SII-SWORD/CoKE huggingface dataset:
Pfam PF19109: Family of unknown function (DUF5796) (family)
Family of proteins of unknown function predominantly found in Halobacteria.
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 PF00200: Disintegrin (domain)
Disintegrins are a family of small proteins from viper venoms that function as potent inhibitors of both platelet aggregation and integrin-dependent cell adhesion . Integrin receptors are involved in cell-cell and cell-extracellular matrix interactions, serving as the final common pathway leading to aggregation via formation of platelet-platelet bridges, which are essential in thrombosis and haemostasis. Disintegrins contain an RGD (Arg-Gly-Asp) or KGD (Lys-Gly-Asp) sequence motif that binds specifically to integrin IIb-IIIa receptors on the platelet surface, thereby blocking the binding of fibrinogen to the receptor-glycoprotein complex of activated platelets. Disintegrins act as receptor antagonists, inhibiting aggregation induced by ADP, thrombin, platelet-activating factor and collagen . The role of disintegrin in preventing blood coagulation renders it of medical interest, particularly with regard to its use as an anti-coagulant .

Disintegrins from different snake species have been characterised: albolabrin, applagin, barbourin, batroxostatin, bitistatin, obtustatin , schistatin , echistatin , elegantin, eristicophin, flavoridin , halysin, kistrin, tergeminin, salmosin  and triflavin.

Disintegrin-like proteins are found in various species ranging from slime mold to humans. Some other proteins known to contain a disintegrin domain are:


 * Some snake venom zinc metalloproteinases  consist of an N-terminal catalytic domain fused to a disintegrin domain. Such is the case for trimerelysin I (HR1B), atrolysin-e (Ht-e) and trigramin. It has been suggested that these proteinases are able to cleave themselves from the disintegrin domains and that the latter may arise from such a post-translational processing.
 * The beta-subunit of guinea pig sperm surface protein PH30 . PH30 is a protein involved in sperm-egg fusion. The beta subunit contains a disintegrin at the N-terminal extremity.
 * Mammalian epididymial apical protein 1 (EAP I) . EAP I is associated with the sperm membrane and may play a role in sperm maturation. Structurally, EAP I consists of an N-terminal domain, followed by a zinc metalloproteinase domain, a disintegrin domain, and a large C-terminal domain that contains a transmembrane region.
Wikipedia: Disintegrins are a family of small proteins from viper venoms that function as potent inhibitors of both platelet aggregation and integrin-dependent cell adhesion.
Pfam PF00195: Chalcone and stilbene synthases, N-terminal domain (domain)
The C-terminal domain of Chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase.          The differences in activity are accounted for by differences in this N-terminal domain.
Pfam PF12544: Lysine-2,3-aminomutase (family)
This domain family is found in bacteria, archaea and eukaryotes, and is typically between 111 and 127 amino acids in length. The family is found in association with [pfam:PF04055]. LAM catalyses the interconversion of L-alpha-lysine and L-beta-lysine, which proceeds by migration of the amino group from C2 to C3 concomitant with cross-migration of the 3-pro-R hydrogen of L-alpha-lysine to the 2-pro-R position of L-beta-lysine.
Pfam PF01843: DIL domain (repeat)
The DIL domain has no known function.
Pfam PF22998: LYC1 GNAT-like C-terminal domain (domain)
This domain is found C-terminal in Lysine acetyltransferase (LYC1) and other related fungal proteins. LYC1 catalyzes the first step the lysine degradation pathway. The domain represented by this entry is  predicted to adopt GNAT-like fold. It is found usually upstream Acetyltransferase GNAT domain ([pfam:PF00583]) suggesting a possible duplication event in these proteins.
Pfam PF02982: Scytalone dehydratase (domain)
Scytalone dehydratases are structurally related to the NTF2 family (see [pfam:PF02136]).
Pfam PF11666: Protein of unknown function (DUF2933) (family)
This bacterial family of 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 PF24188: Family of unknown function (DUF7416) (family)
This entry represents a small uncharacterised enterobacterial phage protein family.  Structure prediction suggests these proteins might adopt 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 PF08634: Mitochondrial protein Pet127 (domain)
Pet127 has been implicated in mitochondrial RNA stability and/or processing and is localised to the mitochondrial membrane. The Pet127 family is part of the PD-(D/E)XK nuclease superfamily including a full set of active site residues.
Pfam PF20609: Putative adhesive domain (group 17) (domain)
The structure model of this domain folds into 10 beta strands arranged in two beta sheets as well as 4-5 elongated alpha helices.  The beta sheets distantly resemble the Collagen_bind ([pfam:PF05737])  domain. It is annotated N-terminal to repeating stalk domains in  bacterial surface proteins. This domain can be found on a  E. faecalis protein encoded by the EF3314 gene, which was  proposed to contribute to the interaction of E. faecalis  with the host and to the bacterial virulence.
Pfam PF13958: Toxin ToxN, type III toxin-antitoxin system (family)
ToxN acts as a toxin, it is part of a type III toxin-antitoxin system. It acts as a ribosome independent endoribonuclease. It interacts with, and is inhibited by, the RNA antitoxin, ToxI. Three ToxN monomers bind to three ToxI monomers to create a trimeric ToxN-ToxI complex.
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF09680: Family of unknown function (family)
This is a family of unknown function. However, family members such as yjcZ has been shown to be sporulation specific and transcribed by the SigK RNA polymerase beginning at t4 of sporulation.
Pfam PF23061: M02D8_5-like, second CUB domain (domain)
This entry represents the second occurrence of the CUB domain in a family of uncharacterised proteins present in nematodes. Consecutive repetitions of this domain are common in this protein family. The CUB domain (for complement C1r/C1s, Uegf, Bmp1) is a structural motif of approximately 110 residues found predominantly in extracellular and plasma membrane-associated proteins, many of which undergo developmental regulation. CUB domains appear to be involved in oligomerisation and/or recognition of substrates and binding  partners.
Pfam PF14323: GxGYxYP putative glycoside hydrolase C-terminal domain (domain)
This family carries a characteristic sequence motif, GxGYxYP, and is a putative glycoside hydrolase. This domain is found in association with [pfam:PF16216]. Associated families are sugar-processing domains.
Pfam PF14190: Domain of unknown function (DUF4313) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 136 and 171 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 PF00260: Protamine P1 (family)
Protamines are small arginine-rich proteins that condense DNA in sperm to almost crystalline packing levels, creating a more hydrodynamic sperm head for efficient swimming and protects the DNA from UV radiation and DNA damage. These proteins bind non-specifically to the DNA and use a multi-step process to loop the DNA. During sperm development, the histones that package DNA in early spermatids are removed from the DNA and replaced in the final stages of spermatid maturation by sperm-specific histones, protamine-like proteins or protamines. Sequence comparisons of vertebrate and invertebrate protamines show that the sequence, structure, and probably function of these proteins evolve independently in vertebrates and various invertebrate groups.
Wikipedia: Protamines are small, arginine-rich, nuclear proteins that replace histones late in the haploid phase of spermatogenesis and are believed essential for sperm head condensation and DNA stabilization. They may allow for denser packaging of DNA in the spermatozoon than histones, but they must be decompressed before the genetic data can be used for protein synthesis. However, part of the sperm's genome is packaged by histones thought to bind genes that are essential for early embryonic development.
Pfam PF18931: Domain of unknown function (DUF5680) (domain)
This family of presumed domains is found in bacteria and archaea. Proteins in this family are typically between 152 and 220 amino acids in length. In some of the proteins this domain is associated with an N-terminal HTH domain, suggesting that they are transcriptional regulators.  This suggests that this may be a previously unidentified ligand binding 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 PF19814: Family of unknown function (DUF6297) (family)
This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 139 and 579 amino acids in length. There is a conserved sequence motif GPV. Some members of this family are hypothetical ABC transporter permeases.
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 PF21446: Long-tail fiber proximal subunit, C-terminal, trimerization domain (repeat)
The long tail fibers of bacteriophage T4 consist of rigid proximal and distal parts, connected by a hinge region. The proximal half- fiber is formed by a parallel homo-trimer of the Long-tail fiber proximal subunit Gp34. This entry represents a region of the C-terminal domain, which forms a long triple beta-helix made up of parallel beta-strands.
Pfam PF12716: Nuclear pore assembly and biogenesis (family)
This is a family of conserved fungal proteins involved in nuclear pore assembly. Apq12 is an integral membrane protein of the nuclear envelope (NE) and endoplasmic reticulum. Its absence leads to a partial block in mRNA export and cold-sensitive defects in the growth and localisation of a subset of nucleoporins, particularly those asymmetrically localised to the cytoplasmic fibrils. The defects in nuclear pore assembly appear to be due to defects in regulating membrane fluidity.
Pfam PF03302: Giardia variant-specific surface protein (family)
During infection, the intestinal protozoan parasite Giardia lamblia virus undergoes continuous antigenic variation which is determined by diversification of the parasite's major surface antigen, named VSP (variant surface protein).
Pfam PF17691: Contingent replication of cDNA 4 (family)
Family members are 18-kDa serine/threonine-rich polypeptides containing a P-loop motif and an SH3-binding region with phosphorylation sites for a variety of protein kinases (cdc2, CDK2, MAPK, CDK5, protein kinase C, Ca(2+)/calmodulin protein kinase 2, casein kinase 2) involved in cell proliferation and differentiation. Functional studies revealed that expression is associated with proliferating and migrating cells in developing brain. Furthermore, it has been suggested that CROC-4 participates in brain-specific c-fos signaling pathways involved in cellular remodeling of brain architecture. C1orf61 expression was also found associated with the progression of liver disease as well as human embryogenesis. It was shown to be up-regulated in hepatic cirrhosis tissues and further up-regulated in primary hepatocellular carcinoma tumors where it was suggested to play a role as a tumor activator.
Pfam PF18277: AbrB C-terminal domain (domain)
This is the C-terminal domain of AbrB protein from Bacillus subtilis. AbrB is a transition state regulator. Functions of AbrB include biofilm formation, antibiotic production, competence development, extracellular enzyme production, motility, and sporulation. The C-terminal domain is responsible for multimerization and, to a lesser extent than the N-terminal domain, also contributes in DNA binding.
Pfam PF23723: Erythroid differentiation-related factor 1-like, TPR repeats (repeat)
This region of tetratricopeptide-like repeats (TPR) is found at the C-terminal end of human Erythroid differentiation-related factor 1 (EDRF1) and similar proteins predominantly found in vertebrates. EDRF1 is a transcription factor involved in erythroid differentiation.
Pfam PF23919: Domain of unknown function (DUF7258) (domain)
This domain is found in uncharacterised proteins from Bacteroidota. It is predicted to adopt a globular structure with SH3-like topology. It is sometimes found N-terminal to [pfam:PF22273].
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 PF19354: Family of unknown function (DUF5931) (family)
This presumed domain is functionally uncharacterised. This domain family is found in actinobacteria, and is approximately 170 amino acids in length. This domain is found at the N-terminus of 2 component signalling proteins which also contain [pfam:PF07730], and [pfam:PF02518]. This domain presumably binds an as yet unknown ligand.
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 PF21210: Putative ATP-dependent RNA helicase, helical bundle (domain)
This domain is found in the putative ATP-dependent RNA helicase from Pyrococcus furiosus (PF2015) and similar archaeal proteins. PF2015 is a Hef helicase that processes flap- or fork-DNA structures. This protein shows an SF2 helicase domain in the N-terminal two-thirds and an XPF/Mus81-type nuclease domain in the C-terminal one-third. The SF2 helicase domain is organised into three structural subdomains. This entry represents the second of them, which is composed of six alpha-helices that are tightly assembled into a hydrophobic core. Its surface is positively charged, suggesting that it is a potential DNA binding region.
Pfam PF09682: Bacteriophage holin of superfamily 6 (Holin_LLH) (family)
Phage_holin_6_1 or Holin_LLH identifies a family of phage holins from a number of phage and prophage regions of Gram-positive bacteria. Like other holins, it is large for holins (about 100-160 amino acids) with stretches of hydrophobic sequence and is encoded adjacent to lytic enzymes. Holin LLH family is found in phage of Firmicutes and have an N-terminal transmembrane segment.
Pfam PF13663: Domain of unknown function (DUF4148) (domain)
This protein family is functionally uncharacterised.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13537: Glutamine amidotransferase domain (domain)
This domain is a class-II glutamine amidotransferase domain found in a variety of enzymes such as asparagine synthetase and glutamine-fructose-6-phosphate transaminase.
Pfam PF16149: Domain of unknown function (DUF4857) (family)
This family consists of uncharacterized proteins around 340 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Pfam PF19148: Family of unknown function (DUF5830) (family)
This is a family of proteins predominantly found in Halobacteria. Some members includes the MarR family transcriptional regulator.
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 PF04755: PAP_fibrillin (family)
This family identifies a conserved region found in a number of plastid lipid-associated proteins (PAPs), and in a number of putative fibrillin proteins.
Pfam PF19836: Family of unknown function (DUF6315) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000081) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650.
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 PF12470: Suppressor of Fused Gli/Ci N terminal binding domain (family)
This domain family is found in eukaryotes, and is typically between 192 and 219 amino acids in length. The family is found in association with [pfam:PF05076]. There is a conserved HGRHFT sequence motif. This family is the C terminal domain of the Suppressor of Fused protein (Su(fu)). Su(fu) is a repressor of the Gli and Ci transcription factors of the Hedgehog signalling cascade. It functions by binding these proteins and preventing their translocation to the nucleus. The C terminal domain is only found in eukaryotic Su(fu) proteins; it is not present in bacterial homologues. The C terminal domain binds to the N terminal of Gli/Ci while the N terminal of Su(fu) binds to the C terminal of Gli/Ci. This dual binding mechanism is likely an evolutionary advancement in this signalling cascade which is not present in bacterial homologues.
Wikipedia: Suppressor of fused homolog is a protein that in humans is encoded by the SUFU gene.
In molecular biology, the protein domain suppressor of fused protein (Sufu) has an important role in the cell. The Sufu is important in negatively regulating an important signalling pathway in the cell, the Hedgehog signalling pathway (HH). This particular pathway is crucial in embryonic development. There are several homologues of Sufu, found in a wide variety of organisms.
Pfam PF23881: Family of unknown function (DUF7234) (family)
This family represents a domain of unknown function, which is found in phage proteins ranging in length from 75 to 88 amino acids. The domain is found in phage that infect Salmonella, Shigella, Serratia, and Enterobacter species.
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 PF23955: Family of unknown function (DUF7284) (family)
This entry represents uncharacterised archaeal proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11495: Archaeal transcriptional regulator TrmB (family)
TrmB is an alpha-glucoside sensing transcriptional regulator. The protein is the transcriptional repressor for gene cluster encoding trehalose/maltose ABC transporter in T.litoralis and P.furiosus. TrmB has lost its DNA binding domain but retained its sugar recognition site. A nonreducing glucosyl residue is shared by all substrates bound to TrmB which suggests that its a common recognition motif.