SII-SWORD/CoKE huggingface dataset:
Pfam PF13904: Coiled-coil domain-containing protein 34 (coiled_coil)
This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known.
Pfam PF17037: Cellulose biosynthesis protein BcsO (family)
This is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria. (Roemling U. and Galperin M.Y. "Bacterial cellulose biosynthesis. Diversity of operons and subunits" (manuscript in preparation)).
Pfam PF00551: Formyl transferase (domain)
This family includes the following members. Glycinamide ribonucleotide transformylase catalyses the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyltetrahydrofolate deformylase produces formate from formyl- tetrahydrofolate. Methionyl-tRNA formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. Inclusion of the following members is supported by PSI-blast. HOXX_BRAJA (P31907) contains a related domain of unknown function. PRTH_PORGI (P46071) contains a related domain of unknown function. Y09P_MYCTU (Q50721) contains a related domain of unknown function.
Pfam PF01483: Proprotein convertase P-domain (domain)
A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.
Pfam PF24765: SAC9 C-terminal domain (domain)
This domain is found C-terminal in SAC9 from Arabidopsis thaliana which is a probable phosphoinositide phosphatase that is involved in modulating phosphoinositide signals during the stress response. This domain is predicted to fold into a beta-sandwich with a similarity to the anaphase promoting complex subunit 10.
Pfam PF00389: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (domain)
This family represents the largest portion of the catalytic domain  of 2-hydroxyacid dehydrogenases as the NAD binding domain is  inserted within the structural domain.
Pfam PF03955: Adenovirus hexon-associated protein (IX) (family)
Hexon (PF01065) is the major coat protein from  adenovirus type 2. Hexon forms a homo-trimer.  The 240 copies of the hexon trimer are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together  by 12 copies of polypeptide IX.
Pfam PF11678: Antibacterial effector protein Tle3, C-terminal domain (domain)
This entry represents the C-terminal domain of Antibacterial effector protein Tle3 from Pseudomonas aeruginosa and similar sequences from proteobacteria. Tle3 is toxic once delivered in the periplasm of prey bacteria.
Pfam PF20862: Family of unknown function (DUF6843) (family)
This protein family includes Putative lipoprotein BA_2398 from Bacillus anthracis and similar proteins from bacteria, predominantly Firmicutes and Bacteroidetes.
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 PF14099: Polysaccharide lyase (domain)
This family includes heparin lyase I, [ec:4.2.2.7]. Heparin lyase I depolymerises heparin by cleaving the glycosidic linkage next to an iduronic acid moiety. The structure of heparin lyase I consists of a beta-jelly roll domain with a long, deep substrate-binding groove and an unusual thumb domain containing many basic residues extending from the main body of the enzyme. This family also includes glucuronan lyase, [ec:4.2.2.14]. The structure glucuronan lyase is a beta-jelly roll.
Pfam PF02016: LD-carboxypeptidase N-terminal domain (domain)
Muramoyl-tetrapeptide carboxypeptidase hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid. The function of this activity is in  murein recycling. This family also includes the microcin c7 self-immunity protein [swissprot:Q47511]. This family corresponds to  Merops family S66.
Pfam PF24390: PRTase-CE (domain)
PRTase-like domain predicted to act as an effector in multiple antiviral immunity systems by targeting nucleotides.
Pfam PF23926: LtfC-like, beta-sandwich domain (domain)
This entry, previously known as DUF7264, represents a domain found in the Minor tail protein Gp6, Collar protein p132, Lateral tail fiber protein C (LtfC) and related phage proteins. This domain folds into a beta-sandwich fold with and extended beta-hairpin that projects away from it. The minor tail proteins Gp6 are likely involved in the assembly or function of the tail structure in bacteriophages. The collar protein p132 forms the T5 phage collar structure, which serves as an anchoring point for the side tail fiber protein pb1, suggesting a role in stabilising the tail fibers and ensuring proper attachment to the host cell. The lateral tail fiber protein C (LtfC) is a component of the DT57C bacteriophage tail tip complex where it forms a dodecameric ring. LtfC adopts a compact, single-domain structure. The LtfC ring is complemented by another lateral tail fiber protein, LtfA. Each of the LtfA monomers is connected to the LtfC assembly in a unique way by augmenting the edges of LtfC beta-sheets with two short beta-strands and thus completing the LtfC beta-sandwich structure.
Pfam PF03506: Influenza C non-structural protein (NS1) (family)
The influenza C virus genome consists of seven single-stranded RNA segments. The shortest RNA segment  encodes a 286 amino acid non-structural protein NS1. This protein contains 6 conserved cysteines that may be functionally important, perhaps binding to a metal ion.
Pfam PF17459: Family of unknown function (DUF5422) (family)
This is a family of unknown function found in Chlamydia. Members of this family have 1-4 predicted trans-membrane regions.
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 PF01554: MatE (family)
The MatE domain
Wikipedia: The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) flippase superfamily is a group of integral membrane protein families. The MOP flippase superfamily includes twelve distantly related families, six for which functional data are available:One ubiquitous family (MATE) specific for drugs - (TC# 2.A.66.1) The Multi Antimicrobial Extrusion (MATE) Family
One (PST) specific for polysaccharides and/or their lipid-linked precursors in prokaryotes - (TC# 2.A.66.2) The Polysaccharide Transport (PST) Family
One (OLF) specific for lipid-linked oligosaccharide precursors of glycoproteins in eukaryotes - (TC# 2.A.66.3) The Oligosaccharidyl-lipid Flippase (OLF) Family
One (MVF) lipid-peptidoglycan precursor flippase involved in cell wall biosynthesis - (TC# 2.A.66.4) The Mouse Virulence Factor (MVF) Family
One (AgnG) which includes a single functionally characterized member that extrudes the antibiotic, Agrocin 84 - (TC# 2.A.66.5) The Agrocin 84 Antibiotic Exporter (AgnG) Family
And finally, one (Ank) that shuttles inorganic pyrophosphate (PPi) - (TC# 2.A.66.9) The Progressive Ankylosis (Ank) Family
Pfam PF00127: Copper binding proteins, plastocyanin/azurin family (domain)
The small blue proteins are single-domain proteins. The domain consists of a Î²-sheet sandwich, composed of eight strands in two sheets, and has predominantly antiparallel Î²-strand topology . This entry represents the blue copper domain.
Blue (type 1) copper proteins constitute a diverse class of proteins, including small blue proteins and multicopper oxidases. They bind copper and are characterised by an intense electronic absorption band near 600 nm .

The most well known members of this class of proteins are the small blue proteins, which includes azurins and plastocyanins. It is a group of monomeric proteins which contain one copper ion per molecule. The plant chloroplastic plastocyanins exchange electrons with cytochrome c6, and the distantly related bacterial azurins exchange electrons with cytochrome c551. This group also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus ; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings ; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) , a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans ; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. This pollen protein is evolutionary related to the above proteins, but seems to have lost the ability to bind copper.
Wikipedia: Azurin is a small, periplasmic, bacterial blue copper protein found in Pseudomonas, Bordetella, or Alcaligenes bacteria. Azurin moderates single-electron transfer between enzymes associated with the cytochrome chain by undergoing oxidation-reduction between Cu(I) and Cu(II). Each monomer of an azurin tetramer has a molecular weight of approximately 14kDa, contains a single copper atom, is intensively blue, and has a fluorescence emission band centered at 308 nm.
Pfam PF00802: Pneumovirus attachment glycoprotein G (family)
This family includes attachment proteins from respiratory synctial virus.  Glycoprotein G has not been shown to have any neuraminidase or hemagglutinin activity (Swiss-Prot). The amino terminus is thought to be cytoplasmic, and the carboxyl terminus extracellular.  The extracellular region contains four completely conserved cysteine residues.
Wikipedia: Respiratory syncytial virus G protein is a glycoprotein produced by respiratory syncytial virus. Some features of the G protein suggest it could be important to respiratory syncytial virus vaccine or antiviral drug target design.
Pfam PF09358: Ubiquitin fold domain (domain)
The ubiquitin fold domain is found at the C-terminus of ubiquitin-activating E1 family enzymes. This domain binds to E2 enzymes.
Pfam PF14512: Putative TM nitroreductase (family)
Compared with the more traditional NADH oxidase/flavin reductase family, this family is a duplication, consisting of two similar domains arranged as the subunits of the dimeric NADH oxidase/flavin reductase with one conserved active site.
Wikipedia: Nitroreductases are a family of evolutionarily related proteins involved in the reduction of nitrogen-containing compounds, including those containing the nitro functional group. Members of this family utilise flavin mononucleotide as a cofactor and are often found to be homodimers.
Pfam PF10588: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (domain)
This entry represents the iron-sulphur binding domain of the G subunit. This domain consists of just two Î±-helices separated by a loop region that coordinates a  cluster through an unusual H-x(3)-C-x(2)-C-x(5)-C motif that includes one His and three Cys residues .
This domain is found in the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. It is also found in subunits from formate dehydrogenase complexes, in particular, the NADP(+)-dependent formate dehydrogenase subunit alpha which is involved in the NADP-dependent reduction of CO2 to format .
Pfam PF17718: Family of unknown function (DUF5563) (family)
This is a family of unknown function found in chordata.
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 PF23471: Cap15, TM helices (domain)
This entry includes CD-NTase-associated protein 15 (Cap15), an effector protein of a CBASS antivirus system. These proteins occur in conserved genome contexts with the SMODS nucleotide synthetase. Cap15 consists of two transmembrane segments (TM) at the N-terminal, represented in this entry, and a compact eight-stranded beta-barrel scaffold that forms a cyclic dinucleotide receptor domain ([pfam:PF18153]) which oligomerises upon activation. Activated Cap15 binds the cyclic nucleotide second messenger 3',3'-cGAMP, re localizes throughout the cell and specifically induces rupture of the inner membrane.
Pfam PF03750: Csm2 Type III-A (family)
Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features.  This family is known as CRISPR (short for Clustered Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-associated) proteins. This entry represents Csm2 Type III-A, a family of Cas proteins also known as TM1810/Csm2.
Wikipedia: CRISPR is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. Each sequence within an individual prokaryotic cell is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes and provide a form of heritable, acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
Pfam PF09771: Transmembrane protein 188 (family)
The function of this family of transmembrane proteins has not, as yet, been determined.
Pfam PF20307: Divergent DnaB-like ATPase (domain)
This domain is found in a divergent DnaB-like helicase of the RecA-ATP-synthetase superfamily of P-loop NTPases found in phages, which is characterised by a modified ATP-binding Walker B motif.
Pfam PF08421: Putative zinc binding domain (domain)
This domain is found at the N-terminus of bacterial methyltransferases and contains four conserved cysteines suggesting a potential zinc binding domain.
Pfam PF10991: Enterobacter phage Enc34, ssDNA-binding protein (domain)
ssDNA-binding protein from Enterobacter phage Enc34 ([swissprot:H6WYG2]) shows a globular shape with a mixed alpha/beta architecture consisting mainly of beta-strands that clearly resembles the oligosaccharide/ oligonucleotide-binding (OB)-fold. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Pfam PF05264: Choristoneura fumiferana antifreeze protein (CfAFP) (family)
This family consists of several antifreeze proteins from the insect Choristoneura fumiferana (Spruce budworm). Antifreeze proteins (AFPs) and  antifreeze glycoproteins (AFGPs) are present in many organisms that must survive sub-zero temperatures. These proteins bind to seed ice crystals and inhibit their growth through an adsorption-inhibition mechanism.
Wikipedia: Antifreeze proteins (AFPs) or ice structuring proteins refer to a class of polypeptides produced by certain animals, plants, fungi and bacteria that permit their survival in temperatures below the freezing point of water. AFPs bind to small ice crystals to inhibit the growth and recrystallization of ice that would otherwise be fatal. There is also increasing evidence that AFPs interact with mammalian cell membranes to protect them from cold damage. This work suggests the involvement of AFPs in cold acclimatization.
Pfam PF00754: F5/8 type C domain (domain)
This domain is also known as the discoidin (DS) domain family.
Wikipedia: Discoidin domain is major protein domain of many blood coagulation factors.
Pfam PF21638: SDA1, C-terminal (domain)
This entry includes SDA1 protein and its homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability. It is a HEAT repeat-containing protein, required for 60S pre-ribosomal subunits export to the cytoplasm and may also be required for 60S ribosomal subunit maturation and accumulation. This entry represents the C-terminal region of SDA1 proteins.
Pfam PF22220: Quiescin sulphydryl oxidase pseudo-Erv domain (domain)
Quiescin sulphydryl oxidase (QSOX) family of enzymes is the only known example of conserved concatenation of disulphide-generating and disulphide-transferring modules within a single polypeptide. Formation and transfer of disulphide bonds in QSOX are mediated by redox-active cysteine pairs in a canonical Cys-X-X-Cys pattern. One of these pair is in the N-terminal thioredoxin-like domain (Trx1). Another is in the C-terminal flavin adenine dinucleotide (FAD)-binding domain (Erv) related to the mitochondrial enzyme Erv1. The middle domain, the so-called pseudo-Erv domain, bridges the Trx1 and Erv domains and is structurally similar to the Erv domain.
Pfam PF00186: Dihydrofolate reductase (domain)
Dihydrofolate reductase (DHFR) (1.5.1.3) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, which can be used inde novosynthesis both certain amino acids, purines and deoxythymidine phosphate (the precursors of DNA synthesis) , and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood .

Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar . The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown  to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself .
Wikipedia: Dihydrofolate reductase, or DHFR, is an enzyme that reduces dihydrofolic acid to tetrahydrofolic acid, using NADPH as an electron donor, which can be converted to the kinds of tetrahydrofolate cofactors used in one-carbon transfer chemistry. In humans, the DHFR enzyme is encoded by the DHFR gene. It is found in the q14.1 region of chromosome 5.
Pfam PF21870: GP180, GOLD domain (domain)
This entry represents the GOLD domain from GPR180, which is associated with TGF-beta signaling, as it regulates the activity of the TGF-beta receptor complex through SMAD3 phosphorylation. Furthermore, GPR180 is also required for the action of Collagen triple helix repeat containing 1 (CTHRC1) to regulate brown and beige adipocyte activity and glucose homeostasis. GPR180 was first to be an orphan Rhodopsin-like GPCR given structural similarities to GPCR transmembrane region, however, it was then confirmed not to signal as a a GPCR. GPR180 is homologous to TMEM145, TMEM181 and WLS, which have been described as GOST proteins (for GOLD domain seven-transmembrane helix proteins) together with TMEM87A/B, GPR107 and GPR108, given they share the same domain architecture consisting of a GOLD domain atop of a membrane-spanning seven-transmembrane helix domain.
Pfam PF09610: Mycoplasma virulence signal region (Myco_arth_vir_N) (domain)
This entry represents the N-terminal region of a family of large, virulence-associated proteins in Mycoplasma arthritidis and smaller proteins in Mycoplasma capricolum. It includes a probable signal sequence or signal anchor, which, in most instances, has four consecutive Lys residues before the hydrophobic stretch.
Pfam PF13283: Bacteriophage N adsorption protein A C-term (family)
The function of this domain is unknown but it is found at the C-terminus of bacteriophage N4 adsorption protein A, in association with an N-terminal region of TPR repeats.
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 PF15728: Domain of unknown function (DUF4679) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 213 and 412 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 PF16279: Domain of unknown function (DUF4927) (family)
This family, around 80 residues, consists of uncharacterized and nuclear receptor coactivator 2 proteins and is mainly found in mammalia species. The specific function of this family is still unknown.
Pfam PF10941: Protein of unknown function DUF2620 (family)
This is a bacterial family of proteins with 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 PF20464: MmeI, N-terminal 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). This domain corresponds to the N-terminal endonuclease, it cuts the two DNA strands at one site simultaneously with enzyme bound at two sites interacting to accomplish the cleavage.