SII-SWORD/CoKE huggingface dataset:
Pfam PF12981: Domain of Unknown Function with PDB structure (DUF3865) (family)
Family based of PDB:3B5P encoded by ZP_00108531 from nitrogen-fixing cyanobacterium Nostoc punctiforme pcc 73102 is a CADD-like protein of unknown function. Superposition between protein structures encoded by CT610 from Chlamydia trachomatis (PDB code 1rwc), pyrroloquinolinquinone synthase C (PqqC, PDB code 1otv) and ZP_00108531 revealed that putative active sites in CT610 and ZP_00108531 are identical. ( REF: http://www.topsan.org/Proteins/JCSG/3B5P).
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 PF13899: Thioredoxin-like (domain)
Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond.
Pfam PF17151: Periplasmic sensor domain (domain)
CHASE7 is a conserved periplasmic sensor domain found in histidine kinases and diguanylate cyclases/phosphodiesterases, including the diguanylate cyclase DgcQ (YedQ) that regulates biofilm formation and motility in Escherichia coli.
Pfam PF02993: Minor capsid protein VI (family)
This minor capsid protein may act as a link between the external capsid and the internal DNA-protein core.              The C-terminal 11 residues may function as a protease cofactor leading to enzyme activation.
Pfam PF04950: 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal (family)
RIBIOP_C is a family of eukaryotic proteins from the C-terminus of pre-rRNA-processing protein or ribosome biogenesis proteins BMS1 and TSR1. These proteins act, in the nucleolus, as a molecular switch during maturation of the 40S ribosomal subunit. This domain, domain IV of translation elongation factor selb, adopts the same fold as translation proteins such as domain II of GTP-elongation factor Tu proteins.
Pfam PF12008: Type I restriction and modification enzyme - subunit R C terminal (domain)
This enzyme has been characterised and shown to belong to a new family of the type I class of restriction and modification enzymes. This family is involved in bacterial defence by making double strand breaks in specific double stranded DNA sequences, e.g. that of invading bacteriophages. EcoR124 is made up of three subunits, HsdR, HsdS and HsdM. The R subunit has ATPase and restriction endonuclease activity. This domain is the C terminal of the R subunit.
Pfam PF09861: Lactate racemase N-terminal domain (domain)
This is the N-terminal domain found in Lactate racemase enzymes [ec:5.1.2.1]. LarA is a nickel-dependent lactate racemase from the larA-E operon of Lactobacillus plantarum, whereas LarB, LarC and LarE are accessory proteins required for the incorporation of Ni in the lactate racemase apoprotein. LarA contains 18 beta-strands and 16 alpha-helices arranged in a novel fold composed of two domains of similar size. This entry represents the N-terminal domain of LarA and related proteins.
Pfam PF14393: Domain of unknown function (DUF4422) (family)
This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 255 and 371 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 PF07893: Protein of unknown function (DUF1668) (repeat)
The hypothetical proteins found in this family are  expressed by Oryza sativa and are 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 PF15086: Uncharacterised protein family UPF0542 (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. There is a conserved LSWKL sequence motif. This family includes human protein C5orf43.
Pfam PF22759: Baseplate hub gp41 (family)
E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Gp41 ia a baseplate cap protein that forms a complex with gp36, gp37 and gp38 proteins. These four proteins are evolutionarily related to the tail tube and adopt a similar fold, consisting of two orthogonally packed beta-sheets that form the inner lumen of the tail.
Pfam PF21492: Ribosomal protein L31p, N-terminal (domain)
Ribosomal protein L31p (bL31, also known as 54S ribosomal protein L36), is a component of the mitochondrial ribosome. Overexpression of bL31m suppresses mutations in the COX2 leader peptide-encoding and initiation codon regions. This entry represents the N-terminal domain of yeast bL31.
Pfam PF04049: Anaphase promoting complex subunit 8 / Cdc23 (repeat)
The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8).
Pfam PF21561: Virus, RNA-directed RNA polymerase L, thumb ring domain (domain)
This domain is found in RNA-directed RNA polymerase L from Bunyavirus La Crosse (L) and similar viral sequences. This entry represents the thumb ring domain, which shows an alpha-beta structure that is structurally homologous to the influenza PB2 N1 and N2 domains.
Pfam PF23937: Family of unknown function (DUF7272) (family)
This entry represents a small family of uncharacterised proteins from phage. The structure of this family does not appear similar to any other known protein or family.
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 PF17643: TssR protein N-terminal barrel domain (domain)
This entry represents the N-terminal small beta barrel domain from the TssR protein.  T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex.
Pfam PF06457: Ectatomin (domain)
Ectatomin is a toxic component from the Ectatomma tuberculatum ant venom.  It is comprised of two subunits, A and B, which  are homologous.  The structure of ectatomin  reveals that each subunit is comprised of two helices and a connecting hinge region, the forms a hairpin structure that is stabilised by disulphide bridges.  The two hinges are connected by a disulphide bond.
Pfam PF04225: Opacity-associated protein A LysM-like domain (domain)
The OapA domain gets its name from the Haemophilus influenzae protein OapA, which is required for the expression of colony opacity, thus opacity- associated protein A. The OapA protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation.  The OapA domain has been shown to bind to peptidoglycan in the E. coli protein YtfB. A screen to identify factors that affect cell division in E. coli discovered that overproducing a fragment of YtfB, including its OapA domain, caused cells to grow as long filaments. OapA domains are commonly associated with other domains that are involved in breaking peptidoglycan cross-links. The OapA domain is distantly related to [pfam:PF01476].
Pfam PF16672: Ragulator complex protein LAMTOR5 (domain)
Hepatitis B X-interacting protein (HBXIP, also known as LAMTOR5) was originally recognised for its association with the X protein of hepatitis B virus (HBV) and ability to down-regulate HBV replication . When complexed to the anti-apoptotic protein survivin, HBXIP interferes with apoptosome assembly, preventing recruitment of pro-caspase-9 to oligomerised APAF1, thereby selectively suppressing apoptosis initiated via the mitochondrial/cytochrome c pathway . HBXIP is one of the Ragulator components that are required for mTORC1 activation by amino acids . It is also part of the AA (amino acid) sensing machinery in human CD4+ T cells .
Wikipedia: Hepatitis B virus X-interacting protein is a protein that in humans is encoded by the HBXIP gene.
Pfam PF22931: SAM domain-like (domain)
This entry represents the SAM (sterile alpha motif) domain of TNK-like subfamily of non-receptor tyrosine-protein kinases. This is a putative protein-protein interaction domain.
Pfam PF16783: FANCM to MHF binding domain (domain)
FANCM-MHF_bd is a structured region on Fanconi anaemia complementation group protein M that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin.
Pfam PF17056: Killer toxin-resistance protein 1 (family)
The killer toxin-resistance protein 1 family are GPI-anchored plasma membrane proteins, found in yeast. They are involved in 1,6-beta-glucan formation and in the assembly and architecture of the cell wall. They also act as plasma membrane receptors for the yeast K1 viral toxin, and are involved in subsequent lethal channel formation. The family also includes Pga1 proteins, which have a role in oxidative stress response and in adhesion and biofilm formation.
Pfam PF09547: Stage IV sporulation protein A, ATPase domain (domain)
SpoIVA is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. This protein assembles into static polymers driven by ATP hydrolysis and is anchored to the outer forespore membrane through its C-terminal domain. This entry represents the ATPase domain located at the N-terminal of SpoIVA. It contains a conserved 'sensor' threonine residue that is involved in coordinating a Mg+2 ion.
Pfam PF00143: Interferon alpha/beta domain (domain)
Type I interferons (alpha, beta) belong to the larger helical cytokine superfamily,which includes growth hormones, interleukins, several colony-stimulating factors and several other regulatory molecules.
Wikipedia: Interferons are a group of signaling proteins made and released by host cells in response to the presence of several viruses. In a typical scenario, a virus-infected cell will release interferons causing nearby cells to heighten their anti-viral defenses.
Pfam PF16708: Lipoprotein confined to pathogenic Mycobacterium (domain)
This is a family of lipoproteins found only in pathogenic mycobacteria. These pathogenic lipoproteins may play a role in host-pathogen interactions. Lipoproteins localised to the cell-envelope of pathogenic bacteria are major determinants of virulence. The proteins are localised to the cell-surface via an N-terminal lipidation carried out by a transferase - pro-lipoprotein diacylglyceryl transferase Lgt - which attaches a diacylglyceride molecule to a sulfur atom from a crucial cysteine, and a consecutively acting lipoprotein signal peptidase LspA that cleaves the signal peptide just before the modified cysteine. When the peptidase is inactivated the pathogen has difficulty in replicating inside macrophages.
Pfam PF13404: AsnC-type helix-turn-helix domain (domain)
The asnC-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 60 amino acids present in transcription regulators of the asnC/lrp family. This family of prokaryotic regulators is named after Escherichia coli asnC and Leucine-responsive Regulatory Protein (lrp), which are a regulator of asparagine synthesis and a global regulator of various operons, respectively . AsnC/lrp-like proteins are present in bacteria and archaea . The DNA-binding asnC-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain.
Pfam PF10986: Protein of unknown function (DUF2796) (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 PF19984: Family of unknown function (DUF6420) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the  istamycin biosynthetic gene cluster from Streptomyces tenjimariensis.
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 PF03483: B3/4 domain (domain)
This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.
Wikipedia: The B3/B4 domain, is found in tRNA synthetase beta subunits, as well as in some non-tRNA synthetase proteins.
Pfam PF12678: RING-H2 zinc finger domain (domain)
There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control.
Pfam PF06290: Plasmid SOS inhibition protein (PsiB) (family)
This family consists of several plasmid SOS inhibition protein (PsiB) sequences.
Pfam PF11382: Copper transport outer membrane protein, MctB (family)
Outer membrane channel protein MctB in Mycobacterium tuberculosis is part of a Cu resistance mechanism that ensures low intracellular Cu levels in the bacterium. Human resistance to bacteria, mediated via IFN-gamma-mediated activation of macrophages, may involve the use of reactive Cu(1) in the presence of hydrogen peroxide, since activated Cu is toxic to bacteria. IFN-gamma stimulates the trafficking of the Cu transporter ATP7a to the vesicles that fuse with phagosome and these phagosomes are found to have a high Cu content and an increased bactericidal activity against E.coli. Using MctB, Mycobacterium tuberculosis may limit the amount of excess Cu within it whole in the host.
Pfam PF03749: Sugar fermentation stimulation protein RE domain (domain)
This family contains Sugar fermentation stimulation proteins. Which is probably a regulatory factor involved in maltose metabolism. SfsA has been shown to bind DNA and it contains a helix-turn-helix motif that probably binds DNA at its C-terminus.
Pfam PF20152: Family of unknown function (DUF6534) (family)
This entry represents a large family of fungal integral membrane 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 PF08636: ER protein Pkr1 (family)
Pkr1 has been identified as an ER protein of unknown function.
Pfam PF20060: Family of unknown function (DUF6459) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 143 and 204 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 PF19914: Wolframin EF-hand domain (domain)
Contains two characteristic copies of the bihelical repeat forming the basic EF-hand unit. The absence of the characteristic calcium-binding motif, suggesting it could self-dimerize or dimerize with other EF-hand-containing proteins.
Pfam PF09859: Oxygenase, catalysing oxidative methylation of damaged DNA (domain)
This family of bacterial sequences is predicted to catalyse oxidative de-methylation of damaged bases in DNA.
Pfam PF02435: Levansucrase/Invertase (repeat)
This Pfam family consists of the glycosyl hydrolase 68 family, including several bacterial levansucrase enzymes, and invertase from zymomonas.
Wikipedia: In molecular biology, glycoside hydrolase family 68 is a family of glycoside hydrolases.
Pfam PF07572: Bucentaur or craniofacial development (family)
Bucentaur or craniofacial development protein 1 (BCNT) in ruminents has a different domain architecture to that in mouse and human. For this reason it has been used as a model for molecular  evolution. Both bovine and human BCNTs are phosphorylated by casein kinase II in vitro.
Pfam PF14390: Putative PD-(D/E)XK family member, (DUF4420) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 310 and 334 amino acids in length.  Advanced homology-detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses have established this family to be a member of the PD-(D/E)XK superfamily.
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 PF21041: XMAP215/Dis1/CLASP, TOG domain (repeat)
This is the tubulin-binding TOG domain of two related families of microtubules (MTs) regulatory proteins, XMAP215/Dis1 and Cytoplasmic Linker ASsociated Proteins CLASP. XMAP215/Dis1 family includes Stu2 from S. cerevisiae, S. pombe Alp14 and Dis1, A. thaliana MOR1, C. elegans Zyg9, D. melanogaster MiniSpindles (MSPS) and human ch-TOG (also known as Cytoskeleton-associated protein 5), which have conserved roles in promoting the assembly of microtubules. CLASP proteins promote MT rescue and suppress MT catastrophe events.
Pfam PF16327: Cytochrome c-type biogenesis protein CcmF C-terminal (family)
This C-terminal region of CcmF, one of the cytochrome c-type biogenesis proteins, is associated at the C-terminal with Cytochrome_C_asm family [pfam:PF01578]. It is possible that it is this domain which delivers reductant to haem on CcmE.
Pfam PF04398: Protein of unknown function, DUF538 (family)
This family consists of several plant 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 PF10881: Protein of unknown function (DUF2726) (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 PF09561: HpaII restriction endonuclease (family)
This family includes the HpaII (recognises and cleaves C^CGG) restriction endonuclease.
Pfam PF05270: Alpha-L-arabinofuranosidase B (ABFB) domain (domain)
This family consists of several fungal alpha-L-arabinofuranosidase B proteins. L-Arabinose is a constituent of plant-cell-wall poly-saccharides. It is found in a polymeric form in L-arabinan, in which the backbone is  formed by 1,5-a- linked l-arabinose residues that can be branched via 1,2-a- and 1,3-a-linked l-arabinofuranose side chains. AbfB hydrolyses  1,5-a, 1,3-a and 1,2-a linkages in both oligosaccharides and  polysaccharides, which contain terminal non-reducing l-arabinofuranoses in side chains.
Pfam PF03304: Mlp lipoprotein family (family)
The Mlp (for Multicopy Lipoprotein) family of lipoproteins is found in Borrelia species. This family were previously known as 2.9 lipoprotein genes. These surface expressed genes may represent new candidate vaccinogens for Lyme disease. Members of this family generally are downstream of four ORFs called A,B,C and D that are involved in hemolytic activity.
Pfam PF10106: Uncharacterized protein conserved in bacteria (DUF2345) (family)
Members of this family are found in various bacterial hypothetical proteins, as well as Rhs element Vgr 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 PF14616: Transcription regulator Rua1, C-terminal (domain)
This entry represents a domain that can be found at the C terminus f fungal proteins such as meiotic expression up-regulated protein 26 from Schizosaccharomyces pombe, Ecm8 from Saccharomyces cerevisiae and Rua1 from Ustilago maydis. Rua1 is a transcription factor and part of the gene cluster that mediates the biosynthesis of the glycolipid biosurfactant ustilagic acid (UA).