SII-SWORD/CoKE huggingface dataset:
Pfam PF21637: Family of unknown function (DUF6856) (family)
This entry includes a set of mycoplasma lipoproteins related to uncharacterized Mycoplasma genitalium lipoprotein MG348.
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 PF24295: Domain of unknown function (DUF7480) (domain)
This domain is found in uncharacterised bacterial proteins. These proteins contain a highly conserved lipoprotein-type signal peptide sequence at the N terminus and two invariant cysteine residues within this domain suggesting their extracytoplasmic localisation.
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 PF17945: Beta/Gamma crystallin (domain)
This is the C-terminal domain found in mucin glycoproteins such as secreted protease of C1 esterase inhibitor from EHEC (StcE). This domain adopts a beta/gamma crystallin fold and has been shown to be dispensable for substrate binding. Furthermore, deletion analysis suggest that lack of the C-terminal resulted in impaired association with the cell surface.
Wikipedia: In anatomy, a crystallin is a water-soluble structural protein found in the lens and the cornea of the eye accounting for the transparency of the structure. It has also been identified in other places such as the heart, and in aggressive breast cancer tumors.
The physical origins of eye lens transparency and its relationship to cataract are an active area of research. Since it has been shown that lens injury may promote nerve regeneration,
crystallin has been an area of neural research. So far, it has been demonstrated that crystallin β b2 (crybb2) may be a neurite-promoting factor.
Pfam PF23633: Guanine-nucleotide exchange factor YEL1 PH domain (domain)
This entry represents a PH domain found in the YEL1 family proteins.  The YEL1 family comprises guanine-nucleotide exchange factors (GEFs) for ARF3, a small GTPase involved in vesicle transport and actin cytoskeleton organization. Members of the YEL1 family are essential for the correct localization of ARF3 to specific cellular sites, such as the bud neck and tip in yeast. They play a crucial role in the polarization of actin patches, which are important for processes like endocytosis and cell shape determination. The conserved function across different species suggests a fundamental role in cellular dynamics related to membrane trafficking and cytoskeletal arrangements.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF08875: Domain of unknown function (DUF1833) (family)
This family of proteins are functionally uncharacterised and are predicted to adopt an all-beta fold. They are often found in gene neighborhoods containing genes for an NlpC peptidase and a  Ubiquitin domain predicted to be involved in tail assembly.
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 PF15372: Domain of unknown function (DUF4600) (family)
Some members of this family are also annotated as coiled-coil domain-containing protein 169 (CCDC169).
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 PF07831: Pyrimidine nucleoside phosphorylase C-terminal domain (domain)
This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, [swissprot:P77826]) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP, [swissprot:P07650]). The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer.
Pfam PF24667: Dynein regulatory complex subunit 7 MORN domain (repeat)
Dynein regulatory complex subunit 7 (DRC7) is a component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. In humans, defective ciliary motility can lead to male infertility and a congenital disorder called primary ciliary dyskinesia (PCD), in which impaired clearance of mucus by the cilia causes chronic respiratory infections. This entry represents the MORN-repeats domain, found in the central region of human DRC7.
Pfam PF11812: Domain of unknown function (DUF3333) (family)
This family of proteins are functionally uncharacterised. This family is only found in bacteria.  This presumed domain is typically between 116 to 159 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 PF04065: Not1 N-terminal domain, CCR4-Not complex component (family)
The Ccr4-Not complex (Not1, Not2, Not3, Not4 and Not5) is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID . This domain is the N-terminal region of the Not proteins.
Pfam PF04234: CopC domain (domain)
CopC is a bacterial blue copper protein that binds 1 atom of copper per  protein molecule.  Along with CopA, CopC mediates copper resistance by sequestration of copper in the periplasm.
Pfam PF00187: Chitin recognition protein (domain)
A number of plant and fungal proteins that bind N-acetylglucosamine (e.g. solanaceous lectins of tomato and potato, plant endochitinases, the wound-induced proteins: hevein, win1 and win2, and the Kluyveromyces lactis killer toxin alpha subunit) contain this domain . The domain may occur in one or more copies and is thought to be involved in recognition or binding of chitin subunits . In chitinases, as well as in the potato wound-induced proteins, the 43-residue domain directly follows the signal sequence and is therefore at the N terminus of the mature protein; in the killer toxin alpha subunit it is located in the central section of the protein.
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF11910: Cyanobacterial and plant NDH-1 subunit O (family)
The proton-pumping NADH:ubiquinone oxidoreductase catalyzes the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organisms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides.  Homologues of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 subcomplexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role in growth of cells at low CO2. Here we report the subunit composition of these two complexes. Fifteen proteins were discovered in NDH-1L including NdhL, a new component of the membrane fragment, and Ssl1690 (designated as NdhO), a novel peripheral subunit. The three nuclear-encoded subunits NdhM,NdhN and NdhO are vital for the functional integrity of the plastidial complex.
Pfam PF08727: Poliovirus 3A protein like (domain)
This domain is found in positive-strand RNA viruses.  The 3A protein is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport.
Pfam PF19741: Family of unknown function (DUF6230) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001774) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a  member from the MS-271 biosynthetic gene cluster from Streptomyces  sp. This family appears to be predominantly found in  Actinobacteria. Some members of this family have been identified as putative cholesterol esterases.
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 PF04392: ABC transporter substrate binding protein (family)
This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.
Pfam PF04920: Beet necrotic yellow vein virus, p31 (family)
This is a family of hypothetical proteins known as p31, mostly from Beet necrotic yellow vein virus. P31, encoded by RNA4, is involved in efficient vector transmission, symptom severity and silencing suppression in roots.
Pfam PF07449: Hydrogenase-1 expression protein HyaE (family)
This family contains bacterial hydrogenase-1 expression proteins approximately 120 residues long. This includes the E. coli protein HyaE, and the homologous proteins HoxO of R. eutropha and HupG of R. leguminosarum. Deletion of the hoxO gene in R. eutropha led to complete loss of the uptake [NiFe] hydrogenase activity, suggesting that it has a critical role in hydrogenase assembly.
Pfam PF12719: Nuclear condensing complex subunits, C-term domain (repeat)
The Cnd1-3 proteins are the three non-SMC (structural maintenance of chromosomes) proteins that go to make up the mitotic condensation complex along with the two SMC protein families, XCAP-C and XCAP-E, (or in the case of fission yeast, Cut3 and Cut14). The five-member complex seems to be conserved from yeasts to vertebrates. This domain is the C-terminal, cysteine-rich domain of Cnd3. The complex shuttles between the nucleus, during mitosis, and the cytoplasm during the rest of the cycle. Thus this family is made up of the C-termini of XCAP-Gs, Ycg1 and Ycs5 members.
Pfam PF05620: SRP-independent targeting protein 2/TMEM208 (family)
This family includes SRP-independent targeting protein 2 (SND2) from yeast and transmembrane protein 208 (TMEM208) from mammals. Both are localized to the endoplasmic reticulum (ER). SND2 works together with SND1 and SND3 in an alternative targeting route to the ER. TMEM208 regulates both ER stress and autophagy. It contains three predicted transmembrane regions. SND2 also known as Env10 in Saccharomyces cerevisiae, and its homologue as Mug69 in Schizosaccharomyces pombe. They were identified as proteins involved in vacuolar processing and morphology and meiosis, respectively.
Pfam PF14519: Macro-like domain (domain)
This domain is an ADP-ribose binding module. It is found in a number of yeast proteins.
Pfam PF02458: Transferase family (family)
This family includes a number of transferase enzymes. These include anthranilate N-hydroxycinnamoyl/benzoyltransferase that catalyses the first committed reaction of phytoalexin biosynthesis. Deacetylvindoline 4-O-acetyltransferase [ec:2.3.1.107] catalyses the last step in vindoline biosynthesis is also a member of this family. The motif HXXXD is probably part of the active site. The family also includes trichothecene 3-O-acetyltransferase.
Pfam PF21130: YgfZ, beta-barrel domain (domain)
YgfZ is a folate-binding protein involved in regulating the level of ATP-dnaA and in the modification of some tRNAs. It consists of a folate-binding domain at the N-terminal ([pfam:PF01571]) and a six-stranded antiparallel beta-barrel at the C-terminal, represented in this entry, with identical topology found at the C-terminal of elongation factors Tu and eEF-1alpha and in the gamma subunit of the initiation factor eIF2.
Pfam PF08292: RNA polymerase III subunit Rpc25 (domain)
Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III.
Pfam PF24588: Domain of unknown function (DUF7613) (domain)
This domain is found in uncharacterised proteins mainly from fungi. It is predicted to fold into a beta-barrel with a PH-like 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 PF23600: Domain of unknown function (DUF7139) (domain)
This entry represents a family of 4 transmembrane helix domains found in archaebacteria. In some proteins these domains are associated with repeats of the [pfam:PF07411] domain. AlphaFold predicts a confident dimeric structure for this 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 PF00257: Dehydrin (family)
LEA (late embryogenesis abundant) proteins were first identified in land plants. Plant LEA proteins have been found to accumulate to high levels during the last stage of seed formation (when a natural desiccation of the seed tissues takes place) and during periods of water deficit in vegetative organs. Later, LEA homologues have also been found in various species . They have been classified into several subgroups in Pfam and according to Bray and Dure .
Dehydrin has been classified as part of the LEA family (D-11 from Dure, or group 2 from Bray) . Dehydrins contribute to freezing stress tolerance in plants and it was suggested that this could be partly due to their protective effect on membranes .

Dehydrins share a number of structural features. One of the most notable features is the presence, in their central region, of a continuous run of five to nine serines followed by a cluster of charged residues. Such a region has been found in all known dehydrins so far with the exception of pea dehydrins. A second conserved feature is the presence of two copies of a lysine-rich octapeptide; the first copy is located just after the cluster of charged residues that follows the poly-serine region and the second copy is found at the C-terminal extremity.
Wikipedia: Dehydrin (DHN) is a multi-family of proteins present in plants that is produced in response to cold and drought stress. DHNs are hydrophilic, reliably thermostable, and disordered. They are stress proteins with a high number of charged amino acids that belong to the Group II Late Embryogenesis Abundant (LEA) family. DHNs are primarily found in the cytoplasm and nucleus but more recently, they have been found in other organelles, like mitochondria and chloroplasts.
Pfam PF13825: Paramyxovirus structural protein V/P N-terminus (family)
This family consists of several Paramyxoviridae structural protein P and V sequences. From a structural point of view, P is the best-characterised protein of the replicative complex. P is organised into two moieties that are functionally and structurally distinct: a C-terminal moiety (PCT) and an N-terminal moiety (PNT). PCT is the most conserved in sequence and contains all regions required for virus transcription, whereas PNT, which is poorly conserved, provides several additional functions required for replication. P protein plays a crucial role in the enzyme by positioning L onto the N/RNA template through an interaction with the C-terminal domain of N. Without P, L is not functional. The N, P, and L proteins of SeV and measles and mumps viruses are functionally equivalent. However, sequence identity between proteins from these viruses is limited, and the viruses have been placed in different genera (Respirovirus, Morbilivirus, and Rubulavirus, respectively).  SeV P protein (568 aa) is a modular protein with distinct functional domains. The N-terminal part of P (PNT) is a chaperone for N and prevents it from binding to non-viral RNA in the infected cell.
Pfam PF14910: S-phase genomic integrity recombination mediator, N-terminal (family)
MMS22L (Methyl methanesulfonate-sensitivity protein 22-like) is found in yeast, plants and vertebrates, and is integrally concerned with DNA forking and repair mechanisms during replication.  MMS22L complexes with TONSL and this complex accumulates at regions of ssDNA associated with distressed replication forks or at processed DNA breaks. Its depletion results in high levels of endogenous DNA double-strand breaks caused by an inability to complete DNA synthesis after replication fork collapse. Thus the complex mediates recovery from replication stress and homologous recombination in vertebrates, yeasts and plants. This family is the more N-terminal region of the proteins.
Pfam PF19467: Family of unknown function (DUF6004) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000033) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a  protein from the calicheamicin biosynthetic gene cluster from  Micromonospora echinospora.
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 PF21034: BCAS3, WD40 repeat (repeat)
BCAS3 microtubule associated cell migration factor (BCAS3, also known as Rhudira in mice) is involved in angiogenesis and metastasis. It participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and and the reorganisation of the actin cytoskeleton at the cell leading edge. BCAS3 plays a regulatory role in autophagic activity; it forms a complex with PHAF1 (C16orf70) which associates with the  preautophagosomal structure during both non-selective and selective autophagy. This is the WD40 repeat domain of BCAS3, which directly binds phosphatidylinositol-3-phosphate. This domain is also found in ATG18-like proteins from Arabidopsis.
Pfam PF07902: gp58-like protein (family)
Sequences found in this family are derived from a number of bacteriophage and prophage proteins. They are similar to gp58 ([swissprot:Q38355]), a minor structural protein of Lactococcus delbrueckii bacteriophage LL-H.
Pfam PF22935: Large ribosomal subunit protein mL44, endonuclease domain (domain)
Large ribosomal subunit protein mL44 (RM44) is a component of the 39S subunit of mitochondrial ribosome. It may play a role in the assembly/stability of nascent mitochondrial polypeptides exiting the ribosome. This entry represents the endonuclease (RNase III-like) domain.
Pfam PF05760: Immediate early response protein (IER) (family)
This family consists of several eukaryotic immediate early response (IER) 2 and 5 proteins. The role of IER5 is unclear although it  play an important role in mediating the cellular response to mitogenic signals. Again, little is known about the function of IER2 although it is thought to play a role in mediating the cellular responses to a variety of extracellular signals.
Pfam PF13098: Thioredoxin-like domain (domain)
Several biological processes regulate the activity of target proteins through changes in the redox state of thiol groups (S2 to SH2), where a hydrogen donor is linked to an intermediary disulphide protein. Such processes include the ferredoxin/thioredoxin system, the NADP/thioredoxin system, and the glutathione/glutaredoxin system . Several of these disulphide proteins share a common structure, consisting of a three-layer Î±/Î²/Î± core.
Wikipedia: The thioredoxin fold is a protein fold common to enzymes that catalyze disulfide bond formation and isomerization. The fold is named for the canonical example thioredoxin and is found in both prokaryotic and eukaryotic proteins. It is an example of an alpha/beta protein fold that has oxidoreductase activity. The fold's spatial topology consists of a four-stranded antiparallel beta sheet sandwiched between three alpha helices. The strand topology is 2134 with 3 antiparallel to the rest.