SII-SWORD/CoKE huggingface dataset:
Pfam PF21204: Ell binding protein Ebp1, C-terminal (domain)
This is the conserved C-terminal domain of Ell binding protein 1 (Ebp1) from S. pombe, which is distantly related to AFF family of proteins from metazoans. This domain is known as AFF4 C-terminal homology domain (CHD) or C-terminal signature sequence (CSS). The function of ebp1 is not clear. It colocalizes with Ell1 and Eaf1, being part of the SEC-like complex that regulates Pol II transcription. This domain has been found in several fungal fungal species, but not in S. cerevisiae.
Pfam PF23521: YKL023C-A (family)
This protein family includes the small uncharacterised protein YKL023C-A from Saccharomyces cerevisiae and similar fungal sequences. This microprotein is predicted to adopt an alpha-helical configuration.
Pfam PF08470: Nontoxic nonhaemagglutinin C-terminal (family)
Bacteria of the Clostridium genus produce protein neurotoxins, which are complexes consisting of neurotoxin (NT), haemagglutinin (HA), nontoxic nonhaemagglutinin (NTNH), and RNA.  The domain described here is found at the C-terminus of the NTNH component.
Pfam PF06739: Beta-propeller repeat (repeat)
This family is related to [pfam:PF00400] and is  likely to also form a beta-propeller. SBBP stands for Seven Bladed Beta Propeller.
Pfam PF02893: GRAM domain (domain)
The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Note the alignment is lacking the last two beta strands and alpha helix.
Wikipedia: The GRAM domain  is found in glucosyltransferases, myotubularins and other membrane-associated proteins. The structure of the GRAM domain is similar to that found in PH domains.
Pfam PF14272: Glycine-rich SFCGS (family)
This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. There are a number of highly conserved motifs including an SFCGSGGAGA motif.
Pfam PF24780: MABP1/WDR62 first WD40 domain (repeat)
This entry represents the second WD40 domain of MABP1 and WDR62. MABP1 (Mitogen-activated protein kinase-binding protein 1) is a negative regulator of NOD2 function, leading to the down-regulation of NOD2-induced processes such as activation of NF-kappa-B signalling, IL8 secretion and antibacterial response. WDR62 is a microcephaly-related, microtubule (MT)-associated protein (MAP) that localises to the spindle pole and regulates spindle organisation by recruiting katanin to the spindle pole by forming a complex with TPX2/Aurora A. The microtubule-binding affinity of WDR62 is autoinhibited through JNK phosphorylation-induced intramolecular interaction. Additionally, WRD62 is implicated in the development of the cerebral cortex influencing both the proliferation and migration of neurons. The WD40 domains of WDR62 mediate the interaction with Aurora A and MT-binding.
Pfam PF02556: Preprotein translocase subunit SecB (family)
This family consists of preprotein translocase subunit SecB. SecB is required for the normal export of envelope proteins out of the  cell cytoplasm.
Pfam PF12893: Putative lumazine-binding (domain)
This is a family of uncharacterised proteins. However, the family belongs to the NTF2-like superfamily of various enzymes, and some of the members of the family are putative dehydrogenases.
Pfam PF04432: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus (domain)
Coenzyme F420 hydrogenase ([ec:1.12.99.1]) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits,.  The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain ([ec:1.2.1.2], [swissprot:P06130]) is also a member of this family. This region is often found in association with the 4Fe-4S binding domain, fer4 ([pfam:PF00037]).
Pfam PF04838: Baculoviridae late expression factor 5 (family)
This is the N-terminal domain of Baculoviridae late expression factor 5, required for late and very late gene expression.
Pfam PF23362: DEAH helicase DHX37 C-terminal domain (domain)
This domain is found in human DEAH-box helicase DHX37 (Dhr1 in yeast) and related proteins. DHX37 is a component of the human SSU processome and plays an important role in processome maturation. The domain represented by this entry folds into an array of alpha helices and it is involved in protein-protein interactions with other components such as PWP2 and WDR36. This domain is also involved in the recruitment of DHX37 to the processome.
Pfam PF13020: Protein NO VEIN, C-terminal (family)
This domain of unknown function is found at the C-terminal of Protein NO VEIN from Arabidopsis, a protein essential for cell fate determination during embryogenesis. It mediates this process through an auxin-dependent pathway. This domain is also found in some restriction endonucleases.
Pfam PF13761: Domain of unknown function (DUF4166) (domain)
This domain is often found at the C-terminus of proteins containing [pfam:PF03435].
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 PF08962: Rv2632c-like (family)
This entry includes a set of Actinobacterial proteins, including Rv2632c from Mycobacterium tuberculosis that is strongly implicated in the onset of non-replicating persistence, and thereby latent tuberculosis. Rv2632c contains a dsRBD-like (2 layers alpha/beta) fold (PDBe:2fgg). It shares remarkable similarity with bacterial hibernation factors, despite very low sequence similarity. Based on this structure it was predicted that Rv1738, highly up-regulated in conditions that mimic the onset of persistence, helps trigger dormancy by association with the bacterial ribosome.
Pfam PF07860: WisP family C-Terminal Region (family)
This family is found at the C-terminus of the Tropheryma whipplei WisP family proteins ().
Pfam PF22202: CRISPR-associated endonuclease C2c1 first helical domain (domain)
This domain is found at the N-terminal end of CRISPR-associated endonuclease Cas12b from Alicyclobacillus acidoterrestris and similar sequences from firmicutes. Cas12b, also known as C2c1, is a type V-B CRISPR-Cas system dual-RNA-guided DNA endonuclease that site-specifically targets and cleaves dsDNA. This domain, together with the second helical domain ([pfam:PF22172]) forms the alpha-recognition (REC) lobe, which recognises a 20bp guide:target heteroduplex in RNAs.
Pfam PF24266: HVO_0163, N-terminal HTH domain (domain)
This HTH domain is found at the N-terminal of the ArsR family transcription regulator HVO_0163 from Haloferax volcanii and similar archaeal sequences
Pfam PF24012: Family of unknown function (DUF7326) (family)
This entry represents a family of uncharacterised phage 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 PF17034: Zinc-ribbon like family (family)
This family is found at the C-terminus of WD40 repeat structures in eukaryotes.
Pfam PF12463: Protein of unknown function (DUF3689) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 399 and 797 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 PF20651: Exocyst complex component EXOC6/Sec15, N-terminal (repeat)
This entry represents a domain found at the N-terminal of Exocyst complex components EXOC6/Sec15, members of the complexes associated with tethering containing helical rods (CATCHR) fold family and homologous to subunits of other multisubunit tethering complexes (MTCs) such as Dsl1, Golgi-associated retrograde protein (GARP) and COG complexes, characterised by a coiled-coild region at the N-terminal and an alpha-helical bundle at the C-terminal. This is a coiled-coil domain of Sec15 that forms an antiparallel zipper with Sec10 and interacts with the antiparallel zipper formed between Exo70-Exo84, which form a four-helical bundle part of the core of the exocyst.
Pfam PF20293: ABC-three component (ABC-3C) system Middle Component 6 (family)
Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. MC6 is a MC unifiable with the HTH fold.
Pfam PF03108: MuDR family transposase (family)
This region is found in plant proteins that are presumed to be the transposases for Mutator transposable elements. These transposons contain two ORFs. The molecular function of this region is unknown.
Pfam PF02598: Putative RNA methyltransferase (family)
This family has a TIM barrel-like fold with a deep C-terminal trefoil knot. The arrangement of its hydrophilic and hydrophobic surfaces are opposite to that of the classic TIM barrel proteins. It is likely to bind RNA, and may function as a methyltransferase.
Pfam PF06794: Uncharacterised protein family (UPF0270) (family)
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Pfam PF08778: HIF-1 alpha C terminal transactivation domain (domain)
Hypoxia inducible factor-1 alpha (HIF-1 alpha) is the regulatory subunit of the heterodimeric transcription factor HIF-1.  It plays a key role in cellular response to low oxygen tension. This region corresponds to the C terminal transactivation domain.
Wikipedia: Hypoxia-inducible factors (HIFs) are transcription factors that respond to decreases in available oxygen in the cellular environment, or hypoxia. They also respond to instances of pseudohypoxia, such as thiamine deficiency. Both hypoxia and pseudohypoxia leads to impairment of adenosine triphosphate (ATP) production by the mitochondria.
Pfam PF10606: Homer-binding domain of metabotropic glutamate receptor (domain)
This is the proline-rich region of metabotropic glutamate receptor proteins that binds Homer-related synaptic proteins. The Homer proteins form a physical tether linking mGluRs with the inositol trisphosphate receptors (IP3R) that appears to be due to the proline-rich "Homer ligand" (PPXXFr). Activation of PI turnover triggers intracellular calcium release. MGluR function is altered in the mouse model of human Fragile X syndrome, a disorder caused by loss of function mutations in the Fragile X messenger ribonucleoprotein 1 Fmr1. Homer 3 (and to a lesser extent Homer 1b/c) has been shown to form a multimeric complex with mGlu1a and the IP3 receptor, indicating that Homers may play a role in the localisation of receptors to their signalling partners.
Pfam PF14029: Protein of unknown function (DUF4244) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 66 and 95 amino acids in length. There is a conserved EYA sequence motif.
Pfam PF14409: Ribosomally synthesized peptide in Herpetosiphon (family)
Ribosomally synthesized peptide that is usually in the gene neighbourhood of a RimK-like ATP-grasp, and an ABC ATPase fused to a papain-like domain. It is often present in multiple tandem gene  copies. Gene contexts suggest that it is modified by the ATP=grasp. It might function in defence or development, or as a peptide antibiotic.
Pfam PF03072: Domain of unknown function (DUF237) (domain)
This is a domain of unknown function found in mycoplasma. It is found at the C-terminal region.
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 PF21309: Complement component 5, CUB domain (domain)
Complement component 5 (C5)  is a component of the lytic complex consisting of factors C5-C9 which attack bacterial cell membranes.  This entry represents the CUB domain.
Pfam PF20664: Family of unknown function (DUF6814) (family)
This family of proteins is functionally uncharacterised. Proteins in this family are predominantly found in Bacteroidetes and are approximately 80 amino acids in length. There are several conserved motifs: IxxGL, FGxY and GEY.
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 PF25078: Domain of unknown function (DUF7801) (domain)
This domain is found in a group of uncharacterised fungal proteins. This domain is often found associated with [pfam:PF15456] and is predicted to show a 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 PF20525: Family of unknown function (DUF6740) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically around 520 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 PF11523: Protein of unknown function (DUF3223) (family)
This 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 PF24172: CdiI immunity protein EcoliA0-like (family)
CDI toxins are expressed by Gram-negative bacteria as part of a mechanism to inhibit the growth of neighbouring cells. This entry represents the inhibitor (CdiI, also called CdiI immunity protein) of the CdiA effector protein from Escherichia coli A0 34/86, and similar proteins.  E.coli A0 CdiI adopts an alpha/beta structure consisting of a central antiparallel beta-sheet and alpha-helices packed on it PDB:5T86.
Pfam PF07421: Neurotensin/neuromedin N precursor (family)
This family contains the precursor of bacterial neurotensin/neuromedin N (approximately 170 residues long). This the common precursor of two biologically active related peptides, neurotensin and neuromedin N. It undergoes tissue-specific processing leading to the formation in some tissues and cancer cell lines of large peptides ending with the neurotensin or neuromedin N sequence.
Wikipedia: Neurotensin is a 13 amino acid neuropeptide that is implicated in the regulation of luteinizing hormone and prolactin release and has significant interaction with the dopaminergic system. Neurotensin was first isolated from extracts of bovine hypothalamus based on its ability to cause a visible vasodilation in the exposed cutaneous regions of anesthetized rats.
Pfam PF14906: Domain of unknown function (DUF4495) (repeat)
This domain family is found in eukaryotes, and is typically between 322 and 336 amino acids in length. There are two conserved sequence motifs: QMW and DLW. Proteins in this family vary in length from 793 to 1184 amino acids.
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 PF01152: Bacterial-like globin (domain)
This family of heme binding proteins are found mainly in bacteria. However they can also be found in some protozoa and plants as well.
Wikipedia: The globins are a superfamily of heme-containing globular proteins, involved in binding and/or transporting oxygen. These proteins all incorporate the globin fold, a series of eight alpha helical segments. Two prominent members include myoglobin and hemoglobin. Both of these proteins reversibly bind oxygen via a heme prosthetic group. They are widely distributed in many organisms.
Pfam PF20473: MmeI, DNA-methyltransferase domain (domain)
Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320)  via a multi-helical spacer (residues 156-300). These are followed  by the target recognition domain (TRD, residues 621-825), and a  final C-terminal helical bundle (residues 826-919).  The DNA is embedded between the TRD and the MTase domain.  The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove. This domain corresponds to the DNA-methyltransferase.  Structurally, it consists of a twisted beta-sheet flanked by  alpha-helices on both sides.
Pfam PF23435: Family of unknown function (DUF7121) (family)
This family represents a group of proteins mainly from halobacteria. Members are predicted to show an 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 PF15480: Domain of unknown function (DUF4640) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 99 and 306 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 PF16488: Argonaute linker 2 domain (family)
ArgoL2 is the second linker domain in eukaryotic argonaute proteins. It starts with two alpha-helices aligned orthogonally to each other followed by a beta-strand involved in linking the two lobes, the PAZ lobe and the Piwi lobe of argonaute to each other. Linker 2 together with the N, PAZ and L1 domains form a compact global fold. Numerous residues from Piwi, L1 and L2 linkers direct the path of the phosphate backbone of nucleotides 7-9, thus allowing DNA-slicing.
Pfam PF08066: PMC2NT (NUC016) domain (domain)
This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components.
Pfam PF16216: GxGYxYP_N 1st domain (domain)
This entry represents a domain that is found repeated in three copies per protein and is likely to be involved in binding the bacterial cell wall. This domain is found in association with [pfam:PF14323].
Pfam PF08251: Mastoparan peptide (family)
Mastoparan (MP) peptides I II and III are extracted from the venom  gland of the Neotropical social wasp Protopolybia exigua(Saussure) They are tetradecapeptides presenting from seven to ten  hydrophobic amino acid residues and from two to four lysine  residues in their primary sequences. These peptide cause the degranulation of mast cells. Protopolybia-MP-I also act causing hemolysis in erythrocytes.
Pfam PF21493: Tubulin-like protein TubZ, C-terminal domain (domain)
Tubulin-like protein TubZ is a tubulin-like, filament forming GTPase, the motor component of the type III plasmid partition system which ensures correct segregation of the pXO1 plasmid. This entry represents the C-terminal GTPase-activating domain of TubZ.
Pfam PF22447: Endonuclease/exonuclease/phosphatase family, ig-like domain (domain)
This entry corresponds to the C-terminal immunoglobulin-like domain of a putative endonuclease/exonuclease/phosphatase from Beutenbergia cavernae (PDB:4ruw).
Pfam PF18268: Hit1 C-terminal (domain)
This domain is found in Hit1 protein (Hit1p) present in Saccharomyces cerevisiae.  Hit1p contributes to C/D small nucleolar RNPs (snoRNPs) stability and pre-RNA maturation kinetics by associating with U3 snoRNA precursors and influencing its 3'-end processing. Snu13p-Rsa1p-Hit1p heterotrimer binds C/D snoRNAs. C/D snoRNAs are essential for the biogenesis of ribosomes and spliceosomes. The domain adopts a Pac-Hit fold that forms a claw which locks the alpha-1 helix of Rsa1p, while the Rsa1p alpha-2 helix packs against the exposed surface of the Hit1p Pac-Hit domain alpha-3 helix.
Pfam PF13259: Gag1-like, clamp domain (domain)
This domain found in a group of sequences from fungi and plants, including Gag1 from Saccharomyces cerevisiae, which interacts with Cka2, the fourth subunit of the eukaryotic kinase CK2. Gag1 is organised into three domains: lock, Gag and Clap (this entry). This domain has three regions: rear, hinge and front. It contains two conserved sequence motifs: IPL and FLVD.