SII-SWORD/CoKE huggingface dataset:
Pfam PF05617: Prolamin-like (domain)
Prolamin_like (in which DUF784 and DUF1278 have been merged) is found to be expressed in the plant embryo sac and to be regulated by the Myb98 transcription factor.  Computational analysis has revealed that members are homologous to the plant prolamin superfamily (Protease inhibitor-seed storage-LTP family, [pfam:PF00234]). In contrast to typical prolamin members that have eight conserved Cys residues forming four pairs of disulfide bonds, this domain contains only six conserved Cys residues that may form three pairs of disulfide bonds.  The domain may have a potential function in lipid transfer or protection during plant embryo sac development and reproduction.
Pfam PF12285: Astroviridae polyprotein 1 (family)
This family of proteins is found in non-structural polyprotein 1 A/AB from Astroviridae. They are typically between 49 and 62 amino acids in length. There are two conserved sequence motifs: QPLDLS and EQQ.
Pfam PF14298: Domain of unknown function (DUF4374) (repeat)
This family of proteins is found in bacteria. Proteins in this family are typically between 406 and 466 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 PF05819: NolX protein (family)
This family consists of Rhizobium NolX and Xanthomonas HrpF proteins. The interaction between the plant pathogen Xanthomonas campestris pv. vesicatoria and its host plants is controlled by hrp genes (hypersensitive reaction and pathogenicity), which encode a type III protein secretion system. Among type III-secreted proteins are avirulence proteins, effectors involved in the induction of plant defence reactions. HrpF is dispensable for protein secretion but required for AvrBs3 recognition in planta, is thought to function as a translocator of effector proteins into the host cell. NolX, a soybean cultivar specificity protein, is secreted by a type III secretion system (TTSS) and shows homology to HrpF of the plant pathogen Xanthomonas campestris pv. vesicatoria. It is not known whether NolX functions at the bacterium-plant interface or acts inside the host cell. NolX is expressed in planta only during the early stages of nodule development.
Pfam PF08235: LNS2 (Lipin/Ned1/Smp2) (domain)
This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain (Pfam: PF04571). SMP2 (also known as PAH1) is involved in plasmid maintenance and respiration, and has been identified as a Mg2+-dependent phosphatidate phosphatase ([ec:3.1.3.4]) that contains a haloacid dehalogenase (HAD)-like domain.  Lipin proteins are involved in adipose tissue development and insulin resistance.
Pfam PF00736: EF-1 guanine nucleotide exchange domain (domain)
This family is the guanine nucleotide exchange domain of EF-1 beta and EF-1 delta chains.
Wikipedia: In molecular biology, the EF1 guanine nucleotide exchange domain is a protein domain found in the beta and delta chains of elongation factors from eukaryotes and archaea.
Pfam PF21133: CCA-adding enzyme, C-terminal domain (domain)
Archaeal CCA-adding enzyme builds and repairs the 3'-end of tRNA. This is the C-terminal domain (tail) of CCA-adding enzyme, which serves as a ruler to ensure that only tRNAs and tRNA-like transcripts are substrates for the enzyme and also contributes to the discrimination between stable and unstable RNA substrates.
Pfam PF20109: Proteobacterial transcriptional regulator-like domain (domain)
This domain is found in transcriptional regulators and similar proteins mainly found in proteobacteria. This domain is found in association with the DNA binding domain [pfam:PF10074] in many proteins. It is predicted to adopt an all-alpha structure.
Pfam PF08946: Osmosensory transporter coiled coil (coiled_coil)
The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function.
Pfam PF23509: MSMEG_3727, PQQ-associated (family)
Members of this entry are restricted to members of the Actinobacteria that synthesise PQQ. These are small proteins 155 amino acids long on average, found regularly next to a much larger protein, a PQQ-dependent oxidoreductase, and might be a companion subunit or an accessory protein such as chaperone involved in cofactor insertion.
Pfam PF24391: HD-CE (domain)
This entry represents an HD-like domain predicted to act as effector in multiples antiviral immunity system by targeting nucleotides.
Pfam PF19295: SufBD protein N-terminal region (family)
This entry represents the N-terminal part of the SufB and SufD proteins which have an N-terminal mostly helical region, and a core domain consisting of a right-handed beta-helix ([pfam:PF01458]).
Pfam PF19655: Family of unknown function (DUF6158) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces  kanamyceticus and appears to be predominantly found in  actinobacteria.
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 PF08109: Lactocin 705 family (family)
This family consists of lactocin 705 which is a bacteriocin produced by Lactobacillus casei CRL 705. Lactocin 705 is a class IIb bacteriocin, whose activity depends upon the complementation of two peptides (705-alpha and 705-beta) of  33 amino acid residues each. Lactocin 705 is active against several Gram-positive bacteria, including food-borne pathogens and is a good candidate to be used for biopreservation of fermented meats.
Pfam PF00893: Small Multidrug Resistance protein (family)
This family is the Small Multidrug Resistance (SMR) family. Several members have been shown to export a range of toxins, including ethidium bromide ( and quaternary ammonium compounds, through coupling with proton influx.
Wikipedia: Small multidrug resistance protein is a family of integral membrane proteins that confer drug resistance to a wide range of toxic compounds by removing them for the cells. The efflux is coupled to an influx of protons. An example is Escherichia coli mvrC P23895 which prevents the incorporation of methyl viologen into cells and is involved in ethidium bromide efflux.
Pfam PF17790: Macroglobulin domain MG1 (domain)
This entry represents the N-terminal macroglobulin domain found in complement proteins C3, C4 and C5.
Pfam PF11392: Oxamate carbamoyltransferase subunit AllH (family)
This entry, previously known as DUF2877, represents the Oxamate carbamoyltransferase subunit AllH and related bacterial proteins. AllH is a component of a carbamoyltransferase involved in the anaerobic nitrogen utilization via the assimilation of allantoin. It catalyses the conversion of oxalurate (N-carbamoyl-2-oxoglycine) to oxamate and carbamoyl phosphate.
Pfam PF05281: Neuroendocrine protein 7B2 precursor (Secretogranin V) (family)
The neuroendocrine protein 7B2 has a critical role in the proteolytic conversion and activation of proPC2, the enzyme responsible for the proteolytic conversion of many peptide hormone precursors. The 7B2 protein acts as an intracellular binding protein for proPC2, facilitates its maturation, and is required for its enzymatic activity. Processing of many important peptide precursors does not occur in 7B2 nulls. 7B2 null mice exhibit a unique form of Cushing's disease with many atypical symptoms, such as hypoglycemia.
Wikipedia: Neuroendocrine protein 7B2 is a protein that in humans is encoded by the SCG5 gene. The protein expressed by this gene is widely distributed in neuroendocrine tissues. It functions as a chaperone protein for the proprotein convertase PC2 by blocking the aggregation of this protein, and is required for the production of an active PC2 enzyme. It is an intrinsically disordered protein that may also function as a chaperone for other aggregating secretory proteins in addition to proPC2. 7B2 has been identified in vertebrates and in invertebrates as low as flatworms and insects. It is also called Sgne1 and Secretogranin V. In C. elegans, it was originally called e7B2 and then renamed Seven B Two. There is a Pfam entry for this protein: Secretogranin_V (PF05281).
Pfam PF24810: Leucine--tRNA ligase, RagD-binding domain (domain)
This is the RagD-binding domain (RBD) of human Leucine--tRNA ligase, a synthetase that catalyses the specific attachment of leucine to its cognate tRNA. This domain shows three helices.
Pfam PF15574: Immunity protein 48 (family)
A predicted immunity protein with an all alpha-helical fold and a conserved HRG motif. Proteins containing this domain are present in heterogeneous poly-immunity loci in polymorphic toxin systems.
Pfam PF14268: YoaP-like (family)
The YoaP-like domain is found at the C-terminus of the B. subtilis YoaP protein [swissprot:O34983].  It is found in bacteria and archaea, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF00583]. There is a single completely conserved residue A that may be functionally important.
Pfam PF21727: Family of unknown function (DUF6863) (domain)
This entry represents an alpha helical bundle domain found at the N-terminus of a small group of putative bacterial toxins. The function of this domain 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 PF17372: Family of unknown function (DUF5394) (family)
This is a family of unknown function found in Rickettsiales.
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 PF22159: Maltose-forming alpha-amylase-like, N-terminal domain (domain)
This domain is found in the maltose-forming alpha-amylase from the hyperthermophilic archaeon Pyrococcus sp. ST04 (PSMA). This enzyme is able to hydrolyse both alpha-1,4-glucosidic and alpha-1,6-glucosidic bonds. PSMA protein consists of two domains: an N-terminal domain with a typical glycoside hydrolase 57 family (beta]/alpha)7-barrel fold and a C-terminal domain composed of alpha-helical bundles. This entry represents the N-terminal domain.
Pfam PF12221: Bacterial membrane protein N terminal (family)
This domain is found in bacteria. This domain is typically between 65 to 81 amino acids in length. This domain is found associated with [pfam:PF01145]. This domain is the N terminal of the bacterial membrane protein HflK. HflK complexes with HflC to form a membrane protease which is modulated by the GTPase HflX. The N terminal domain of HflK is the membrane spanning region which anchors the protein in the bacterial membrane.
Pfam PF23356: PEP5/VPS11 TPR (repeat)
This entry represents the TPR segment found in Pep5-like zinc finger protein from Schizosaccharomyces pombe (also known as Vps11) and its orthologues from human, mouse and A. thaliana Vacuolar protein sorting-associated protein 11 (VPS11). Vps11 aggregates with other Vps proteins to form the homotypic fusion and protein sorting complex (HOPS), which promotes the fusion of late endosomes and autophagosomes with lysosomes. Pep5 (also known as Vps11) was initially isolated as a protease deficient mutant, and has function in protein trafficking and vacuole biogenesis pathways.
Pfam PF14574: C-terminal domain of RACo the ASKHA domain (domain)
This family includes reductive activator of CoFeSP (RACo) proteins, [swissprot:Q3ACS2]. Structure analysis of RACo indicate that it contains 4 regions: N-terminal region [pfam:PF00111] (residues 3-94) binding the [2Fe-2S] cluster, a linker region (residues 95-125), the middle region (residues 126-206), and the large C-terminal domain (residues 207-630). This entry is specific for the C-terminal domain which harbors the ATP-binding site. Structural studies show that the C-terminal domain contains the conserved beta-beta-beta-alpha-beta-alpha-beta-alpha topology characteristic of the ASKHA (acetate and sugar kinases/heat shock protein 70/actin). Despite the low-sequence identity shared between members of the ASKHA super family, they show a common central fold. Members of the ASKHA include proteins that catalyze phosphoryl transfers or hydrolysis of ATP in a variety of biological contexts. Asp, Asn, Glu, and Gln residues are well conserved in the core of the ASKHA proteins, where they interact with the phosphates of ATP and the bound Mg2+ ions.
Pfam PF17333: Beta defensin 136 (domain)
Beta-defensins are small cationic peptides that have triple-stranded beta-sheet structure. They are characterized by the presence of multiple cysteine residues (forming three distinctive intramolecular disulfide bridges) and a highly similar tertiary structure known as the defensin motif. All beta-defensin genes encode a precursor peptide that consists of a hydrophobic, leucine-rich signal sequence, a pro-sequence, and a mature six-cysteine defensin motif at the carboxy terminus. They exhibit broad-spectrum antimicrobial properties and contribute to mucosal immune responses at epithelial sites. Several beta-defensins family members have been shown to play essential roles in sperm maturation and fertility in rats, mice and humans. In addition to the wide spectrum of antimicrobial activity, mammalian beta-defensins have been reported to have other roles in the immune system, such as the chemotactic ability for immature dendritic cells and memory T-cells via chemokine receptor-6 demonstrated by human beta-defensin-2. This entry contains beta-defensins such as DEFB136 [swissprot:Q30KP8], the mouse homologue Defb42 [swissprot:Q8BVB5] and Ostricacin-3 [swissprot:P85115].
Wikipedia: Beta defensins  are a family of vertebrate defensins. The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonization.
Pfam PF23722: DEX1 beta-sandwich (domain)
Protein defective in exine formation DEX1 is a factor required for proper pollen wall formation in Arabidopsis thaliana and other plant sequences. This entry represents the beta sandwich found towards the C-terminus of DEX1 in plants. Mutations in DEX1 are associated with changes in the microspore membrane and primexine formation, which disrupt normal deposition of sporopollenin. DEX1 is suggested to be a either a component of the primexine matrix or the ER and participates in the assembly of primexine precursors. DEX1 has been identified as a Ca2+ binding protein involved in regulating rice tapetal cell degradation and pollen formation.
Pfam PF09293: T4 RNase H, C terminal (domain)
Members of this family are found in T4 RNaseH ribonuclease, and adopt a SAM domain-like fold, consisting of a bundle of four/five helices. These residues may have a role in providing a docking site for other proteins or enzymes in the replication fork.
Pfam PF22157: Sucrose hydrolase-like, C-terminal domain (domain)
This domain is found at the C-terminal end of Sucrose hydrolase from Xanthomonas campestris (SupH, [swissprot:Q6UVM5]) and similar bacterial sequences. SupH shows a central domain that consists of an eight-stranded alpha/beta barrel ([pfam:PF00128]). This beta-stranded domain is located on a side of the barrel fold.
Pfam PF05067: Manganese containing catalase (domain)
Catalases are important antioxidant metalloenzymes that catalyse disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and this family that is a structurally distinct family containing non-heme manganese.
Pfam PF08825: E2 binding domain (domain)
E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades.  This is an E2 binding domain that is found on NEDD8 activating E1 enzyme.  The domain resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains.
Wikipedia: NEDD8-activating enzyme E1 catalytic subunit is a protein that in humans is encoded by the UBA3 gene.
Pfam PF00231: ATP synthase (domain)
The ATPase F1 complex gamma subunit forms the central shaft that connects the F0 rotary motor to the F1 catalytic core. The gamma subunit functions as a rotary motor inside the cylinder formed by the Î±(3)Î²(3) subunits in the F1 complex . The most conserved region of the gamma subunit is its C terminus, which seems to be essential for assembly and catalysis.
F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (7.1.2.2) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the Î±(3)Î²(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.
Wikipedia: Gamma subunit of ATP synthase F1 complex forms the central shaft that connects the Fo rotary motor to the F1 catalytic core. F-ATP synthases are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits, while the Fo ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria.
Pfam PF18886: Repeats of unknown function (DUF5649) (repeat)
This entry represents a series of potential beta-helix repeats found in a variety of putative bacterial adhesin proteins.
Pfam PF05812: Herpesvirus BLRF2 protein (family)
This family consists of several Herpesvirus BLRF2 proteins.
Pfam PF17336: Family of unknown function (DUF5368) (family)
This is a family of unknown function found in Proteobacteria and predicted to contain 2 trans-membrane regions.
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 PF11808: Phosphate regulon sensor protein PhoR (family)
This family is only found in bacteria. Family members include PhoR. A member of the two-component regulatory system PhoR/PhoB involved in the phosphate regulon genes expression. PhoR is the bifunctional histidine autokinase/phospho-PhoB phosphatase that donates a phosphoryl group to PhoB when environmental Pi is limiting and removes the phosphoryl group from phosphorylated PhoB (PhoB-P) when environmental Pi is abundant.
Pfam PF01610: Transposase (family)
Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204 ([swissprot:Q50911]), IS1001 ([swissprot:Q06126]), IS1096 ([swissprot:Q50440]) and IS1165 [swissprot:Q48788].
Pfam PF09820: Predicted AAA-ATPase (family)
This family contains many hypothetical bacterial proteins.  This family was previously the N-terminal part of the Pfam DUF1703 ([pfam:PF08011]) family before it was split into two.  This region is predicted to be an AAA-ATPase domain.
Pfam PF14240: YHYH protein (family)
This domain family is found in bacteria, eukaryotes and viruses, and is typically between 141 and 198 amino acids in length. There is a conserved YHYH sequence motif.
Pfam PF11990: Protein of unknown function (DUF3487) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 121 to 136 amino acids in length. This protein has a conserved RLN sequence motif.
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 PF19573: Domain of unknown function (DUF6089) (domain)
This family of membrane bound beta barrel proteins is functionally uncharacterised. This family of proteins is found in Bacteroidetes bacteria. Proteins in this family are typically between 227 and 265 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 PF15285: Beclin-1 BH3 domain, Bcl-2-interacting (domain)
The BH3 domain is a short motif known to bind to Bcl-xLs. This interaction is important in apoptosis.