SII-SWORD/CoKE huggingface dataset:
Pfam PF23709: Mycofactocin precursor peptide (family)
This protein family includes Mycofactocin precursor peptide from Mycobacterium tuberculosis (MftA) and similar short sequences from actinobacteria. MftA is a 29-residues long precursor peptide that leads to mycofactocin (MFT) after extensive post-translational modifications by enzymes encoded by adjacent genes. Mycofactocin acts as a redox cofactor of nicotinamide-dependent oxidoreductases encoded in the same locus.
Pfam PF22255: Baseplate hub protein gp44-like, second domain (domain)
This domain is found in Baseplate hub protein gp44 from Escherichia phage Mu and similar proteins found in tailed bacteriophages and proteobacterial prophages. This domain is located C-terminal to [pfam:PF21683] and N-terminal to [pfam:PF21929].
Pfam PF03470: XS zinc finger domain (domain)
This domain is a putative nucleic acid binding zinc finger found in proteins that also contain an XS domain.
Pfam PF00853: Runt domain (domain)
The AML1 gene is rearranged by the t(8;21) translocation in acute myeloid leukemia . The gene is highly similar to the Drosophila melanogaster segmentation gene runt and to the mouse transcription factor PEBP2 alpha subunit gene . The region of shared similarity, known as the Runt domain, is responsible for DNA-binding and protein-protein interaction.

In addition to the highly-conserved Runt domain, the AML-1 gene product carries a putative ATP-binding site (GRSGRGKS), and has a C-terminal region rich in proline and serine residues. The protein (known as acute myeloid leukemia 1 protein, oncogene AML-1, core-binding factor (CBF), alpha-B subunit, etc.) binds to the core site, 5'-pygpyggt-3', of a number of enhancers and promoters.
Wikipedia: The Runt domain  is an evolutionary conserved protein domain. The AML1/RUNX1 gene is rearranged by the t(8;21) translocation in acute myeloid leukemia. The gene is highly similar to the Drosophila melanogaster segmentation gene runt and to the mouse transcription factor PEBP2 alpha subunit gene. The region of shared similarity, known as the Runt domain, is responsible for DNA-binding and protein-protein interaction.
Pfam PF21229: TdIF1, C-terminal (domain)
This domain is found in Deoxynucleotidyltransferase terminal- interacting protein 1 from humans (TdIF1) and similar proteins conserved from nematodes to mammals. TdIF1 is part of a histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. It is organised into two domains. This entry represents the C-terminal domain, which shows a structure related to the SKI/SNO/DAC domain ([pfam:PF02437]) and is involved in the interaction with both DNA and nucleosomes.
Pfam PF19801: Family of unknown function (DUF6284) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis. This family appears to be predominantly found in  Actinoabactteria.
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 PF21091: FACT complex subunit SPT16, C-terminal domain (domain)
FACT (facilitates chromatin transactions) is a general chromatin factor that acts to reorganise nucleosomes. SPT16 is a subunit of this complex that is conserved among eukaryotes, from yeast to humans. This entry represents the C-terminal domain of SPT16, which wraps around the DNA binding surface of H2A-H2B.
Pfam PF22617: Homocitrate synthase post-HMGL domain-like (domain)
This entry represents domain found in diverse homologues of Homocitrate synthase (HCS). This domain follows the catalytic domain and is required for the enzymatic activity.
Pfam PF11940: Domain of unknown function (DUF3458) Ig-like fold (domain)
This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. The domain has an Ig-like fold. This domain is found associated with [pfam:PF01433].
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 PF19091: Family of unknown function (DUF5779) (family)
Family of unknown function predominantly found in Halobacteria.
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 PF09307: CLIP, MHC2 interacting (domain)
Members of this family are found in class II invariant chain-associated peptide (CLIP), and are required for association with class II major histocompatibility complex (MHC) in the MHC class II processing pathway.
Pfam PF00491: Arginase family (domain)
The ureohydrolase superfamily includes arginase (3.5.3.1), agmatinase (3.5.3.11), formiminoglutamase (3.5.3.8) and proclavaminate amidinohydrolase (3.5.3.22) . These enzymes show trimeric or hexameric structures and share a 3-layer Î±-Î²-Î± structure , playing important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways.

Arginase, which catalyses the conversion of arginine to urea and ornithine, is one of the five members of the urea cycle enzymes that convert ammonia to urea as the principal product of nitrogen excretion . There are several arginase isozymes that differ in catalytic, molecular and immunological properties. Deficiency in the liver isozyme leads to argininemia, which is usually associated with hyperammonemia.

Agmatinase hydrolyses agmatine to putrescine, the precursor for the biosynthesis of higher polyamines, spermidine and spermine. In addition, agmatine may play an important regulatory role in mammals.
Wikipedia: A ureohydrolase is a type of hydrolase enzyme. The ureohydrolase superfamily includes arginase, agmatinase, formiminoglutamase and proclavaminate amidinohydrolase. These enzymes share a 3-layer alpha-beta-alpha structure, and play important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways.
Pfam PF13165: Six-cysteine peptide SCIFF (family)
Members of this protein family are essentially universal in the class Clostidia and therefore highly abundant in the  human gut microbiome. This short peptide is designated  SCIFF, for Six Cysteines in Forty-Five residues. It is a  presumed ribosomal natural product precursor, always  found associated with a yet-uncharacterised radical SAM  protein that resembles other peptide modification radical  SAM enzymes and is designated SCIFF radical SAM maturase.
Pfam PF02104: SURF1 family (family)
This entry includes SURF1 and Shy1 proteins. The surfeit locus 1 gene (SURF1 or surf-1) encodes a conserved protein of about 300 amino-acid residues that seems to be involved in the biogenesis of cytochrome c oxidase . Vertebrate SURF1 is evolutionary related to yeast protein Shy1, which is a mitochondrial inner membrane protein required for assembly of cytochrome c oxidase . There seems to be two transmembrane regions in these proteins, one in the N-terminal, the other in the C-terminal.

Defects in SURF1 are a cause of Leigh syndrome (LS). LS is a severe neurological disorder characterised by bilaterally symmetrical necrotic lesions in subcortical brain regions that is commonly associated with systemic cytochrome c oxidase (COX) deficiency .
Pfam PF13315: Protein of unknown function (DUF4085) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 101 and 269 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 PF12253: Chromatin assembly factor 1 subunit A dimerization domain (family)
The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the largest, known as A/p150, which is uniquely required for the progression of S phase in mouse cells, independently of its ability to promote histone deposition but dependent on its ability to interact with HP1 (heterochromatin protein 1)-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. It contains a HP1-CAF-1 interaction module that functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. p150 plays a key role in embryonic differentiation. This entry represents the dimerization domain of p150.
Pfam PF02189: Immunoreceptor tyrosine-based activation motif (conserved_site)
T cell receptor (TCR) is a complex multi-protein cell surface receptor composed of the ligand-sensing TCR heterodimer and three signaling subunits. These signaling subunits contain cytoplasmic immunoreceptor tyrosine-based activation motifs (ITAMs) with a consensus sequence of YxxL/Ix6-12YxxL/I. The two tyrosines are phosphorylated by a Src kinase, Lck or Fyn. Binding of the dually phosphorylated ITAM peptide reorients the two SH2 domains relative to each other, destabilizing inhibitory interactions made by the linker connecting the SH2 and kinase domains.
Wikipedia: An immunoreceptor tyrosine-based activation motif (ITAM) is a conserved sequence of four amino acids that is repeated twice in the cytoplasmic tails of non-catalytic tyrosine-phosphorylated receptors, cell-surface proteins found mainly on immune cells. Its major role is being an integral component for the initiation of a variety of signaling pathway and subsequently the activation of immune cells, although different functions have been described, for example an osteoclast maturation.
Pfam PF15856: Domain of unknown function (DUF4727) (family)
This family of proteins is found in vertebrates. There are a number of conserved cysteines, but the domain is not a zinc-finger.
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 PF09558: Protein of unknown function (DUF2375) (family)
Two members of this family are found in Colwellia psychrerythraea (strain 34H / ATCC BAA-681) and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by PEP_anchor (IPR013424).
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 PF20600: Exodeoxyribonuclease X-like C-terminal (domain)
This short domain is found at the C-terminal of Exodeoxyribonuclease 10 (ExoX) from Escherichia coli (strain K12) and it is functionally uncharacterised. This domain is found in bacteria and eukaryotes There is a conserved FGKY/H sequence motif.
Pfam PF16562: N-terminal domain of E3 ubiquitin-protein ligase HECW1 and 2 (domain)
HECW_N is a domain on E3 ubiquitin-protein ligases that lies upstream of the C2 domain; its function is not clearly understood, except perhaps to determine the substrate spectrum of the ligase.
Pfam PF12377: Duffy binding protein N terminal (family)
This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with [pfam:PF05424]. This family contains the N terminus of the Duffy receptor binding domain.
Wikipedia: In molecular biology, Duffy binding proteins are found in Plasmodium. Plasmodium vivax and Plasmodium knowlesi merozoites invade Homo sapiens erythrocytes that express Duffy blood group surface determinants. The Duffy receptor family is localised in micronemes, an organelle found in all organisms of the phylum Apicomplexa.
Pfam PF20138: Family of unknown function (DUF6528) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 311 and 340 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 PF24815: WDHD1 HMG box (domain)
This entry represents the HMG box found at the C-terminal of WDHD1 (also known as AND-1), an adaptor molecule crucial for DNA replication. This domain binds DNA.
Pfam PF24053: Domain of unknown function (DUF7356) (domain)
This domain is found in uncharacterised plant proteins. It is predicted to adopt a globular structure with similarity to Fibronectin type III-like domains.
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 PF11164: Protein of unknown function (DUF2948) (family)
This family of proteins with unknown function appear to be restricted to Proteobacteria.
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 PF08537: Fungal Nap binding protein NBP1 (family)
NBP1 is a nuclear protein which has been shown in Saccharomyces cerevisiae to be essential for the G2/M transition of the cell cycle.
Pfam PF18279: Werner helicase-interacting protein 1 ubiquitin-binding domain (domain)
This domain is found in the Werner helicase-interacting protein 1 present in Homo sapiens. The domain is a zinc finger responsible and has a zinc-coordinating B-B-A fold. WRNIP1 UBZ binds ubiquitin in a similar manner to Rad18 UBZ.
Pfam PF02087: Nitrophorin (domain)
Nitrophorins are haemoproteins found in saliva of blood-feeding insects . Saliva of the blood-sucking bug Rhodnius prolixus (Triatomid bug) contains four homologous nitrophorins, designated NP1 to NP4 in order of their relative abundance in the glands . As isolated, nitrophorins contain nitric oxide (NO) ligated to the ferric (FeIII) haem iron. Histamine, which is released by the host in response to tissue damage, is another nitrophorin ligand. Nitrophorins transport NO to the feeding site. Dilution, binding of histamine and increase in pH (from pH ~5 in salivary gland to pH ~7.4 in the host tissue) facilitate the release of NO into the tissue where it induces vasodilatation.

The salivary nitrophorin from the hemipteran Cimex lectularius (Bed bug) has no sequence similarity to R. prolixus nitrophorins. It is suggested that the two classes of insect nitrophorins have arisen as a product of the convergent evolution .

3-D structures of several nitrophorin complexes are known . The nitrophorin structures reveal lipocalin-like eight-stranded Î²-barrel, three Î±-helices and two disulphide bonds, with haem inserted into one end of the barrel. Members of the lipocalin family are known to bind a variety of small hydrophobic ligands, including biliverdin, in a similar fashion (see  for review). The haem iron is ligated to His59. The position of His59 is restrained through water-mediated hydrogen bond to the carboxylate of Asp70. The His59-Fe bond is bent ~15 degrees out of the imidazole plane. Asp70 forms an unusual hydrogen bond with one of the haem propionates, suggesting the residue has an altered pKa. In NP1-histamine structure, the planes of His59 and histamine imidazole rings lie in an arrangement almost identical to that found in oxidised cytochrome b5.
This entry represents the nitrophorin structural domain.
Pfam PF07138: Baculovirus protein AC11 (family)
This family of baculovirus proteins is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV) protein AC11 (Orf11). ac11 is an early gene essential for budded-virus production and occlusion-derived-virus envelopment.
Pfam PF06379: L-rhamnose-proton symport protein (RhaT) (family)
This family consists of several bacterial L-rhamnose-proton symport protein (RhaT) sequences.
Pfam PF06822: Protein of unknown function (DUF1235) (family)
This family contains a number of viral proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF07189: Splicing factor 3B subunit 10 (SF3b10) (family)
This family consists of several eukaryotic splicing factor 3B subunit 10 (SF3b10) proteins. SF3b10 is a 10 kDa subunit of the splicing factor SF3b. SF3b associates with the splicing factor SF3a and a 12S RNA unit to form the  U2 small nuclear ribonucleoproteins complex. SF3b10 and SF3b14b are also thought to facilitate the interaction of U2 with the branch site.
Pfam PF02947: flt3 ligand (domain)
The flt3 ligand is a short chain cytokine with a 4 helical bundle fold.
Pfam PF12133: Betacoronavirus NS6 protein (family)
This entry represents non-structural protein NS6 (also known as non-structural protein 6, accessory protein 6, or X3 protein), which is highly conserved among SARS-related coronaviruses. (This is distinct from NSP6 which is encoded on the replicase polyprotein). Proteins in this family are typically between 42 to 63 amino acids in length. NS6 is located in the endoplasmic reticulum. It has been reported that NS6 can increase the cellular gene synthesis and it can also induce apoptosis through Jun N-terminal kinase and Caspase-3 mediated stress. This protein can modulate host antiviral responses by inhibiting synthesis and signalling of IFN-beta, via NS6 interaction with host N-Myc (and STAT) interactor (Nmi) protein and suppressing the translocation of signal transducer and activator of transcription 1 (STAT1).
Pfam PF16225: Domain of unknown function (DUF4884) (family)
This family consists of several uncharacterized proteins around 90 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Pfam PF04956: TrbC/VIRB2 pilin (family)
TrbC is a pilin found in bacterial type IV secretion systems. The protein undergoes three processing steps before gaining its mature cyclic structure. This family also contains VIRB2 type IV secretion proteins. This alignment contains two predicted transmembrane helices.
Pfam PF21667: Nop5, N-terminal domain (domain)
This entry represents the N-terminal domain of archaeal Nop5, a Nop56/58 homologue which are pre-RNA processing ribonucleoproteins (RNP). This domain is very well conserved and mediates a stable interaction with fibrillarin, playing a role in both RNP assembly and methyltransferase activity.
Pfam PF14066: Protein of unknown function (DUF4256) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 190 amino acids in length.
Pfam PF23361: BBS7 platform domain (domain)
This entry represents the platform domain of BBS7. BBS7 is one of the BBS proteins that form the BBSome complex found in vertebrates and nematodes, including humans, mice, and Caenorhabditis elegans. BBSome complex is required for ciliogenesis and the assembly and movement of intraflagellar transport proteins along the ciliary membrane.
Pfam PF12153: LPS binding domain of CAP18 (C terminal) (domain)
This domain family is found in eukaryotes, and is approximately 30 amino acids in length, and the family is found in association with [pfam:PF00666]. CAP18 is a protein which is derived from rabbit granulocytes. It has two domains, an N terminal DUF and a C terminal Gram negative LPS binding domain. This domain is the C terminal domain.
Pfam PF17331: GFD1 mRNA transport factor (conserved_site)
Following transcription, mRNA is processed, packaged into messenger ribonucleoprotein (mRNP) particles, and transported through nuclear pores (NPCs) to the cytoplasm. Gfd1 is one of several factors that, although not essential for mRNA export, enhances the efficiency of the process, either by facilitating integration of different steps in the gene expression pathway or by increasing the rate of key steps. Gfd1 localizes to the cytoplasm and nuclear rim. It interacts with a number of components of the mRNA export machinery in yeast. Most notably, Gfd1 interacts with the Dbp5-activating protein, Gle1, the cytoplasmic nucleoporin Nup42/Rip1, the putative RNA helicase, Dbp5, and a protein implicated in mRNA export, Zds1. Gfd1 forms a complex with Nab2 both in vitro and in vivo in which Gfd1 binds to the N-terminal domain of Nab2. The crystal structure, together with complementary NMR data, indicated that residues 126-150 of Gfd1 form a single alpha-helix that binds primarily to helix 2 of Nab2-N. Gfd1 functions to co-ordinate Dbp5 and Gle1 to facilitate the removal of Nab2 from mRNPs at the cytoplasmic face of nuclear pores.
Pfam PF20091: Alpha/beta hydrolase domain (domain)
This entry represents a protein that belongs to the alpha/beta hydrolase superfamily. Although proteins in this family are uncharacterised they are likely to have an enzymatic activity.