SII-SWORD/CoKE huggingface dataset:
Pfam PF11217: Protein of unknown function (DUF3013) (family)
This bacterial family of proteins with unknown function appear to be restricted to Firmicutes.
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 PF11310: Protein of unknown function (DUF3113) (family)
This family of proteins has no known function. It has a highly conserved sequence.
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 PF08995: Necrosis inducing protein-1 (domain)
Necrosis inducing protein-1, a fungal avirulence protein produced by plants, consists of two parts containing beta-sheets of two and three anti-parallel strands, respectively. Five intramolecular disulfide bonds, stabilise these parts and their position with respect to each other, providing a high level of stability.
Pfam PF24252: CdrL-like, middle region (domain)
This domain is centrally located in CdrL (cell division regulator long, HVO_0583) from Haloferax volcanii and similar sequences from halobacteria. CdrL shows [pfam:PF01402] at the N-terminal end and [pfam:PF12773] at the C-terminal.
Pfam PF25127: Domain of unknown function (DUF7819) (domain)
This domain is found towards the C-terminal end of human Calcium homeostasis endoplasmic reticulum protein (CHERP), which is involved in calcium homeostasis, growth and proliferation. This domain is usually found associated with [pfam:PF01585]. Its specific function is unknown. It shows highly conserved GWE and GLYE/DxY/F motifs.
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 PF10897: Protein of unknown function (DUF2713) (family)
This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. This entry may represent a pseudogene.
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 PF01787: Ilarvirus coat protein (family)
This family consists of various coat proteins from the ilarviruses part of the Bromoviridae, members include apple mosaic virus and prune dwarf virus. The ilarvirus coat protein is required to initiate replication of the viral genome in host plants.  Members of the Bromoviridae have a positive stand ssRNA genome with no DNA stage in there replication.
Pfam PF09778: Guanylylate cyclase (family)
Members of this family of proteins catalyse the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate.
Pfam PF00217: ATP:guanido phosphotransferase, C-terminal catalytic domain (domain)
The substrate binding site is located in the cleft between N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain.
Wikipedia: In molecular biology, the ATP:guanido phosphotransferase family is a family of structurally and functionally related enzymes, that reversibly catalyse the transfer of phosphate between ATP and various phosphagens. The enzymes belonging to this family include:Glycocyamine kinase, which catalyses the transfer of phosphate from ATP to guanidoacetate.
Arginine kinase, which catalyses the transfer of phosphate from ATP to arginine.
Taurocyamine kinase, an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to taurocyamine.
Lombricine kinase, an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to lombricine.
Smc74, a cercaria-specific enzyme from Schistosoma mansoni.
Creatine kinase (CK), which catalyses the reversible transfer of high energy phosphate from ATP to creatine, generating phosphocreatine and ADP.
Pfam PF00543: Nitrogen regulatory protein P-II (domain)
P-II modulates the activity of glutamine synthetase. It is a tetrameric protein encoded by the glnB gene, a component of the adenylation cascade involved in the regulation of GS activity.
Wikipedia: The PII family comprises a group of widely distributed signal transduction proteins found in nearly all Bacteria and also present in Archaea and in the chloroplasts of Algae and plants. PII form barrel-like homotrimers with a flexible loop, namely T-loop, emerging from each subunit. PII proteins have extraordinary sensory properties; they can exist in a vast range of structural status accordingly to the levels of ATP, ADP and 2-oxogluratate. These metabolites interact allosterically with PII in three conserved binding sites located in the lateral cavity between each PII subunit. ATP and ADP bind competitively to the nucleotide binding whereas the 2-oxoglutarate only interacts with PII in the presence of MgATP.
Pfam PF24806: Family of unknown function (DUF7706) (family)
This entry represents an uncharacterised family of bacterial proteins. Structure prediction ([swissprot:B2VAQ8] AF3 iPTM=0.93) suggests that these proteins form dimers. The monomer is composed of three alpha helices. STRING provides some weak evidence that these proteins may be immunity proteins or perhaps part of a plasmid addiction system.
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 PF23094: MBTPS1, third Ig-like domain (domain)
This domain is found in the family of serine proteases such as MBTPS1 and SBT6.1 that are involved in regulated intramembrane proteolysis (RIP) of various substrates, playing a crucial role in cellular signaling and regulation. The MBTPS1 proteases cleave after hydrophobic or small residues, with a preference for Arg or Lys at the P4 position. They are responsible for the proteolytic activation of sterol regulatory element-binding proteins (SREBPs), cyclic AMP-dependent transcription factors (ATF6 and ATF6B), and other factors like BDNF, GNPTAB, and FAM20C. In plants, SBT6.1 participate in stress response signaling and cell wall remodeling by processing factors like BZIP17 and pectinesterases. The domain represented by this entry is predicted to fold into a globular structure with an Ig-like fold.
Pfam PF02152: Dihydroneopterin aldolase (domain)
This enzyme [ec:4.1.2.25] catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate.
Wikipedia:  The enzyme dihydroneopterin aldolase catalyzes the chemical reaction2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8- dihydropteridine  2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + glycolaldehyde
Pfam PF04773: FecR protein (family)
FecR is involved in regulation of iron dicitrate transport. In the absence of citrate FecR inactivates FecI. FecR is probably a sensor that recognises iron dicitrate in the periplasm.
Pfam PF08924: Rv2525c-like, glycoside hydrolase-like domain (domain)
This domain is found in uncharacterised bacterial proteins, including the putative peptidoglycan hydrolase Rv2525c from Mycobacterium tuberculosis. It has been proposed to function as a peptidoglycan hydrolase with glycosidase activity regarding structural studies showed that this domain has a typical TIM-barrel-like fold, characteristic of glycoside hydrolases. However, it displays esterase activity toward p-nitrophenyl esters of various acyl chain length in vitro.
Pfam PF24274: T2SS substrate NttE (family)
This entry represents the type II secretion system substrate NttE from Legionella pneumophila and relate proteins found mainly in Legionellales species. NttE structure is composed of two intertwined alpha/beta domains, each of which is consisting of an antiparallel beta-sheet and alpha-helices packed on it. This protein forms stable dimers and the dimer interface is contributed by the C-terminal domain. The N-terminal domain of NttE is mobile which is likely essential for its function in modifying the bacterial cell surface and/or during intracellular infection.
Pfam PF12336: SOX transcription factor (family)
This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found in association with [pfam:PF00505]. There are two conserved sequence motifs: KKDK and LPG. This family is made up of SOX transcription factors. These are involved in upregulation of nestin, a neural promoter.
Wikipedia: SOX genes encode a family of transcription factors that bind to the minor groove in DNA, and belong to a super-family of genes characterized by a homologous sequence called the HMG-box. This HMG box is a DNA binding domain that is highly conserved throughout eukaryotic species. Homologues have been identified in insects, nematodes, amphibians, reptiles, birds and a range of mammals. However, HMG boxes can be very diverse in nature, with only a few amino acids being conserved between species.
Pfam PF02940: mRNA capping enzyme, beta chain (domain)
The beta chain of mRNA capping enzyme has triphosphatase activity.  The function of the capping enzyme also depends on the guanylyltransferase activity conferred by the alpha chain (see [pfam:PF01331])
Pfam PF23015: Zinc finger found in WIZ protein (domain)
This entry represents a C2H2 type zinc finger found in the WIZ proteins.
Pfam PF19082: Family of unknown function (DUF5773) (family)
This is a family of uncharacterised proteins of unknown function found in Phycodnaviridae.
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 PF19498: Protein of unknown function (DUF6033) (family)
This family of proteins is functionally uncharacterised. This family of proteins is primarily found in Clostridia. Proteins in this family are typically between 212 and 271 amino acids in length.
Pfam PF18227: LepB GAP domain C-terminal subdomain (domain)
This subdomain is found in the Rab1 GTPase-activating protein (GAP) domain of GAP LepB present in Legionella pneumophilia. LepB inactivates Rab1, a key regulator of the secretory vesicular trafficking machinery, by acting as a GTPase-activating protein. LepB is also an antagonist of DrrA, which promotes Rab1. LepB acts by an atypical RabGAP mechanism that is reminiscent of classical GAPs. This is the C-terminal subdomain of the GAP domain and consists of an unusual fold.
Pfam PF14560: Ubiquitin-like domain (domain)
This entry contains ubiquitin-like domains.
Wikipedia: Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ubiquitously. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Four genes in the human genome code for ubiquitin: UBB, UBC, UBA52 and RPS27A.
Pfam PF10680: RNA polymerase I specific transcription initiation factor (domain)
Initiation of transcription of ribosomal DNA (rDNA) in yeast involves an interaction of upstream activation factor (UAF) with the upstream element of the promoter, to form a stable UAF-template complex. UAF, together with the TATA-binding transcription initiation factor protein TBP, then recruits an essential core factor to the promoter, to form a stable preinitiation complex. This Rrn9 domain, which seems to be constrained to fungi, is the two highly conserved regions of proteins which form one of the subunits of UAF and appears to be the region responsible for the interaction with TBP. The family includes the S.pombe Arc1 protein, [swissprot:Q10204], which is found to be essential for the accumulation of condensin at kinetochores.
Pfam PF01937: Damage-control phosphatase ARMT1-like domain (domain)
This domain is widely distributed in all domains of life and occur in stand-alone form and as C-terminal fusions to pantothenate kinase (PanK) in plants and animals. They are metal-dependent phosphatases involved in metabolic damage-control processes termed "damage pre-emption" or "housecleaning". S.cerevisiae Damage-control phosphatase YMR027W and the human orthologue Damage-control phosphatase ARMT1 (also known as C6orf211) are involved in response to DNA damage, a damage pre-emption function. Crystal structure of Damage-control phosphatase At2g17340 from Arabidopsis revealed a novel protein fold and several conserved residues coordinating a metal ion (probably Mg2+), which exhibits a high degree of conservation, suggesting that the metal-binding site is central for the function.
Pfam PF05190: MutS family domain IV (domain)
This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with [pfam:PF01624], [pfam:PF05188], [pfam:PF05192] and [pfam:PF00488]. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair;  other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal  carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds in part with globular domain IV,  which is involved in DNA binding, in Thermus aquaticus MutS as characterised in.
Pfam PF18442: E3 gp78 Ube2g2-binding region (G2BR) (domain)
The activity of RING finger ubiquitin ligases (E3) is dependent on their ability to facilitate transfer of ubiquitin from ubiquitin-conjugating enzymes (E2) to substrates. The G2BR domain within the E3 gp78 binds selectively and with high affinity to the E2 Ube2g2. Binding to the G2BR results in conformational changes in Ube2g2 that affect ubiquitin loading. The Ube2g2-G2BR interaction also causes a 50-fold increase in affinity between the E2 and RING finger. Hence, the Ube2g2-binding region (G2BR) is required for the function of gp78. In yeast, Ubc7p, the ortholog of Ube2g2, is recruited by Cue1p to the ER membrane. Cue1p directly binds Ubc7p through a stretch of 50 aa domain analogous to G2BR, i.e. suggesting that this domain which activates ERAD and Hrd1p stimulating ubiquitylation, might be the yeast equivalent of the G2BR domain.
Pfam PF05246: Protein of unknown function (DUF735) (family)
This family consists of several uncharacterised Borrelia burgdorferi (Lyme disease spirochete) 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 PF02877: Poly(ADP-ribose) polymerase, regulatory domain (domain)
Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a  carboxyl 40 kDa fragment is still catalytically active.
Pfam PF04051: Transport protein particle (TRAPP) component (family)
TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits.  This family contains many TRAPP family proteins.  The Bet3 subunit is one of the better characterised TRAPP proteins and has a dimeric structure with hydrophobic channels.  The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues.  Bet3 is proposed to localise TRAPP to the Golgi.
Pfam PF01695: IstB-like ATP binding protein (domain)
This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences.  The function of this protein is unknown, but it may perform a transposase function.
Pfam PF01340: Met Apo-repressor, MetJ (domain)
Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change . MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated.

MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer .

The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein Î²-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs .
Pfam PF01819: Levivirus coat protein (domain)
The Levivirus coat protein forms the bacteriophage coat that encapsidates the viral RNA.  180 copies of this protein form the virion shell. The MS2 bacteriophage coat protein controls two distinct processes: sequence-specific RNA encapsidation and repression of replicase translation-by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication.
Pfam PF20657: Family of unknown function (DUF6811) (family)
This family of proteins is functionally uncharacterised. Proteins in this family are approximately 90 amino acids in length and are predominantly found in Deltaproteobacteria. There are several conserved motifs: ExCxGCxR, PxxKW, GxCNFATH and KxNPLKASK.
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 PF15690: Nuclear receptor-interacting protein 1 repression 4 (family)
This domain is the fourth (C-terminal) repression domain of nuclear receptor-interacting protein 1.
Wikipedia: Nuclear receptor-interacting protein 1 (NRIP1) also known as receptor-interacting protein 140 (RIP140) is a protein that in humans is encoded by the NRIP1 gene.
Pfam PF00564: PB1 domain (domain)
The PB1 (Phox and Bem1) domain, comprising about 80 amino acid residues, is conserved among animals, fungi, amoebas, and plants. It functions as a protein binding module through PB1-mediated heterodimerization or homo-oligomerization .
Pfam PF14445: Prokaryotic RING finger family 2 (family)
RING finger family found sporadically in bacteria and archaea, and  associated with other components of the ubiquitin-based signaling  and degradation system, including ubiquitin and the E1 and E2  proteins. The bacterial versions contain transmembrane helices.
Pfam PF17475: Clostridial binary toxin B/anthrax toxin PA domain 2 (domain)
This domain forms the middle beta sandwish domain in anthrax toxin.
Wikipedia: The AB toxins are two-component protein complexes secreted by a number of pathogenic bacteria, though there is a pore-forming AB toxin found in the eggs of a snail. They can be classified as Type III toxins because they interfere with internal cell function. They are named AB toxins due to their components: the "A" component is usually the "active" portion, and the "B" component is usually the "binding" portion. The "A" subunit possesses enzyme activity, and is transferred to the host cell following a conformational change in the membrane-bound transport "B" subunit. T
Pfam PF24597: DOP1 middle TPR domain (repeat)
DOP1 is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organisation of multicellular structures in the filamentous fungus Emericella nidulans (Aspergillus nidulans). Dop1 homologues are found in mammals, where they may play a role in regulating membrane trafficking of cargo proteins. Together with ATP9A and MON2, it regulates SNX3 retromer-mediated endosomal sorting of WLS away from lysosomal degradation. In S. cerevisiae, it is required for normal cellular morphogenesis. Loss of Dop1 activity affects endosome to Golgi transport and causes a severe perturbation of the organization of the endoplasmic reticulum; Mon2 a relative of large Arf exchange factors, recruits Dop1 to the Golgi apparatus. These are long proteins consisting of TPRs; this entry represents a domain found at the middle region of DOP1.