SII-SWORD/CoKE huggingface dataset:
Pfam PF11518: Protein of unknown function (DUF3221) (family)
This family of proteins with unknown function appears to be restricted to Bacillus. Some members in this family of proteins are annotated as YobA however this cannot be confirmed. YobA is a protein with 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 PF04232: Stage V sporulation protein S (SpoVS) (family)
In Bacillus subtilis this protein interferes with sporulation at an early stage and this inhibitory effect is overcome by SpoIIB and SpoVG.  SpoVS seems to play a positive role in allowing progression beyond stage V of sporulation.  Null mutations in the spoVS gene block sporulation at stage V, impairing the development of heat resistance and coat assembly.
Pfam PF14119: Domain of unknown function (DUF4288) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 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 PF05415: Beet necrotic yellow vein furovirus-type papain-like endopeptidase (family)
Corresponds to Merops family C36. This protease involved in processing the viral polyprotein.
Pfam PF01973: 6-hydroxymethylpterin diphosphokinase MptE-like (family)
This domain can be found in a group of proteins, including archaeal 6-hydroxymethylpterin diphosphokinase (6-HMDPK), known as MptE, which catalyses the formation of 6-hydroxymethyl-7,8-dihydropterin diphosphate (6-HMDP) from 6-HMD and ATP. 6-HMDP is the precursor of the pterin containing moiety of the essential C1-carriers tetrahydrofolate and tetrahydromethanopterin. This entry also includes a number of uncharacterised proteins from bacteria.
Pfam PF05609: Lamina-associated polypeptide 1, AAA+ activator domain (domain)
Torsin-1A-interacting proteins 1 and 2 (TOIP 1/2), also known as LAP1 proteins (Lamina-associated polypeptide 1) are type 2 integral membrane proteins with a single membrane-spanning region of the inner nuclear membrane. These proteins interact with and activate Torsin A, an AAA+ ATPase localised to the endoplasmic reticulum (ER) through a perinuclear domain and forms a heterohexameric (LAP1-Torsin)3 ring that targets Torsin to the nuclear envelope. LAP1 has an atypical AAA+ fold and provides an arginine finger to the Torsin A active site to promote its ATPase activity. A single mutation in Torsin A causes early onset primary dystonia, a painful and severely disabling neuromuscular disease. This entry represents the C-terminal AAA+ activator domain of LAP1.
Pfam PF17357: Facilitor Of iron transport 1 and 2 (family)
Fit proteins (facilitor of iron transport) found on Saccharomyces cerevisiae cell wall are mannoproteins implicated in the siderophore-iron bound transport. This domain family can be found in FIT1 and FIT2 proteins in Saccharomycetaceae. The FIT1-3 cell wall mannoproteins are attached to the beta-glucan layer through a GPI (glycosylphosphatidylinoisitol) anchor. They are very rich in serine and threonine residues (40-50 % serine and threonine) and bear several short repeat of 6-7 amino acids sequence. The exact domain function is unknown.
Pfam PF22276: Tetracyclin repressor-like, C-terminal domain (domain)
This domain is found at the C-terminal end of Nucleoid occlusion factor SlmA from Escherichia coli and similar transcriptional repressors from proteobacteria. SlmA is required for the nucleoid occlusion (NO) phenomenon, which prevents Z-ring formation and cell division over the nucleoid. It is organised into two domains, a small N-terminal [pfam:PF00440] and a C-terminal domain (this entry). This domain shows an all-alpha configuration. This region mediates dimerisation.
Pfam PF03278: IpaB/EvcA family (family)
This family includes IpaB, which is an invasion plasmid antigen from  Shigella, as well as EvcA from E. coli [swissprot:Q9ZNF1]. Members of this family seem to be involved in pathogenicity of some enterobacteria. However the exact function of this component is not clear.
Pfam PF19571: ACT domain pair (domain)
This entry represents a pair of ACT domains. These domains bind to amino acids and often form regulatory subunits of enzymes. Proteins in this family are found in bacteria and archaea. Proteins in this family are approximately 140 amino acids in length.
Wikipedia: In molecular biology, the ACT domain is a protein domain that is found in a variety of proteins involved in metabolism. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The ACT domain is named after three of the proteins that contain it: aspartate kinase, chorismate mutase and TyrA. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure.
Pfam PF10248: Myelodysplasia-myeloid leukemia factor 1-interacting protein (family)
This entry is the conserved central region of a group of proteins that are putative transcriptional repressors. The structure contains a putative 14-3-3 binding motif involved in the subcellular localisation of various regulatory molecules, and it may be that interaction with the transcription factor DREF could be regulated through this motif. DREF regulates proliferation-related genes in Drosophila. Mlf1IP is expressed in both the nuclei and the cytoplasm and thus may have multi-functions.
Pfam PF07316: Protein of unknown function (DUF1463) (family)
This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be found exclusively in Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown.
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 PF22801: GLD-3 1st KH domain (aka KH2) (domain)
This KH domain is found in the C. elegans GLD-3 protein. GLD-3 is a protein required maternally for germline survival and embryogenesis. This domain is known as the KH2 domain based on a prior identification of five KH domains in the GLD-3 protein. However, based on recent structure predictions using AlphaFold is appears that the KH1 domain is not a KH domain at all. Therefore the 1st KH domain is known as KH2. This is the first KH domain of the globular structure unit also formed by KH3, KH4 and KH5.
Pfam PF22846: CATSPERG C-terminal domain (domain)
The CATSPER (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4, it functions as an alkalinisation-activated calcium channel. This complex is involved in sperm cell hyperactivation, a process needed for sperm motility, which is essential late in the preparation of sperm for fertilisation. This complex requires four auxiliary subunits (beta, gamma, delta and epsilon), which play a role in channel assembly. These are multidomain proteins which share a similar domain organisation. This entry represents the C-terminal domain of CATSPERG, which covers the Stem domain and the transmembrane helix, involved in the association with the channel domain.
Pfam PF14077: Alternative WD40 repeat motif (family)
WD repeats are short subdomains of about 40 amino acids and fold into 4 antiparallel beta hairpins. This domain here has been detected on the C-terminus of WD repeat-containing protein 18 during target selection by the Joint Center for Structural Genomics.
Pfam PF18288: Fumarylacetoacetase N-terminal domain 2 (domain)
This is domain is found in the N-terminal region of Fumarylacetoacetate (FAA) hydrolase ([pfam:PF01557]). Family members of this domain include Pseudogulbenkiania ferrooxidans and Cupriavidus gilardii.
Pfam PF14568: SMI1-KNR4 cell-wall (domain)
Members of this family are related to the SMI1/KNR4-like or SUKH superfamily of proteins.
Pfam PF06529: Vertebrate interleukin-3 regulated transcription factor (family)
This family includes vertebrate transcription factors, some of which are regulated by IL-3/adenovirus E4 promoter binding protein. Others were found to strongly repress transcription in a DNA-binding-site-dependent manner.
Pfam PF16690: Methylmalonic aciduria and homocystinuria type C family (domain)
MMACHC, also known as Cyanocobalamin reductase / alkylcobalamin dealkylase, is involved in the intracellular processing of vitamin B12 by catalyzing two reactions: the reductive decyanation of cyanocobalamin in the presence of a flavoprotein oxidoreductase and the dealkylation of alkylcobalamins through the nucleophilic displacement of the alkyl group by glutathione . Mutations in the MMACHC gene have been linked to a disease known as Methylmalonic aciduria and homocystinuria, cblC type (OMIM 277400), the most common inborn error of vitamin B(12) (cobalamin) metabolism. The C-terminal region of this protein folds similarly to TonB, a bacterial protein involved in energy transduction for cobalamin uptake .

The structure of MMACHC reveals it to be the most divergent member of the NADPH-dependent flavin reductase family that can use FMN or FAD to catalyze reductive decyanation; it is also the first enzyme with glutathione transferase (GST) activity that is unrelated to the GST superfamily in structure and sequence .
Wikipedia: Methylmalonic aciduria and homocystinuria type C protein (MMACHC) is a protein that in humans is encoded by the MMACHC gene.
Pfam PF18679: ThcOx helix turn helix domain (domain)
This is a winged helix turn helix domain which is found in cyanobactin oxidase ThcOx N-terminal region. The oxidase converts thiazolines to thiazoles.
Pfam PF13754: Domain of unknown function (domain)
This is a family of uncharacterised Clostridiales proteins.
Pfam PF14342: Domain of unknown function (DUF4396) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 167 and 310 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 PF01893: Uncharacterised protein family UPF0058 (domain)
This archaebacterial protein has no known function.
Pfam PF17622: Viral unique long protein 16 (family)
This family contains members such as UL16 found in the human cytomegalovirus (HCMV). It is an immunoevasin which subverts NKG2D-mediated immune responses by retaining a select group of diverse NKG2D ligands inside the cell. UL16 is a heavily glycosylated 50 kDa type I trans-membrane glycoprotein. The ectodomain folds into a modified version of the a variable (V-type) (immunoglobulin Ig)-like domain. The N-terminal plug region (amino acids 27-50) is covalently linked to the Ig-like core with a disulfide bond. UL16 protein utilizes a three-stranded beta-sheet to engage the alpha-helical surface of the MHC class I-like MICB platform domain. Residues at the center of this beta-sheet mimic a central binding motif employed by the structurally unrelated C-type lectin-like NKG2D to facilitate engagement of diverse NKG2D ligands.
Pfam PF05576: PS-10 peptidase S37 (family)
These serine proteases have been found in Streptomyces species.
Pfam PF02135: TAZ zinc finger (family)
The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1.  The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC.
Wikipedia: In molecular biology, TAZ zinc finger domains are zinc-containing domains found in the homologous transcriptional co-activators CREB-binding protein (CBP) and the P300. CBP and P300 are histone acetyltransferases that catalyse the reversible acetylation of all four histones in nucleosomes, acting to regulate transcription via chromatin remodelling. These large nuclear proteins interact with numerous transcription factors and viral oncoproteins, including p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1, and are involved in cell growth, differentiation and apoptosis. Both CBP and P300 have two copies of the TAZ domain, one in the N-terminal region, the other in the C-terminal region. The TAZ1 domain of CBP and P300 forms a complex with CITED2, inhibiting the activity of the hypoxia inducible factor (HIF-1alpha) and thereby attenuating the cellular response to low tissue oxygen concentration. Adaptation to hypoxia is mediated by transactivation of hypoxia-responsive genes by hypoxia-inducible factor-1 (HIF-1) in complex with the CBP and p300 transcriptional coactivators.
Pfam PF16799: C-terminal membrane-localisation domain of ion-channel, VCN1 (coiled_coil)
VCN1_C is the short C-terminal region of voltage-gated proton channel 1 proteins in higher eukaryotes. The domain is necessary for achieving the dimeric architecture, two monomers form a dimer via parallel alpha-helical coiled-coil interaction. but it is also essential for localising the protein to an intracellular membrane.
Pfam PF05800: Gas vesicle synthesis protein GvpO (family)
This family consists of archaeal GvpO proteins which are required for gas vesicle synthesis. The family also contains two related sequences from Streptomyces coelicolor.
Pfam PF17231: Family of unknown function (DUF5305) (family)
This family consists of several hypothetical 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 PF01184: GPR1/FUN34/yaaH family (family)
The Ady2 protein in ([swissprot:P25613]) is required for acetate in Saccharomyces cerevisiae, and is probably an acetate transporter. A homologue in Yarrowia lipolytica (GPR1) has a role in acetic acid sensitivity.
Pfam PF06984: Mitochondrial 39-S ribosomal protein L47 (MRP-L47) (family)
This family represents the N-terminal region (approximately 8 residues) of the eukaryotic mitochondrial 39-S ribosomal protein L47 (MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure.
Pfam PF07992: Pyridine nucleotide-disulphide oxidoreductase (domain)
This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases.  This domain is actually a small NADH binding domain within a larger FAD binding domain.
Pfam PF23320: Polycomb protein SUZ12-like, Zn domain (domain)
This entry represents the C2H2-type zinc finger domain (Zn) of human Polycomb protein SUZ12, a component of the PRC2 complex, which methylates 'Lys-9' and 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. This domain is necessary to mediate stable binding of the TR domain of Jarid2, another component of the PRC2 complex, and the C-terminal domain of EPOP (C17orf96, a scaffold protein that bridges with the elongin BC complex). It shows a beta -sheet and an alpha helix on one side. This entry is often found associated with [pfam:PF09733].
Pfam PF05789: Baculovirus VP1054 protein (family)
This family consists of several VP1054 proteins from the Baculoviruses. VP1054 is a virus structural protein required for nucleocapsid assembly.
Pfam PF16073: Starter unit:ACP transacylase in aflatoxin biosynthesis (family)
SAT is the N-terminal starter unit:ACP transacylase of the aflatoxin biosynthesis pathway.  SAT selects the hexanoyl starter unit from a pair of specialised fungal fatty acid synthase subunits (HexA/HexB) and transfers it onto the polyketide synthase A acyl-carrier protein to prime polyketide chain elongation. The family is found in association with [pfam:PF02801], [pfam:PF00109], [pfam:PF00550], [pfam:PF00975], [pfam:PF00698].
Pfam PF24678: Domain of unknown function (DUF7658) (domain)
This is a presumed domain found towards the C-terminal of a group of uncharacterised sequences from C. elegans and similar proteins from nematodes.
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 PF19435: Integrator complex subunit 14, beta-barrel domain (domain)
This entry represents the central beta-barrel domain of Integrator complex subunit 14 (IntS14), a component of the integrator complex which is involved in the transcription of small nuclear RNAs (snRNA) and their 3'-box-dependent processing. This complex is also involved in the 3'-end processing of the U7 snRNA, and the spliceosomal snRNAs U1 and U5. IntS14 interacts with IntS13, both of them consist of an N-terminal von-Willebrand type A like domain (VWA),  followed by a central beta-barrel domain and a C-terminal alpha-helical domain connected through a linker. The interface involves all domains of both proteins, both beta-barrel domains form the centre of the complex and contribute to the major contact between Ints13-IntS14.
Pfam PF02683: Cytochrome C biogenesis protein transmembrane domain (domain)
This entry represents the transmembrane domain of Cytochrome C biogenesis proteins also known as disulphide interchange proteins,  such as DsbD from E. coli and DipZ from Mycobacterium. These proteins posses a protein disulphide isomerase like domain that is  not found within the aligned region of this family. DsbA and DsbC, periplasmic proteins of E. coli, are two key players  involved in disulphide bond formation. DsbD generates a reducing  source in the periplasm, which is required for maintaining proper  redox conditions. DipZ is essential for maintaining cytochrome c  apoproteins in the correct conformations for the covalent attachment  of haem groups to the appropriate pairs of cysteine residues.
Wikipedia: The Disulfide bond oxidoreductase D (DsbD) family is a member of the Lysine Exporter (LysE) Superfamily. A representative list of proteins belonging to the DsbD family can be found in the Transporter Classification Base.
Pfam PF10751: Protein of unknown function (DUF2535) (family)
This family of proteins with unknown function appears to be restricted to Bacillus spp.
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 PF24424: FNG domain (domain)
This entry shows a beta sandwich structure that shows similarity to known carbohydrate binding domain families CBM61 and CBM70. This domain is found at the N-terminus of proteins that contain repeated domains, suggesting these proteins may act as carbohydrate binding adhesins. This domain contains a conserved FNG sequence after which the domain is named.
Pfam PF01145: SPFH domain / Band 7 family (family)
This family has been called SPFH, Band 7 or PHB domain. Recent phylogenetic analysis has shown this domain to be a slipin or Stomatin-like integral membrane domain conserved from protozoa to mammals.
Pfam PF05392: Cytochrome C oxidase chain VIIB (family)
Cytochrome oxidase subunit VIIB is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport . The X-ray structure of azide-bound fully oxidized cytochrome c oxidase from bovine heart at 2.9 A resolution has been determined .
Pfam PF17418: Sporulation delaying protein SdpA (family)
Spore formation by the bacterium Bacillus subtilis is an elaborate developmental process that is triggered by nutrient limitation. Cells that have entered the pathway to sporulate produce and export a killing factor and a signaling protein that act cooperatively to block sister cells from sporulating and to cause them to lyse. The sporulating cells feed on the nutrients thereby released, which allows them to keep growing rather than to complete morphogenesis. Entry into sporulation is governed by the regulatory protein Spo0A (master regulator of sporulation). Upon Spo0A phosphorylation, it represses the expression of abrB, a negative regulator of skfABCEFGH and sdpAB, leading to the transcriptional activation of sdpAB operon. The production of SdpAB is essential for the SDP toxin. SDP is a 42-amino-acid, ribosomally synthesized AMP which contains a disulfide bond between two cysteine residues located at the N terminus. SDP acts by rapidly collapsing the proton motive force thereby inducing autolysin mediated lysis on neighboring species and non-biofilm producing B. subtilis cells (which do not produce SdpI) to respond by moving away, while autolysis would release nutrients that can be readily used to promote biofilm growth. SdpAB proteins are required to produce SDP from SdpC33-203. This domain family is found in SdpA proteins which are predicted to be a 158-amino-acid proteins suggest to be primarily cytoplasmic.
Pfam PF11364: Protein of unknown function (DUF3165) (family)
Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is 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 PF04163: Tht1-like nuclear fusion protein (family)
Nuclear fusion protein KAR5 is an integral membrane protein that is thought to be required for the fusion of nuclear envelopes during karyogamy .