macroglobulin (α2M) or alpha-2-macroglobulin is a large plasma protein found in the blood. It is mainly produced by the liver, and also locally synthesized by macrophages, fibroblasts, and adrenocortical cells. In humans it is encoded by the A2M gene.
Pfam PF06433: Methylamine dehydrogenase heavy chain (MADH) (repeat)
Methylamine dehydrogenase ([ec:1.4.99.3]) a periplasmic quinoprotein found in several methyltrophic bacteria. Induced when grown on methylamine as a carbon source MADH catalyses the oxidative deamination of amines to there corresponding aldehydes.  MADH is a hetero- tetramer, comprised of two heavy chains (H) and two light chains (L).  The H-chain forms a beta-propeller like structure.
Pfam PF00224: Pyruvate kinase, barrel domain (domain)
This is the barrel domain of pyruvate kinases. This domain represents the beta/alpha barrel and the small beta-barrel domain inserted within it. The active site is found in a cleft between the two domains.
Pfam PF05749: Rubella membrane glycoprotein E2 (family)
Rubella virus (RV), the sole member of the genus Rubivirus within the family Togaviridae, is a small enveloped, positive strand RNA virus.  The nucleocapsid consists of 40S genomic RNA and a single species of capsid protein which is enveloped within a host-derived lipid bilayer containing two viral glycoproteins, E1 (58 kDa) and E2 (42-46 kDa).  In virus infected cells, RV matures by budding either at the plasma membrane, or at the internal membranes depending on the cell type and enters adjacent uninfected cells by a membrane fusion process in the endosome, directed by E1-E2 heterodimers. The heterodimer formation is crucial for E1 transport out of the endoplasmic reticulum to the Golgi and plasma membrane. In RV E1, a cysteine at position 82 is crucial for the E1-E2 heterodimer formation and cell surface expression of the two proteins.
Pfam PF18255: DNA processing protein A sterile alpha motif domain (domain)
This is the N-terminal domain found in DNA processing protein A (DprA) present in Streptococcus pneumoniae. DprA has recently been discovered to be a transformation-dedicated RecA loader. Transformation is believed to play a major role in genetic plasticity. This domain is known as the sterile alpha motif (SAM) domain. DprAs are able to form a type of dimer through SAM-SAM interactions, also known as N/N interactions.
Pfam PF22632: Dihydroxybiphenyl dioxygenase BphC D1 (domain)
This domain is found in dihydroxybiphenyl dioxygenase BphC and related proteins. This enzyme contains a non-heme iron atom and plays an important role in degrading biphenyl/polychlorinated biphenyls (PCBs).
Pfam PF16828: GAG-binding domain on surface antigen (domain)
GAGBD is a domain on the surface antigen of the swine pathogen Streptococcus suis and related species. This domain expresses three clusters of basic residues, largely lysines, that are critical for heparin-binding and cell adhesion during bacterium-host cell adhesion. The GAGBD domain binds to the host cell surface glycosaminoglycans or GAGs of the Streptococcus.
Pfam PF01445: Viral small hydrophobic protein (family)
The SH (small hydrophobic) protein is a membrane protein of uncertain function.
Pfam PF24369: Family of unknown function (DUF7525) (family)
This family includes a group of short archaeal proteins. Members are predicted to adopt an alpha-helical configuration.
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 PF19000: Family of unknown function (DUF5729) (family)
This is a highly conserved domain of unknown function found in Platyhelminthes, with many of the sequences annotated as being the small conductance calcium-activated potassium channel protein. However, the location suggests that this domain belongs to the intracellular amino terminus of these transmembrane proteins, near the calcium-activated SK potassium channel.
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 PF14929: TAF RNA Polymerase I subunit A (repeat)
TATA box binding protein associated factor RNA Polymerase I subunit A is found in eukaryotes and is encoded by the gene TAF1A in humans. Its function is to aid transcription of DNA into RNA by binding to the promoter at the -10 TATA box site. It is a component of the transcription factor SL1/TIF-IB complex, involved in PIC assembly (pre-initiation complex) during RNA polymerase I-dependent transcription. The rate of PIC formation depends on the rate of association of this protein. This protein also stabilises nucleolar transcription factor 1/UBTF on rDNA.
Wikipedia: The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II.
Pfam PF07867: Protein of unknown function (DUF1654) (family)
This family consists of proteins from the Pseudomonadaceae.
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 PF22284: Family of unknown function (DUF6961) (family)
This is a family of small, about 60 residues in length, bacterial proteins. They are predicted to adopt a globular structure consisting of three helices. The N- and C-terminal helices contain highly conserved aromatic residues in addition to the nearly invariant glycines located at the interhelical connecting loops.
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 PF17722: Intraflagellar transport-associated protein (family)
Intraflagellar transport-associated protein (IFTAP, C11ORF74) interacts with the IFT-A complex and is accumulated at the distal tip in the absence of an IFT-A subunit IFT139. In IFTAP-knockout (KO) cells, the BBSome components cannot enter cilia. However, IFTAP-KO mice demonstrated no obvious anatomical abnormalities associated with ciliary dysfunctions.
Pfam PF18883: Autochaperone Domain Type 1 (repeat)
This entry represents the autochaperone domain of type 1 (AC-1) in the Type Va Secretion System (T5aSS). Autotransporters (ATs) belong to a family of modular proteins secreted by the Type V, subtype a, secretion system (T5aSS) and considered as an important source of virulence factors in lipopolysaccharidic diderm bacteria (archetypical Gram-negative bacteria). The AC of type 1 with beta-fold appears as a prevalent and conserved structural element exclusively associated to beta-helical AT passenger.
Pfam PF09105: Elongation factor SelB, winged helix (domain)
SelB (Selenocysteine-specific elongation factor) is a transcription factor necessary for the incorporation of selenocysteine into proteins and binds both transfer RNA (tRNA) and mRNA.. This entry represents a domain that adopts a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. In SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit.
Pfam PF10671: Toxin co-regulated pilus biosynthesis protein Q (family)
The toxin-coregulated pilus (TCP) of Vibrio cholerae and the soluble TcpF protein that is secreted via the TCP biogenesis apparatus are essential for intestinal colonisation in the disease of cholera. TcpQ is part of an outer membrane complex of the TCP biogenesis apparatus, comprised of TcpC and TcpQ, and the TcpQ is required for proper localisation of TcpC to the outer membrane. The domain is found in other Proteobacterial species apart from Vibrio.
Pfam PF08464: Geminivirus AC4/5 conserved region (family)
This domain is found in replication initiator (Rep) associated proteins such as AC5 in the Geminivirus/Begomovirus.
Pfam PF19867: Family of unknown function (DUF6340) (repeat)
This family of proteins is found in bacteria and it is functionally uncharacterised. Members in this family are about 350 amino acids in length and are likely to contain TRP repeats.
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 PF24770: CFAP74 second Ig-like domain (domain)
This entry represents the second Ig-like domain of CFAP74, a protein that is part of the central apparatus of the cilium axoneme and may play a role in cilium movement. It may play an important role in sperm architecture and function.
Pfam PF08810: Kinase associated protein B (domain)
This bacterial protein forms an anti-parallel beta sheet with an extending alpha helical region.
Pfam PF22719: Short NACHT-associated C-Terminal domain, family 12 (domain)
The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors.
Pfam PF06541: Putative ABC-transporter type IV (family)
CmpB is a family of membrane proteins that are likely to be part of a two-component type IV ABC-transporter system. Families can transport multiple drugs including ethidium and fluoroquinolones. UniProtKB:Q83XH0 is a member of TCDB family 3.A.1.121.4.
Pfam PF15842: Domain of unknown function (DUF4718) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 130 and 224 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 PF01419: Jacalin-like lectin domain (repeat)
Proteins containing this domain are lectins.  It is found in 1 to 6 copies in these proteins. The domain is also found in the animal prostatic spermine-binding protein ([swissprot:P15501]).
Wikipedia: In molecular biology, the jacalin-like lectin domain is a mannose-binding lectin domain with a beta-prism fold consisting of three 4-stranded beta-sheets, with an internal pseudo 3-fold symmetry. Some lectins in this group stimulate distinct T- and B-cell functions, such as Jacalin, which binds to the T-antigen and acts as an agglutinin. This domain is found in 1 to 6 copies in lectins. The domain is also found in the salt-stress induced protein from rice and an animal prostatic spermine-binding protein.
Pfam PF04382: SAB domain (family)
This presumed domain is found in proteins containing FERM domains [pfam:PF00373].  This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain.
Pfam PF09218: Domain of unknown function (DUF1959) (domain)
This domain is found in a set of uncharacterised Archaeal hypothetical proteins. Its function has not, as yet, been described.
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 PF05099: Tellurite resistance protein TerB (family)
This family contains the TerB tellurite resistance proteins from a a number of bacteria.
Pfam PF10611: Protein of unknown function (DUF2469) (family)
Member proteins often found in Actinomycetes clustered with signal peptidase and/or RNAse-HII.
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 PF00277: Serum amyloid A protein (family)
The serum amyloid A (SAA) proteins comprise a family of vertebrate amphipathic alpha-helical apolipoproteins that associate predominantly with high density lipoproteins (HDL). They play a role in the mobilisation of cholesterol for tissue repair and regeneration. The synthesis of these proteins is greatly increased (as much as a 1000 fold) in inflammation, being a major acute phase reactant together with C-reactive protein. They act as cytokine-like proteins that are involved in cell-cell communication and in inflammatory, immunologic, neoplastic and protective pathways. Prolonged elevation of plasma SAA levels, as in chronic inflammation, results in a pathological condition, called amyloidosis, which is characterised by the highly insoluble accumulation of SAA in several tissues. During chronic inflammation, SAA association with HDL can change its protein and lipid composition which abrogates the HDL anti-atherogenic properties, contributing to a pro-atherogenic state.
Pfam PF11239: Protein of unknown function (DUF3040) (family)
Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
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 PF01376: Heat-labile enterotoxin beta chain (domain)
Escherichia coli heat-labile enterotoxin is a bacterial protein toxin with an AB5 multimer structure, in which the B pentamer has a membrane-binding function and the A chain (IPR001144) is needed for enzymatic activity . The B subunits are arranged as a donut-shaped pentamer, each subunit participating in ~30 hydrogen bonds and 6 salt bridges with its two neighbours .

The A subunit has a less well-defined secondary structure. It predominantly interacts with the pentamer via the C-terminal A2 fragment, which runs through the charged central pore of the B subunits. A putative catalytic residue in the A1 fragment (Glu112) lies close to a hydrophobic region, which packs two loops together. It is thought that this region might be important for catalysis and membrane translocation .
Wikipedia: In molecular biology, the heat-labile enterotoxin family includes Escherichia coli heat-labile enterotoxin and cholera toxin (Ctx) secreted by Vibrio cholerae.
Pfam PF04270: Streptococcal histidine triad protein (family)
All members of this family are proteins from Streptococcal species.  The proteins are characterised by having a HxxHxH motif that usually occurs multiple times throughout the protein. The histidine triad is predicted to bind metal cations, in particular Zn2+. The zinc is transferred, on the surface of the streptococcus from the Strep_his_triad protein, a zinc scavenger, to apo-ADCAII, a cell-surface lipoprotein transporter that leads to Zn2+ uptake into the bacterium.
Pfam PF16392: Ig-like domain (domain)
This family around 100 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides and Parabacteroides species. The function of this family remains unknown. It has an Ig like fold.
Pfam PF24986: RimM PRC barrel domain (domain)
This entry represents a PRC-barrel domain found in the RimM protein family.  The RimM family comprises ribosome maturation factors essential for the final assembly of the 30S ribosomal subunit, particularly the head region. These proteins facilitate the efficient processing of 16S rRNA and may function both before and after RbfA during 16S rRNA maturation. RimM proteins have a specific affinity for free 30S ribosomal subunits but not for 70S ribosomes. The PRC barrel domain within these proteins binds to ribosomal protein uS19, playing a crucial role in the assembly process. In some organisms, RimM is one of several proteins, including Era, RbfA, and RsgA/YjeQ, that assist in the late stages of 30S subunit assembly, ensuring the correct assembly of head-associated ribosomal proteins and preventing the accumulation of precursor rRNA forms.
Pfam PF19179: E3 ubiquitin-protein ligase TTC3/DZIP3 domain (domain)
This domain is found in E3 ubiquitin-protein ligases TTC3 and DZIP3 and its function is unknown. TTC3 mediates ubiquitination and degradation of phosphorylated Akt, apparently its preferable target. DZIP3 is also able to bind RNA through a Lys-rich region which enhances is ubiquitination activity. It is suggested that RNA-binding proteins or ribonucleoprotein particles might be physiological targets for this enzyme, which could be important during viral infections, especially for those replicating through RNA intermediates. This domain is also found in uncharacterised proteins found in viruses.
Pfam PF09336: Vps4 C terminal oligomerisation domain (domain)
This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation.
Pfam PF05315: ICEA Protein (family)
This family consists of several ICEA proteins from Helicobacter pylori. Helicobacter pylori infection causes gastritis and peptic ulcer disease, and is classified as a definite carcinogen of gastric cancer. ICEA1 is  speculated to be associated with peptic ulcer disease.