SII-SWORD/CoKE huggingface dataset:
Pfam PF02156: Glycosyl hydrolase family 26 (domain)
This entry represents a domain found in the glycosyl hydrolase family 26 members. Glycoside hydrolases (GHs) play a critical role in both eukaryotes and prokaryotes, where they fulfill numerous important functions such as substrate acquisition and the remote remodelling of cell walls and the glycan decorations of glycoproteins. GH family 26 consists mainly of endo-beta-1,4- mannanases (mannanases) (3.2.1.78), although some members of this family display beta- 1,3-xylanase activity. Proteins containing this domain also include the enzyme endogluconase H (3.2.1.4), which catalyses the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. The family 26 GHs are members of clan GH-A .

The GH26 catalytic domain exhibits the architecture of the classical (Î²/Î±)8-barrel folding motif characteristic of a clan-GH-A member. Two Glu residues located respectively on strands Î²4 and Î²7 act as the catalytic acid/base and nucleophile in a double-displacement mechanism .
Wikipedia: In molecular biology, glycoside hydrolase family 26 is a family of glycoside hydrolases.
Pfam PF17992: Agarase CBM like domain (domain)
This is the N-terminal CBM-like domain in exo-beta-agarase proteins ([ec:3.2.1.81]) found in the marine microbe Saccharophagus degradans. This enzyme catalyzes a critical step in the metabolism of agarose by S. degradans through cleaving agarose oligomers into neoagarobiose products that can be further processed into monomers. The CBM-like domain is structurally very similar to some CBM families. A loop in the CBM-like domain is involved in forming the roof of the active site channel. The contribution of the CBM-like domain to formation of the active site of the enzyme supports a role in substrate recognition explaining the exo-mode of beta-agarase action.
Pfam PF13565: Homeodomain-like domain (domain)
Wikipedia: A homeobox is a DNA sequence, around 180 base pairs long, that regulates large-scale anatomical features in the early stages of embryonic development. Mutations in a homeobox may change large-scale anatomical features of the full-grown organism.
Pfam PF18335: ATP-dependent RecD-like DNA helicase SH3 domain (domain)
This is an SH3 (SRC homology domain 3) domain found in RecD helicases (EC 3.6.4.12) that belong to the bacterial Superfamily 1B (SF1B). This superfamily of helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life. Structural analysis indicate that the extension of the 5'-tail of the unwound DNA duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit. The process involves this SH3 domain that binds to a region of the RecB subunit. Studies of RecD in E. coli also revealed that the SH3 domain interacts with the ssDNA tail in a location different to that normally occupied by a peptide in canonical eukaryotic SH3 domains, thus retaining the potential to bind peptide at the same time as the ssDNA tail.
Pfam PF21672: COMMD2-7/10, HN domain (domain)
The COMMD (Copper Metabolism Murr1 (Mouse U2af1-rs1 region 1) Domain) proteins are highly conserved in metazoans and unicellular protozoa. There are ten family members that play key roles in intracellular trafficking and in the regulation of transcription. A hallmark of the COMMD family members is a highly conserved C-terminal sequence of 70-80 amino acids called the COMM domain, which has no known structure. This entry represents the N-terminal domain of these proteins, which is referred to as the HN (helical N-terminal) domain, is more variable in sequence across the ten proteins. Therefore, this entry includes COMMD2-7/10, while COMMD1 HN domain is represented in [pfam:PF17221], COMMD9 HN domain in [pfam:PF20923]. Human (and the mammalian homologues) COMMD6 lacks the HN domain, however, it is present in COMMD6 from other species, such as Xenopus sp. This helical N-terminal domain has a globular architecture and is composed of a six-helix bundle with a meander topology.
Pfam PF21380: Nrd1/Seb1, domain 2 (domain)
Nrd1 is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein, part of the Nrd1-Nab3-Sen1 (NNS) complex which is involved in the termination and processing of short RNA polymerase II transcripts. Seb1 is the Nrd1 homologue from S. pombe that is essential for cell viability and binds directly to Rpb7 subunit of RNA polymerase II. It functions in terminating all classes of Pol II-transcribed genes genome-wide. These proteins have a RNA-recognition motif (RRM, [pfam:PF00076]) fused to a second alpha/beta domain described as domain 2 (also referred to as the split domain, SD, in) from Nrd1 and Seb1. This domain is essential and forms a rigid body with the canonical RRM that interacts with RNA.
Pfam PF21485: Translation initiation factor 5A-like, N-terminal (domain)
This is the N-terminal domain of Translation initiation factor 5A from eukaryotes and archaea, which has a SH2-like fold. These proteins are involved in translation elongation and eIF5A is specifically required to promote peptide-bond formation between consecutive proline residues. This entry also includes Woronin body major protein Hex1, which is similar to eIF5A.
Pfam PF00392: Bacterial regulatory proteins, gntR family (domain)
This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.
Wikipedia: In molecular biology, the GntR-like bacterial transcription factors are a family of transcription factors.
Pfam PF05647: Tandem-repeating region of mucin, epiglycanin-like (repeat)
The unusual mucin, epiglycanin, is membrane-bound at the C-terminus but has a long region of this tandem-repeat at the N-terminus. It was the first mucin identified to be associated with the malignant behaviour of carcinoma cells. Mouse Muc21/epiglycanin is thought to be a highly glycosylated molecule, which makes it likely that its function is dependent on its glycoforms. Cells expressing Muc21 are significantly less adherent to each other and to extracellular matrix components than control cells, and this loss of adhesion is mediated by the TR portion of Muc21. This family also now contains the repeat that was the C. elegans protein of unknown function (DUF801).
Pfam PF07521: Zn-dependent metallo-hydrolase RNA specificity domain (conserved_site)
The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in [pfam:PF00753] and are common to all metallo-beta-lactamases. This, the fifth motif, appears to be specific to Zn-dependent metallohydrolases such as ribonuclease J 2 which are involved in the processing of mRNA. This domain adds essential structural elements to the CASP-domain and is unique to RNA/DNA-processing nucleases, showing that they are pre-mRNA 3'-end-processing endonucleases.
Pfam PF11173: Protein of unknown function (DUF2960) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF13559: Domain of unknown function (DUF4129) (domain)
This presumed domain is found at the C-terminus of proteins that contain a transglutaminase core domain. The function of this domain is unknown. The domain has a conserved TXXE motif.
Pfam PF19401: Family of unknown function (DUF5976) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000624) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
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 PF15326: Testis expressed sequence 15 (family)
TEX15 is a family of eukaryotic proteins that is required for chromosomal synapsis and meiotic recombination. TEX15 regulates the loading of DNA repair proteins onto sites of double-stranded-breaks and, thus, its absence causes a failure in meiotic recombination. Two polymorphisms in the TEX15 gene could be considered the genetic risk factors for spermatogenic failure in the Chinese Han population.
Pfam PF14958: ATPase PAAT-like (family)
This family is found in eukaryotes. It represents the ATPase protein associated with ABC transporters (PAAT) and related proteins. PAAT is formed of a nucleotide-binding domain (NBD)-like domain and a signal for intramitochondrial sorting. PAAT interacts with the mitochondrial inner membrane ABC proteins: ABCB7, ABCB8 and ABCB10. It is involved in maintenance of mitochondrial homeostasis and cell survival.
Pfam PF08779: Betacoronavirus NS7A protein (domain)
This entry corresponds to the Human SARS virus NS7A protein (also known as 7a, accessory protein 7a, X4 and U122). The structure of this protein shows similarities to the immunoglobulin like fold and a known member of the immunoglobulin (Ig) domain superfamily, which suggests a binding activity to integrin I domains. In SARS-CoV-infected cells, the NS7A protein is expressed and retained intra-cellularly within the Golgi network. NS7A has been implicated to function during the replication cycle of SARS-CoV.
Wikipedia: ORF7a is a gene found in coronaviruses of the Betacoronavirus genus. It expresses the Betacoronavirus NS7A protein, a type I transmembrane protein with an immunoglobulin-like protein domain. It was first discovered in SARS-CoV, the virus that causes severe acute respiratory syndrome (SARS). The homolog in SARS-CoV-2, the virus that causes COVID-19, has about 85% sequence identity to the SARS-CoV protein.
Pfam PF02844: Phosphoribosylglycinamide synthetase, N domain (domain)
Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see [pfam:PF00289]). This domain is structurally related to the PreATP-grasp domain.
Pfam PF06053: Domain of unknown function (DUF929) (domain)
Family of proteins from the archaeon Sulfolobus, with undetermined function. According to structure prediction this protein has a thioredoxin 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 PF12506: Protein of unknown function (DUF3713) (family)
This family of proteins is found in mycobacteria. Proteins in this family are typically around 1200 amino acids in length. Mycoplasma contain three homologues in this family per genome.
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 PF05406: WGR domain (domain)
This domain is found in a variety of polyA polymerases as well as the E. coli molybdate metabolism regulator [swissprot:P33345] and other proteins of unknown function. I have called this domain WGR after the most conserved central motif of the domain. The domain is found in isolation in proteins such as [swissprot:Q9JN21] and is between 70 and 80 residues in length. I propose that this may be a nucleic acid binding domain.
Pfam PF06213: Cobalamin biosynthesis protein CobT (family)
This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid.
Wikipedia: Cobalt chelatase (EC 6.6.1.2) is an enzyme that catalyzes the chemical reactionATP + hydrogenobyrinic acid a,c-diamide + Co2+ + H2O  ADP + phosphate + cob(II)yrinic acid a,c-diamide + H+
Pfam PF13961: Domain of unknown function (DUF4219) (domain)
This domain is very short and is found at the N-terminal of many Gag-pol polyprotein and related proteins. There is a highly conserved YxxWxxxM 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 PF13285: Domain of unknown function (DUF4073) (family)
This family is frequently found at the C-terminus of bacterial proteins carrying the family, Metallophos [pfam:PF00149].
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 PF24922: Acyl-CoA-binding domain-containing protein 4-like, C-terminal (domain)
This domain is found at the C-terminal end of Acyl-CoA-binding domain-containing protein 4 from Arabidopsis thaliana (ACBP4) and similar plant proteins. ACBP4 plays a role in the biosynthesis of membrane lipids including galactolipids and phospholipids. This domain is predicted to have an all-alpha helical configuration and is often found associated to Kelch-type beta-propeller domains and an Acyl CoA binding domain ([pfam:PF00887]).
Pfam PF13286: Phosphohydrolase-associated domain (domain)
This domain is found on bacterial and archaeal metal-dependent phosphohydrolases.
Pfam PF17620: Family of unknown function (family)
Family members found in alphabaculoviruses such as orf45 have been implicated in late gene expression when linked to orf41.
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 PF02303: Helix-destabilising protein (domain)
This family contains the bacteriophage helix-destabilising protein, or single-stranded DNA binding protein, required for DNA synthesis.
Pfam PF06243: Phenylacetic acid degradation B (family)
Phenylacetic acid degradation protein B (PaaB) is thought to be part of  a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation.
Pfam PF15786: PET assembly of cytochrome c oxidase, mitochondrial (family)
PET117 is a family of eukaryotic proteins found from fungi and plants to human. It is likely to be involved in the assembly of cytochrome C oxidase, and is found in the mitochondrion.
Pfam PF16629: Armadillo-associated region on APC (disordered)
Arm_APC_u3 is a semi-unstructured region lying immediately downstream of the armadillo fold before the beta-catenin binding motifs, APC_crr, [pfam:PF05923], on APC or adenomatous polyposis coli proteins in higher eukaryotes.  The function is not known.
Pfam PF14949: ARF7 effector protein C-terminus (family)
This family represents the C-terminus of the ARF7 effector protein (ARF7EP). ARF7EP interacts with ADP-ribosylation factor-like protein 14 and unconventional myosin-Ie and through this interaction controls movement of MHC-II-containing vesicles along the actin cytoskeleton in dendritic cells. It contains a conserved CXCXXXXCXXCXXXCXXCXXXXCXXXCXC motif in it's C-terminal half.
Pfam PF17052: Cap associated factor (family)
In eukaryotes, the translation of mRNA is initiated by the binding of eIF4F complex, which is composed of eIF4E, eIF4A and eIF4G proteins. elF4E-binding proteins (4E-BPs) are involved in translational regulation through their interaction with eIF4E. There are two elF4E-binding proteins (4E-BPs) found in S. cerevisiae, Caf20 and Eap1. This entry represents Caf20 (also known as p20), which competes with elF4G for binding to elF4E and interferes with the formation of the elF4F complex, hence inhibiting translation. It is needed for the induction of pseudohyphal growth in response to nitrogen limitation.
Pfam PF18884: Bacterial TSP3 repeat (domain)
This entry contains a novel bacterial thrombospondin type 3 repeat which differs from the typical consensus by containing a glutamate in place of one of the calcium binding aspartate residues.
Pfam PF19224: pATOM36 family (family)
This entry represents the trypanosome Peripherally associated ATOM36 protein which has been shown to complement a deletion of the Mim1/Mim2 complex in yeast. The integral MOM protein, peripheral archaic translocase of the outer membrane 36 (pATOM36), in analogy to the MIM complex, is involved in the assembly and/or membrane insertion of a small subset of MOM proteins including subunits of the main trypanosomal outer membrane protein translocase (ATOM complex).
Pfam PF23380: VIN3-like, C-terminal domain (domain)
This domain is found at the C-terminal end of Protein Vernalization Insensitive 3 from Arabidopsis thaliana (VIN3) and similar plant sequences. VIN3 plays a central role in vernalization by mediating the initial transcriptional repression of the homeotic gene FLC, a floral repressor, after a cold treatment. This domain, predicted to adopt an all-alpha structure, is often found associated with [pfam:PF07227] and [pfam:PF23376].
Pfam PF00517: Retroviral envelope protein (family)
This family includes envelope protein from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from human and simian immunodeficiency viruses (HIV and SIV) which mediate membrane fusion during viral entry. The family also includes bovine immunodeficiency virus, feline immunodeficiency virus and Equine infectious anaemia (EIAV). The family also includes the Gp36 protein from mouse mammary tumour virus (MMTV) and human endogenous retroviruses (HERVs).
Wikipedia: Gp41 also known as glycoprotein 41 is a subunit of the envelope protein complex of retroviruses, including human immunodeficiency virus (HIV). Gp41 is a transmembrane protein that contains several sites within its ectodomain that are required for infection of host cells. As a result of its importance in host cell infection, it has also received much attention as a potential target for HIV vaccines.
Pfam PF11938: TLR4 regulator and MIR-interacting MSAP (family)
This family of proteins, found from plants to humans, is PRAT4 (A and B), a Protein Associated with Toll-like receptor 4. The Toll family of receptors - TLRs - plays an essential role in innate recognition of microbial products, the first line of defence against bacterial infection. PRAT4A influences the subcellular distribution and the strength of TLR responses and alters the relative activity of each TLR. PRAT4B regulates TLR4 trafficking to the cell surface and the extent of its expression there. TLR4 recognizes lipopolysaccharide (LPS), one of the most immuno-stimulatory glycolipids constituting the outer membrane of the Gram-negative bacteria.           This family has also been described as a SAP-like MIR-interacting protein family.
Pfam PF19239: GIY-YIG domain-containing protein (domain)
This is a family of proteins that contain the GIY-YIG domain, predominantly found in Bacteria, Fungi and plants (i.e. in Protein EFFECTOR OF TRANSCRIPTION 1,2 and 3 from Arabidopsis) but also in viruses. This is a well characterised domain among the members of the GYI-YIG endonuclease family, which is involved in several cellular processes such as DNA repair and recombination and transfer of mobile genetic elements.
Pfam PF19197: Family of unknown function (DUF5872) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in viruses and Bacteria.
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 PF10676: Spore germination protein gerPA/gerPF (family)
This is a bacterial family of proteins that are required for the formation of functionally normal spores.  Proteins in this family may be involved in establishing normal coat structure and/or permeability which could control the access of germinants to their receptor.
Pfam PF17592: Family of unknown function (DUF5489) (family)
This is a family of unknown function found in Alphafusellovirus.
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 PF00580: UvrD/REP helicase N-terminal domain (domain)
The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. [swissprot:P23478], [swissprot:P08394] have large insertions near to the carboxy-terminus relative to other members of the family.
Pfam PF13410: Glutathione S-transferase, C-terminal domain (domain)
This domain is closely related to [pfam:PF00043].
Wikipedia: Glutathione S-transferase, C-terminal domain  is a structural domain of glutathione S-transferase (GST).
Pfam PF23366: HVO_0234-like, beta propeller (repeat)
This family represents a group of proteins mainly from halobacteria, including HVO_0234 from Haloferax volcanii ([swissprot:D4GZH9]). Members are predicted to adopt a beta -propeller configuration.