SII-SWORD/CoKE huggingface dataset:
Pfam PF00830: Ribosomal L28 family (family)
The ribosomal 28 family includes L28 proteins from bacteria and chloroplasts.  The L24 protein from yeast [swissprot:P36525] also contains a region of similarity to prokaryotic L28 proteins. L24 from yeast is also found in the large ribosomal subunit
Pfam PF19886: Domain of unknown function (DUF6359) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is primarily found in bacteria. This entry may represent an Ig-like fold.
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 PF08541: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal (domain)
This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III [ec:2.3.1.41], the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria.
Pfam PF12268: Protein of unknown function (DUF3612) (family)
This domain family is found in bacteria, and is approximately 180 amino acids in length. The family is found in association with [pfam:PF01381].
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 PF09772: Transmembrane protein 26 (family)
The function of this family of transmembrane proteins has not, as yet, been determined.
Pfam PF20590: Domain of unknown function (DUF6791) (domain)
This presumed domain is functionally uncharacterised. This domain family is found, and is approximately 160 amino acids in length. The domain is found in sequences that belong to the Thif family and is in association with [pfam:PF00899], located at its N-terminal.
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 PF05176: ATP10 protein (family)
ATP 10 is essential for the assembly of a functional mitochondrial ATPase complex.
Wikipedia: In molecular biology, ATP10 protein (mitochondrial ATPase complex subunit ATP10) is an ATP synthase assembly factor. It is essential for the assembly of the mitochondrial F1-F0 complex. A yeast nuclear gene (ATP10) encodes a product that is essential for the assembly of a functional mitochondrial ATPase complex. Mutations in ATP10 induce a loss of rutamycin sensitivity in the mitochondrial ATPase, but do not affect the respiratory enzymes. ATP10 has a molecular weight of 30,293 Da and its primary structure is not related to any known subunit of the yeast or mammalian mitochondrial ATPase complexes. ATP10 is associated with the mitochondrial membrane. It is suggested that the ATP10 product is not a subunit of the ATPase complex but rather a protein required for the assembly of the F0 sector of the complex.
Pfam PF24693: Family of unknown function (DUF7660) (domain)
This family represents a set of uncharacterised bacterial proteins. Structure prediction shows them to be composed of three alpha helices.
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 PF18944: Family of unknown function (DUF5691) (repeat)
This is a family of unknown function. Some family members overlap with [pfam:PF13646].
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 PF02636: Putative S-adenosyl-L-methionine-dependent methyltransferase (family)
This family is a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase. In eukaryotes it plays a role in mitochondrial complex I activity.
Pfam PF08672: Anaphase promoting complex (APC) subunit 2 (domain)
The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases.  Ubiquitin ligases catalyse the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2), to the substrate protein.
Pfam PF07336: Putative stress-induced transcription regulator (family)
The structure of one member of the ABATE domain family consists of a two-domain organisation, with the N-terminal domain presenting a new fold called the ABATE domain that may bind an as yet unknown ligand. The C-terminal domain forms a treble-clef zinc-finger that is likely to be involved in DNA binding. suggests a role as stress-induced transcriptional regulator. Further computational analyses sugeests a role as a stress-induced transcriptional regulator. Members of this family are found in Streptomyces, Rhizobium, Ralstonia, Agrobacterium and Bradyrhizobium species.
Pfam PF13888: Myelin gene regulatory factor C-terminal domain 2 (domain)
This domain is found further downstream of Peptidase_S74, [pfam:PF13884], and MRF_C1, [pfam:PF13887].  The function is not known.
Pfam PF25073: Domain of unknown function (DUF7797) (domain)
This domain is found in a group of uncharacterised plant proteins. This domain is often found associated with [pfam:PF00628] and is predicted to have an all-alpha helical configuration.
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 PF12750: Maff2 family (family)
This family of short membrane proteins are related to the protein Maff2. Maff2 lies just outside the direct repeats of a tetracycline resistance transposable element. This protein may contain transmembrane helices.
Pfam PF02381: MraZ protein, putative antitoxin-like (family)
This small 70 amino acid domain is found duplicated in a family of bacterial proteins. These proteins may be DNA-binding transcription factors (Pers. comm. A Andreeva & A Murzin). It is likely, due to the similarity of fold, that this family acts as a bacterial antitoxin like the MazE antitoxin family.
Pfam PF11667: Putative zincin peptidase (family)
This family of proteins has a conserved HEXXH motif, suggesting the members are putative peptidases of zincin fold.
Pfam PF12025: Phage protein C (family)
This family of phage proteins is functionally uncharacterised. Proteins in this family are typically between 68 to 86 amino acids in length.
Pfam PF01528: Herpesvirus glycoprotein M (family)
The herpesvirus glycoprotein M (gM) is an integral membrane protein predicted to contain 8 transmembrane segments. Glycoprotein M is not essential for viral replication.
Pfam PF06522: NADH-ubiquinone reductase complex 1 MLRQ subunit (family)
The MLRQ subunit of mitochondrial NADH-ubiquinone reductase complex I is nuclear and is found in plants, insects, fungi and higher metazoans. It appears to act within the membrane and, in mammals, is highly expressed in muscle and neural tissue, indicative of a role in ATP generation.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF21700: Delta-like/Jagged, EGF-like domain (domain)
This entry represents a EGF-like domain found in delta-like, jagged and Wnt inhibitory factor 1, which are involved in different signalling pathways.
Pfam PF15338: p53-regulated apoptosis-inducing protein 1 (family)
TPIP1 is a family of eukaryotic proteins whose expression is induced by wild-type p53. Ectopically expressed TPIP1, which is localised within mitochondria, leads to apoptotic cell death through dissipation of mitochondrial A(psi)m. Phosphorylation of p53 Ser-46 regulates the transcriptional activation of TPIP1, thereby mediating p53-dependent apoptosis.
Pfam PF10297: Minimal binding motif of Hap4 for binding to Hap2/3/5 (conserved_site)
In Saccharomyces cerevisiae, the haem-activated protein complex Hap2/3/4/5 plays a major role in the transcription of genes involved in respiration. Hap4_Hap_bind is the essential domain of Hap4 which allows it to associate with Hap2, Hap3 and Hap5 to form the Hap complex.
Pfam PF03089: Recombination activating protein 2 (repeat)
V-D-J recombination is the combinatorial process by which the huge range of immunoglobulin and T cell binding specificity  is generated from a limited amount of genetic material.  This process is synergistically activated by RAG1 and RAG2 in developing lymphocytes.  Defects in RAG2 in humans are a cause of severe combined immunodeficiency B cell negative and Omenn syndrome.
Wikipedia: The recombination-activating genes (RAGs) encode parts of a protein complex that plays important roles in the rearrangement and recombination of the genes encoding immunoglobulin and T cell receptor molecules. There are two recombination-activating genes RAG1 and RAG2, whose cellular expression is restricted to lymphocytes during their developmental stages. The enzymes encoded by these genes, RAG-1 and RAG-2, are essential to the generation of mature B cells and T cells, two types of lymphocyte that are crucial components of the adaptive immune system.
Pfam PF12747: DdrB-like protein (family)
This family includes the Deinococcus DdrB protein which is a ssDNA binding protein. This family also includes some possibly distantly related cyanobacterial proteins. However, these are not strongly supported. The structure of DdrB is known.
Pfam PF22416: Lmo2445-like, C-terminal domain (domain)
This domain is found at the C-terminal end of the Lmo2445 protein from Listeria monocytogenes. This domain shows a immunoglobulin -like fold.
Pfam PF22857: Male-specific sperm protein Mst87F (family)
This family includes Male-specific sperm protein Mst87F from Drosophila melanogaster, the product of a transcript expressed in the germline from late pupal stages onward that overlaps with one of the enhancers of the pri transcriptional unit, which encodes the smORF peptides represented in [pfam:PF22856].
Pfam PF02390: Putative methyltransferase (family)
This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting  a putative methyltransferase activity.
Pfam PF22562: UBA-like domain (domain)
This entry represents a UBA domain.
Pfam PF25031: SBSPON-like, C-terminal (domain)
This domain is found at the C-terminal end of human Somatomedin-B and thrombospondin type-1 domain-containing protein (SBSPON) and similar animal sequences. This domain is usually found associated with [pfam:PF19028].
Pfam PF13942: YfhG lipoprotein (family)
This family includes the YfhG protein from E. coli [swissprot:P0AD44]. Members of this family have an N-terminal lipoprotein attachment site. The members of this family are functionally uncharacterized.
Pfam PF02775: Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (domain)
A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown  that some of these enzymes are structurally related. The thiamin diphosphate-binding fold comprises two different functional modules, the pyridine-binding (Pyr) and pyrophosphate-binding (PP) modules. This represents the TPP binding domain which localizes at the C-terminal of TPP enzymes and in some members has been described as the PP-binding module.
Pfam PF17442: Functional domain of U62 and UL91 proteins (domain)
Human herpesvirus 6A (HHV-6A) and HHV-6B are classified as roseoloviruses and are highly prevalent in the human population. Roseolovirus reactivation in an immunocompromised host can cause severe pathologies. Human cytomegalovirus (HCMV) is responsible for significant diseases in developing fetus as well as in an immunocompromised host. During their productive cycle, herpesviruses have a regulated temporal cascade of gene expression that can be divided into three general stages: immediate-early (IE), early (E), and late (L). Following viral DNA replication, late viral genes that mainly encode structural proteins start to be transcribed, ultimately leading to the assembly and release of infectious particles. This domain family is found in Human herpesvirus 6A and 6B (HHV-6A/B) as well as HCMV. Family members are shown to be involved in late gene expression such as UL91 in Human Cytomegalovirus [swissprot:F5HFJ8]. This functional domain is located on the N-terminal (1-71 amino acids) of full-length UL91. It has been found to suffice for transcriptional activation of true-late genes within the nucleus of infected cells. In other words, UL91 is fully functional as a 71-aa N-terminal polypeptide and This small 71-aa polypeptide contains all protein-protein interaction motifs crucial to mediate transcriptional activation.
Pfam PF06133: Control of competence regulator ComK, YlbF/YmcA (family)
YlbF Is a family of short Gram-positive and archaeal proteins that includes both YlbF and YmcA which may interact synergistically. The family is necessary for correct biofilm formation, as null mutants of ymcA and ylbF fail to form pellicles at air-liquid interfaces and grow on solid media as smooth, undifferentiated colonies. During development, YmcA, YlbF and YaaT, family PSPI, [pfam:PF04468], interact directly with one another forming a stable ternary complex, in vitro. All three proteins are required for competence, sporulation and the formation of biofilms. The YmcA-YlbF-YaaT complex affects the phosphotransfer between Spo0F and Spo0B, thus accelerating the production of Spo0A~P. The three processes of biofilm formation, mature spore formation and competence all require the active, phosphorylated form of Spo0A, as Spo0A-P.
Wikipedia: In microbiology, genetics, cell biology, and molecular biology, competence is the ability of a cell to alter its genetics by taking up extracellular DNA from its environment through a process called transformation. Competence can be differentiated between natural competence and induced or artificial competence. Natural competence is a genetically specified ability of bacteria that occurs under natural conditions as well as in the laboratory. Artificial competence arises when cells in laboratory cultures are treated to make them transiently permeable to DNA. Competence allows for rapid adaptation and DNA repair of the cell.
Pfam PF07528: DZF N-terminal domain (domain)
The function of this domain is unknown. It is often found associated with [pfam:PF00098] or [pfam:PF00035]. This domain has been predicted to belong to the nucleotidyltransferase superfamily.
Pfam PF14532: Sigma-54 interaction domain (domain)
Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent  interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems  and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section.

The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction . The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.
Pfam PF11452: Protein of unknown function (DUF3000) (family)
This is a bacterial family of uncharacterised 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 PF20477: Family of unknown function (DUF6719) (family)
This family is functionally uncharacterised. This family of proteins is found in proteobacteria. Proteins in this family are typically 74 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 PF04536: TPM domain (domain)
This family was first named TPM domain after its founding proteins: TLP18.3, Psb32 and MOLO-1. In Arabidopsis, this domain is called the thylakoid acid phosphatase -TAP - domain and has a Rossmann-like fold. In plants, the family resides in the thylakoid lumen attached to the outer membrane of the chloroplast/plastid. It is active in the photosystem II.
Wikipedia: The TPM domain family is named after the three founding proteins TLP18.3, Psb32 and MOLO-1. TPM domains have a characteristic fold composed of α helices flanking four central β strands. The TPM fold has not been found in other protein domains to date. TPM was previously referred to as "DUF477" and "Repair_PSII".
Pfam PF02903: Alpha amylase, N-terminal ig-like domain (domain)
O-Glycosyl hydrolases (3.2.1.) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
E or "early" set domains are associated with the catalytic domain of the cyclomaltodextrinase (CDase) and pullulan-degrading enzymes at the N-terminal end. The N-terminal domain of the CDase and pullulan-degrading enzymes may be related to the immunoglobulin and/or fibronectin type III superfamilies. This domain may be involved in homodimeric/tetrameric/dodecameric interactions. Enzymes containing this domain belong to family 13 (GH13) of the glycosyl hydrolases. Members of this subgroup include CDase, maltogenic amylase, and neopullulanase, all of which are capable of hydrolyzing all or two of the following three types of substrates: cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by cleavage of alpha-1,4 glycosidic bonds whereas alpha-amylases essentially lack activity on CDs and pullulan. They also catalyze transglycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules .
Wikipedia: In molecular biology, glycoside hydrolase family 13 is a family of glycoside hydrolases.
Pfam PF13426: PAS domain (domain)
This domain is found in many signalling proteins in which it functions as a sensor domain. It recognises FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Wikipedia: A Per-Arnt-Sim (PAS) domain is a protein domain found in all kingdoms of life. Generally, the PAS domain acts as a molecular sensor, whereby small molecules and other proteins associate via binding of the PAS domain. Due to this sensing capability, the PAS domain has been shown as the key structural motif involved in protein-protein interactions of the circadian clock, and it is also a common motif found in signaling proteins, where it functions as a signaling sensor.
Pfam PF21553: Methionyl-tRNA formyltransferase, C-terminal domain (domain)
This domain is found at the C-terminal end of Methionyl-tRNA formyltransferase from Acetivibrio thermocellus and similar bacterial sequences. This domain is usually found associated with [pfam:PF00551].
Pfam PF05368: NmrA-like family (family)
NmrA is a negative transcriptional regulator of various fungi, involved in the post-translational modulation of the  GATA-type transcription factor AreA. NmrA lacks the canonical GXXGXXG NAD-binding motif and has altered residues at the catalytic triad,  including a Met instead of the critical Tyr residue. NmrA may bind  nucleotides but appears to lack any dehydrogenase activity. It lacks  most of the active site residues of the SDR (short-chain  dehydrogenases/reductases) family, but has an NAD(P)-binding motif  similar to the extended SDR family, GXXGXXG. This domain can also be found in other atypical SDRs, such as HSCARG  (an NADPH sensor) and PCBER (phenylcoumaran benzylic ether  reductase).
Pfam PF10113: FeGP cofactor biosynthesis protein, fibrillarin family (family)
Members of this family of proteins include archaeal fibrillarin homologs also known as HcgG which is involved in biosynthesis of Iron-guanylylpyridinol (FeGP) cofactor.
Pfam PF21752: Probable sensor domain DACNG (domain)
This entry represents a potential sensor domain found at the N-terminal of bacterial diadenylate cyclases, which is typically followed by the DAC ([pfam:PF02457]) domain. This domain may have five alpha-helices and four beta-strands according to structure predictions.
Pfam PF04450: Peptidase of plants and bacteria (family)
These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens.
Pfam PF22392: Cmr7b-like, BtrG-like domain (domain)
This entry represents a BtrG-like domain present in Cmr7b protein from Sulfolobus solfataricus. Cmr7b is involved in the CRISPR/Cas pathway. CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids).
Pfam PF03394: Poxvirus E8 protein (family)
This entry represents a family of poxvirus proteins that includes Protein E8 from Vaccinia virus, which is also known as Protein OPG070. This protein may play a role in the biogenesis of the viral factories by recruiting and wrapping DNA replication sites in endoplasmic reticulum derived membranes. It binds DNA in vitro with this binding likely to be modulated by phosphorylation by the viral kinase F10L .