SII-SWORD/CoKE huggingface dataset:
Pfam PF02696: Protein adenylyltransferase SelO (family)
SelO and its homologues are widespread among most eukaryotic taxa, and are also common in many major bacterial taxa. SelO is a conserved pseudokinase that transfers AMP from ATP to Ser, Thr, and Tyr residues on protein substrates (AMPylation). It contains a protein kinase fold with ATP flipped in the active site. In eukaryotes, it is a mitochondrial protein that may be involved in redox biology.
Pfam PF01253: Translation initiation factor SUI1 (domain)
In budding yeast (Saccharomyces cerevisiae), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation . SUI1 is a protein of 108 residues. Close homologues of SUI1 have been found  in mammals, insects and plants. SUI1 is also evolutionary related to:


 * Hypothetical proteins from bacteria such as Escherichia coli (YciH) or Haemophilus influenzae (HI1225).
 * Hypothetical proteins from archaea such as Methanococcus jannaschii (MJ0463).


Two eukaryotic proteins also seem to contain a C-terminal SUI1-like domain. These are:


 * Density-regulated protein (gene: DENR). This protein is found in mammals, insects, nematodes, plants and fungi.
 * Ligatin (gene: LGTN). This protein is found in mammals and insects.
Wikipedia: In molecular biology, the single-domain protein SUI1 is a translation initiation factor often found in the fungus, Saccharomyces cerevisiae but it is also found in other eukaryotes and prokaryotes as well as archaea. It is otherwise known as Eukaryotic translation initiation factor 1 (eIF1) in eukaryotes or YciH in bacteria.
Pfam PF16315: Domain of unknown function (DUF4955) (repeat)
This family consists of uncharacterized proteins around 850 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown.
Pfam PF12837: 4Fe-4S binding domain (domain)
This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich.
Pfam PF01630: Hyaluronidase (domain)
Glycoside hydrolase family 56 GH56 comprises enzymes with only one known activity; hyaluronidase 3.2.1.35.

The venom of Apis mellifera (Honeybee) contains several biologically-active peptides and two enzymes, one of which is a hyaluronidase . The amino acid sequence of bee venom hyaluronidase contains 349 amino acids, and includes four cysteines and a number of potential glycosylation sites . The sequence shows a high degree of similarity to PH-20, a membrane protein of mammalian sperm involved in sperm-egg adhesion, supporting the view that hyaluronidases play a role in fertilisation .

PH-20 is required for sperm adhesion to the egg zona pellucida; it is located on both the sperm plasma membrane and acrosomal membrane . The amino acid sequence of the mature protein contains 468 amino acids, and includes six potential N-linked glycosylation sites and twelve cysteines, eight of which are tightly clustered near the C terminus .
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.
Wikipedia: In molecular biology, glycoside hydrolase family 56 is a family of glycoside hydrolases.
Pfam PF14623: Hint-domain (domain)
This short domain is a conserved region of intein-containing proteins from lower eukaryotes.
Pfam PF10786: HI_0552 protein family (family)
This family is conserved in Firmicutes and Proteobacteria. Several members are annotated as being glucose-6-phosphate 1-dehydrogenase but there is no evidence supporting this. In H. influenzae, it corresponds to [swissprot:P44311] (HI_0558).
Pfam PF06237: Solute carrier family 52, riboflavin transporter (family)
This family includes animal riboflavin transporters belonging to the Solute carrier family 52 (SLC52). They are plasma membrane proteins that transport vitamin B2 (riboflavin, RF) into cells. In case of infection by retroviruses, they act as cell receptors to retroviral envelopes similar to the porcine endogenous retrovirus (PERV-A). These proteins belong to the MFS superfamily.
Pfam PF02633: Creatinine amidohydrolase (family)
Creatinine amidohydrolase ([ec:3.5.2.10]), or creatininase, catalyses  the hydrolysis of creatinine to creatine.
Wikipedia: In enzymology, a creatininase (EC 3.5.2.10) is an enzyme that catalyses the hydrolysis of creatinine to creatine, which can then be metabolised to urea and sarcosine by creatinase.creatinine + H2O  creatine
Pfam PF12989: Domain of unknown function, B. Theta Gene description (DUF3873) (family)
Based on Bacteroides thetaiotaomicron gene BT_2286, a putative uncharacterized protein.  As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or other bacterial species vs when in culture.
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 PF03464: eRF1 domain 2 (domain)
The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown.  Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.
Pfam PF12896: Anaphase-promoting complex, cyclosome, subunit 4 (domain)
Apc4 is one of the larger of the subunits of the anaphase-promoting complex or cyclosome. This family represents the long domain downstream of the WD40 repeat/s that are present on the Apc4 subunits. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. Results in C.elegans show that the primary essential role of the spindle assembly checkpoint is not in the chromosome segregation process itself but rather in delaying anaphase onset until all chromosomes are properly attached to the spindle.  the APC/C is likely to be required for all metaphase-to-anaphase transitions in a multicellular organism.
Pfam PF07988: LMSTEN motif (conserved_site)
This region of Myb proteins has previously been described as the transcriptional activation domain present in the vertebrate c-Myb and A-Myb, but neither vertebrate B-Myb proteins nor Myb proteins of invertebrates. Because vertebrate B-Myb (but neither A-Myb nor c-Myb) can partially complement Drosophila Myb null mutants, this region appears to have been a relatively recent insertion.
Pfam PF22331: Sas-6-like, oligomerization domain (domain)
This entry represents the coiled-coil region of Sas-6 from Chlamydomonas reinhardtii, which mediates oligomerization. In human, Sas-6 is essential for the onset of procentriole formation and accumulates on the torus where Plk4 has focused.
Pfam PF15394: Domain of unknown function (DUF4616) (family)
This protein family is a domain of unknown function found at the C-terminal domain of the proteins. This protein family is found in eukaryotes. Proteins in this family are typically between 166 and 538 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 PF02950: Conotoxin (domain)
Conotoxins are small snail toxins that block ion channels.
Wikipedia: A conotoxin is one of a group of neurotoxic peptides isolated from the venom of the marine cone snail, genus Conus.
Pfam PF10656: Hypothetical protein of unknown function (DUF2483) (family)
This is a family of proteins found in bacteriophage particularly of the SA bacteriophages 11, Mu50B, family, homologous to phi-ETA orf16.
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 PF08958: Domain of unknown function (DUF1871) (domain)
This set of hypothetical proteins is produced by prokaryotes pertaining to the Bacillus genus.
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 PF16835: Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) (domain)
SF3A2 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp21 (subunit 1). with Prp21 wrapping around Prp11.
Pfam PF05131: Pep3/Vps18/deep orange beta-propeller domain (repeat)
This region is found in a number of protein identified as involved in golgi function and vacuolar sorting. The molecular function of this region is unknown. This domain adopts a beta propeller structure. The members of this family contain a C-terminal ring finger domain.
Pfam PF07076: Protein of unknown function (DUF1344) (family)
This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF18165: Predicted pPIWI-associating nuclease (domain)
Predicted nuclease effector domain associating with prokaryotic PIWI-centered conflict systems.
Pfam PF23863: CdsD PD1 domain (domain)
This domain is found in CdsD from Chlamydia trachomatis ([swissprot:O84671]) and similar sequences. CdsD is a structural contact-dependent secretion (Cds) protein that forms part of the basal body of the type III secretion system (T3SS) injectisome of the bacteria. The periplasmic part of this protein contains 3 domains: PD1 (represented in this entry), PD2 ([pfam:PF22598]) and PD3 ([pfam:PF04972]), all of them sharing the same alpha-beta-beta-alpha-beta topology, known as the BON fold.
Pfam PF01726: LexA DNA binding domain (domain)
This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA  binding motif. This domain is found associated with [pfam:PF00717] the auto-proteolytic  domain of LexA [ec:3.4.21.88].
Wikipedia: The LexA repressor or LexA is a transcriptional repressor that represses SOS response genes coding primarily for error-prone DNA polymerases, DNA repair enzymes and cell division inhibitors. LexA forms de facto a two-component regulatory system with RecA, which senses DNA damage at stalled replication forks, forming monofilaments and acquiring an active conformation capable of binding to LexA and causing LexA to cleave itself, in a process called autoproteolysis.
Pfam PF21851: Family of unknown function (DUF6910) (repeat)
The function of this family of proteins is unknown. They are predicted to adopt a five-bladed beta-propeller and are probably distantly related to apyrase.
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 PF22806: Protein M, C-terminal (domain)
This domain is found in proteins from Mycoplasmaceae, including Uncharacterized protein MG281 from Mycoplasma genitalium, also known as protein M. This virulence protein consists of two domains and N- and C-terminal fragments. This entry represents the C-terminal region, which is probably disordered.
Pfam PF11712: Endoplasmic reticulum-based factor for assembly of V-ATPase (family)
The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterised member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localised to the endoplasmic reticulum.
Pfam PF19226: DisA glycoprotein (family)
This entry corresponds to a putative viral glycoprotein.
Pfam PF00926: 3,4-dihydroxy-2-butanone 4-phosphate synthase (family)
3,4-Dihydroxy-2-butanone 4-phosphate is biosynthesised from ribulose 5-phosphate and serves as the biosynthetic precursor for the xylene ring of riboflavin. Sometimes found as a bifunctional enzyme with [pfam:PF00925].
Wikipedia: The enzyme 3,4-dihydroxy-2-butanone 4-phosphate synthase (RibB) EC 4.1.99.12 catalyses the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate, the latter serving as the biosynthetic precursor for the xylene ring of riboflavin. In Photobacterium leiognathi, the riboflavin synthesis genes ribB, ribE, ribH and ribA all reside in the lux operon. RibB is sometimes found as a bifunctional enzyme with GTP cyclohydrolase II that catalyses the first committed step in the biosynthesis of riboflavin. No sequences with significant homology to DHBP synthase are found in the metazoa.
Pfam PF00271: Helicase conserved C-terminal domain (domain)
The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pfam PF14381: EDR1/CTR1/ARMC3, peptidase-like (domain)
This entry represents a peptidase-like domain mainly found in proteins from plants, including serine/threonine-protein kinases EDR1 and CTR1 from Arabidopsis thaliana. EDR1 regulates disease resistance and ethylene-induced senescence, and is also involved in stress response signalling and cell death regulation. CTR1 acts as a negative regulator in the ethylene response pathway. It phosphorylates the cytosolic C-terminal domain of EIN2, preventing the signaling in the absence of ethylene. This entry also includes proteins from animals, such as ARMC3, which is essential for male fertility and sperm motility. During spermatogenesis, promotes the autophagic degradation of excessive ribosomes, providing energy resources for mitochondria and thus ensuring sperm flagellar motility.
Pfam PF10838: Protein of unknown function (DUF2677) (family)
Members in this family of proteins are annotated as UL121 however currently no function is known.
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 PF06452: Carbohydrate family 9 binding domain-like (domain)
CBM9_1 is a C-terminal domain on bacterial xylanase proteins, and it is tandemly repeated in a number of family-members.  The CBM9 module binds to amorphous and crystalline cellulose and a range of soluble di- and monosaccharides as well as to cello- and xylo- oligomers of different degrees of polymerisation. Comparison of the glucose and cellobiose complexes during crystallisation reveals surprising differences in binding of these two substrates by CBM9-2. Cellobiose was found to bind in a distinct orientation from glucose, while still maintaining optimal stacking and electrostatic interactions with the reducing end sugar.
Pfam PF19297: QcrA subunit N-terminal region (family)
This entry describes the N-terminal region of the QcrA subunit which is part of respiratory complex III. This region includes anchoring transmembrane helical regions.
Pfam PF10980: Protein of unknown function (DUF2787) (family)
This bacterial family of proteins has no known function. The conserved hypothetical protein VC1805 from Vibrio cholerae belongs to this group. It adopts a monomeric assembly, showing an unusual topology with a flat seven-stranded anti-parallel beta-sheet and two helices located on the same side of the sheet. It has some structural homology with the human protein p32 and binds to the complement protein C1q, which suggests a possible role in the adherence of the bacteria to the intestinal wall.
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 PF21804: Transposase protein (family)
This entry represents a family of transposase proteins. The structure prediction shows closest similarity to the TN5 transposase protein.
Pfam PF19858: Bacterial oxidoreductases, C-terminal (domain)
This is the C-terminal domain of predicted bacterial oxidoreductases. This domain is related to [pfam:PF02894], and it is likely to be an alpha/beta-domain involved in substrate binding and oligomerization.
Pfam PF24304: Anti-CRISPR Suppressor AcrIIA4 (family)
This entry represents the Anti-CRISPR Suppressor AcrIIA4 encoded by Listeria monocytogenes prophages. AcrIIA4 preferentially targets critical residues essential for PAM duplex recognition, as well as it blocks target DNA access to the key catalytic residues lining the RuvC pocket of Cas9. AcrIIA4 adopts a fold composed of a three-stranded beta-sheet with three alpha-helices positioned along one face of the beta-sheet.
Pfam PF04948: Poxvirus A51 protein (family)
This entry represents Vaccinia virus A51, also known as Protein OPG181, and its homologues from poxvirus. This protein associates with ubiquitin and stabilises host microtubules, promotes viral protein stability, and plays an essential role in viral replication in vertebrate cells .
Pfam PF05391: Lsm interaction motif (conserved_site)
This short motif is found at the C-terminus of Prp24 proteins and probably interacts with the Lsm proteins to promote U4/U6 formation.
Pfam PF00718: Polyomavirus coat protein (domain)
This entry represents the major capsid protein VP1 (viral protein 1) from Polyomaviruses, such as Murine polyomavirus (strain P16 small-plaque) (MPyV) . Polyomaviruses are dsDNA viruses with no RNA stage in their life cycle. The virus capsid is composed of 72 icosahedral units, each of which is composed of five copies of VP1. The virus attaches to the cell surface by recognition of oligosaccharides terminating in alpha(2,3)-linked sialic acid. The capsid protein VP1 forms a pentamer. The complete capsid is composed of 72 VP1 pentamers, with a minor capsid protein, VP2 or VP3, inserted into the centre of each pentamer like a hairpin. This structure restricts the exposure of internal proteins during viral entry. Polyomavirus coat assembly is rigorously controlled by chaperone-mediated assembly. During viral infection, the heat shock chaperone hsc70 binds VP1 and co-localises it in the nucleus, thereby regulating capsid assembly .
Wikipedia: Major capsid protein VP1 is a viral protein that is the main component of the polyomavirus capsid. VP1 monomers are generally around 350 amino acids long and are capable of self-assembly into an icosahedral structure consisting of 360 VP1 molecules organized into 72 pentamers. VP1 molecules possess a surface binding site that interacts with sialic acids attached to glycans, including some gangliosides, on the surfaces of cells to initiate the process of viral infection. The VP1 protein, along with capsid components VP2 and VP3, is expressed from the "late region" of the circular viral genome.
Pfam PF18198: Dynein heavy chain AAA lid domain (domain)
This family represents the AAA lid domain found neat the C-terminal region of dynein heavy chain.
Wikipedia: Dyneins are a family of cytoskeletal motor proteins that move along microtubules in cells. They convert the chemical energy stored in ATP to mechanical work. Dynein transports various cellular cargos, provides forces and displacements important in mitosis, and drives the beat of eukaryotic cilia and flagella. All of these functions rely on dynein's ability to move towards the minus-end of the microtubules, known as retrograde transport; thus, they are called "minus-end directed motors". In contrast, most kinesin motor proteins move toward the microtubules' plus-end, in what is called anterograde transport.
Pfam PF06304: Protein of unknown function (DUF1048) (family)
This family includes LftS, a soluble globular cytoplasmic protein of unknown function. It is suggested that LftS acts in aurantimycin A sensing or in removal of LftR from its operator sites.