SII-SWORD/CoKE huggingface dataset:
Pfam PF12098: Protein of unknown function (DUF3574) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are typically between 144 to 163 amino acids in length. This protein has a conserved TPRF sequence motif.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF16183: Kinesin-associated (family)
This short domain is found in some kinesin-like proteins (KIF1, KIF13, KIF14). It is found between the motor domain (IPR001752) and the forkhead-associated (FHA) domain (IPR000253). Its function is unknown.
Pfam PF23370: Capsid protein Vp20 (family)
This entry represents the capsid protein Vp20 from apple-latent spherical virus (ALSV) and related picorna-like plant viruses. This protein is encoded in a polyprotein that is cleaved into three capsid proteins, Vp25, Vp20 and Vp24, which all have jellyroll folds and form one protomer; 60 copies of this unit compose one virion. Vp25, Vp20 and Vp24 contribute to capsid stabilization. Vp25 and Vp20 form more extensive interactions with their neighbours and likely form a rigid capsid frame that supports the looser Vp24 protrusions.
Pfam PF11858: Domain of unknown function (DUF3378) (family)
This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 80 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 PF16473: 3'-5' exoribonuclease Rv2179c-like domain (domain)
This is a highly divergent 3' exoribonuclease family. The proteins constitute a typical RNase fold, where the active site residues form a magnesium catalytic centre. The protein of the solved structure readily cleaves 3' overhangs in a time-dependent manner. It is similar to DEDD-type RNases and is an unusual ATP-binding protein that binds ATP and dATP. It forms a dimer in solution and both protomers in the asymmetric unit bind a magnesium ion through Asp-6 in SwissProt:P9WJ73. Proteins containing this domain also include 3'-5' exonuclease dexA from bacteriophage T4. It may play a role in the final step of host DNA degradation, by scavenging DNA into mononucleotides.
Pfam PF00373: FERM central domain (domain)
This domain is the central structural domain of the FERM domain.
Wikipedia: In molecular biology, the FERM domain is a widespread protein module involved in localising proteins to the plasma membrane. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus in the majority of proteins in which it is found.
Pfam PF06128: Shigella flexneri OspC protein (family)
This family consists of the Shigella flexneri specific protein OspC. The function of this family is unknown but it is thought that Osp proteins may be involved in post invasion events related to virulence. Since bacterial pathogens adapt to multiple environments during the course of infecting a host, it has been proposed that Shigella evolved a mechanism to take advantage of a unique intracellular cue, which is mediated through MxiE, to express proteins when the organism reaches the eukaryotic cytosol.
Pfam PF02442: Lipid membrane protein of large eukaryotic DNA viruses (family)
The four families of large eukaryotic DNA viruses, Poxviridae, Asfarviridae, Iridoviridae, and Phycodnaviridae, referred to collectively as nucleocytoplasmic large DNA viruses or NCLDV, have all been shown to have a lipid membrane, in spite of the major differences in virion structure. The paralogous genes L1R and F9L encode membrane proteins that have a conserved domain architecture, with a single, C-terminal transmembrane helix, and an N-terminal, multiple-disulfide-bonded domain. The conservation of the myristoylated, disulfide-bonded protein L1R/F9L in most of the NCLDV correlates with the conservation of the thiol-disulfide oxidoreductase E10R which, in vaccinia virus, is required for the formation of disulfide bonds in L1R and F9L.
Pfam PF19458: Family of unknown function (DUF5995) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000354) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This  includes a protein from the friulimicin A biosynthetic gene  cluster from Actinoplanes friuliensis.
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 PF10129: OpgC protein (family)
This domain, found in various hypothetical and OpgC prokaryotic proteins. It is likely to act as an acyltransferase enzyme.
Pfam PF09732: Cactus-binding C-terminus of cactin protein (domain)
CactinC_cactus is the C-terminal 200 residues of the cactin protein which are necessary for the association of cactin with IkappaB-cactus as one of the intracellular members of the Rel complex. The Rel (NF-kappaB) pathway is conserved in invertebrates and vertebrates. In mammals, it controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo. Most members of the family also have a Cactin_mid domain [pfam:PF10312] further upstream.
Pfam PF17886: HSP20-like domain found in ArsA (domain)
This domain is found at the C-terminus of ArsA like proteins. This domain is related to HSP20.
Pfam PF10115: Transcriptional activator HlyU (family)
This domain, found in various hypothetical prokaryotic proteins, has no known function. One of the sequences in this family corresponds to the transcriptional activator HlyU, indicating a possible similar role in other members.
Pfam PF20259: tRNA methyl transferase PRC-barrel domain (domain)
This family represents a central PRC-barrel domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs.
Pfam PF06315: Isocitrate dehydrogenase kinase/phosphatase (AceK) kinase domain (domain)
This the C-terminal protein kinase domain of bacterial isocitrate dehydrogenase kinase/phosphatase (AceK) proteins ([ec:2.7.1.116]). It has a classic bi-lobe protein kinase fold with the ATP-binding cleft located at the interface between the two lobes. The N-terminal lobe comprises a twisted antiparallel beta-sheet of five strands and two alpha-helices. The C-terminal lobe is larger and mainly alpha-helical, with some stretches of antiparallel beta-strands.
Pfam PF23450: KIAA2026 helical domain (domain)
This entry represents an helical domain found in the uncharacterised protein KIAA2026 from human and similar sequences, whose function is currently unknown. This domain is found towards the N-terminal and may adopt an all-helical structure.
Pfam PF08121: Waglerin family (family)
This family consists of the lethal peptides (waglerins)  that are found in the venom of Trimeresurus wagleri.  Waglerins are 22-24 residue lethal peptides and are  competitive antagonist of the muscle nicotinic receptor  (nAChR). Waglerin-1 possesses a distinctive selectivity  for the alpha-epsilon interface binding site of the mouse  nAChR.
Pfam PF05678: VQ motif (conserved_site)
This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor [swissprot:Q9LDH1]. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors (Bateman A pers. obs.).
Pfam PF10965: Protein of unknown function (DUF2767) (family)
This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
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 PF20450: Papillomavirus E1, DNA-binding domain (domain)
This is the DNA-binding domain (DBD) of Papillomavirus E1 protein, a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein [pfam:PF00508] at the origin of replication (ori). This domain is found in the central region of E1 and binds DNA at specific sites of viral origin, and also binds cooperatively with E2-DBD. This domain comprises a five-stranded antiparallel beta-sheet flanked by alpha helices on each side. This domain binds originally as a dimer in which each monomer binds to one half-site of the palindromic E1 binding site, and promotes the  assembly of the hexameric helicase on the ori. E1 has a domain architecture and function similar to SV40 T-antigen.
Pfam PF22240: Type ISP restriction-modification enzyme, coupler domain (domain)
Type ISP restriction-modification (RM) enzymes cleave random DNA between distant target sites when two enzymes collide following convergent ATP-driven translocation. This entry represents the all-helical coupler domain of type ISP RM enzymes, which links the ATPase to the MTase and the C-terminal TRD (target recognition domain) domains and seems to play a key role in transferring conformational strain during initiation.
Pfam PF02374: Anion-transporting ATPase (domain)
This Pfam family represents a conserved domain, which is sometimes repeated, in an anion-transporting ATPase. The ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell.
Wikipedia: Arsenite resistance (Ars) efflux pumps of bacteria may consist of two proteins, ArsB and ArsA, or of one protein. ArsA proteins have two ATP binding domains and probably arose by a tandem gene duplication event. ArsB proteins all possess twelve transmembrane spanners and may also have arisen by a tandem gene duplication event. Structurally, the Ars pumps resemble ABC-type efflux pumps, but there is no significant sequence similarity between the Ars and ABC pumps. When only ArsB is present, the system operates by a pmf-dependent mechanism, and consequently belongs in TC subclass 2.A. When ArsA is also present, ATP hydrolysis drives efflux, and consequently the system belongs in TC subclass 3.A. ArsB therefore appears twice in the TC system but ArsA appears only once. These pumps actively expel both arsenite and antimonite.
Pfam PF20332: Family of unknown function (DUF6627) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 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 PF17190: RecG N-terminal helical domain (domain)
This four helical bundle domain is found at the N-terminus of bacterial RecG proteins.
Pfam PF22357: AF1548-like, C-terminal (domain)
This domain is found at the C-terminal end of the uncharacterised protein AF_1548 from Archaeoglobus fulgidus and similar prokaryotic proteins. This domain is often found associated with [pfam:PF04471].
Pfam PF16085: Bacteriophage holin Hol, superfamily III (family)
Phage_holin_6_2 is a family of holins classified as 1.E.20 in the TC database. The hol gene (PRF9) product (117 aas) of Pseudomonas aeruginosa PAO1 exhibits a hydrophobicity profile similar to holins of P2 and phiCTX phages with two peaks of hydrophobicity that might correspond to either one or two TMSs. Hol functions in conjunction with the lytic enzyme, Lys, a glycosyl hydrolase that breaks-up the murein in the bacterial cell-wall, causing lysis of the cell and hence entry of phage particles. Several members are annotated as pyocin R2_PP when encoded on the chromosome.
Pfam PF05502: Dynactin p62 family (family)
Dynactin is a multi-subunit complex and a required cofactor for most, or all, of the cellular processes powered by the microtubule-based motor cytoplasmic dynein. p62 binds directly to the Arp1 subunit of dynactin.
Wikipedia: Dynactin is a 23 subunit protein complex that acts as a co-factor for the microtubule motor cytoplasmic dynein-1. It is built around a short filament of actin related protein-1 (Arp1).
Pfam PF13305: Tetracyclin repressor-like, C-terminal domain (domain)
This domain is around 80 amino acids in length.  It is found to the C-terminus of a DNA-binding helix-turn-helix domain. This domain may be involved transcriptional regulation predicted to belong to the TetR family. This domain contains three conserved residues (WHG) near the C-terminus.
Pfam PF06191: Protein of unknown function (DUF995) (family)
Family of uncharacterised Proteobacteria 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 PF18745: Secreted Novel AID/APOBEC-like Deaminase 2 (family)
A family of secreted AID/APOBEC like deaminases found in ray-finned fishes.
Pfam PF02086: D12 class N6 adenine-specific DNA methyltransferase (family)
In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. There are 2 major classes of DNA methyltransferase that differ in the nature of the modifications they effect. The members of one class (C-MTases) methylate a ring carbon and form C5-methylcytosine (see IPR001525). Members of the second class (N-MTases) methylate exocyclic nitrogens and form either N4-methylcytosine (N4-MTases) or N6-methyladenine (N6-MTases). Both classes of MTase utilise the cofactor S-adenosyl-L-methionine (SAM) as the methyl donor and are active as monomeric enzymes .

N-6 adenine-specific DNA methylases (2.1.1.72) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. Such enzymes are found in the three existing types of bacterial restriction-modification systems (in type I system the A-Mtase is the product of the hsdM gene, and in type III it is the product of the mod gene). All of these enzymes recognise a specific sequence in DNA and methylate an adenine in that sequence. It has been shown  that A-Mtases contain a conserved motif Asp/Asn-Pro-Pro-Tyr/Phe in their N-terminal section, this conserved region could be involved in substrate binding or in the catalytic activity. The structure of N6-MTase TaqI (M.TaqI) has been resolved to 2.4 A . The molecule folds into 2 domains, an N-terminal catalytic domain, which contains the catalytic and cofactor binding sites, and comprises a central 9-stranded Î²-sheet, surrounded by 5 helices; and a C-terminal DNA recognition domain, which is formed by 4 small Î²-sheets and 8 Î±-helices. The N- and C-terminal domains form a cleft that accommodates the DNA substrate. A classification of N-MTases has been proposed, based on conserved motif (CM) arrangements . According to this classification, N6-MTases that have a DPPY motif (CM II) occuring after the FxGxG motif (CM I) are designated D12 class N6-adenine MTases.
Wikipedia: In biochemistry, the DNA methyltransferase family of enzymes catalyze the transfer of a methyl group to DNA. DNA methylation serves a wide variety of biological functions. All the known DNA methyltransferases use S-adenosyl methionine (SAM) as the methyl donor.
Pfam PF18193: Fibrillin 1 unique N-terminal domain (domain)
This is the N-terminal domain of human fibrillin-1. Fibrillin is a primary constituent of microfibrils in the extracellular matrix of many elastic and non-elastic connective tissues. This domain, known as the fibrillin unique N-terminal (FUN) domain, constitutes the minimal interaction site for the fibrillin C terminus. The FUN domain has homologs in the human proteins LTBP-1L/2 and VWCE, which are also associated with a C-terminal EGF-like domain.
Pfam PF00908: dTDP-4-dehydrorhamnose 3,5-epimerase (domain)
This family catalyse the isomerisation of dTDP-4-dehydro-6-deoxy -D-glucose with dTDP-4-dehydro-6-deoxy-L-mannose. The EC number of this enzyme is 5.1.3.13.
Wikipedia: In enzymology, a dTDP-4-dehydrorhamnose 3,5-epimerase is an enzyme that catalyzes the chemical reactiondTDP-4-dehydro-6-deoxy-D-glucose  dTDP-4-dehydro-6-deoxy-L-mannose
Pfam PF20314: Family of unknown function (DUF6610) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 304 and 335 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 PF11658: Cellulose biosynthesis protein BcsG (family)
CBP_BcsG is a component of bacterial cellulose synthase complex that plays a role in biofilm formation in bacteria. It is a Zn(2+)-dependent phosphoethanolamine transferase that catalyses transfer of phosphoethanolamine residues from membrane phosphatidylethanolamine  to the glucosyl residues in the nascent cellulose chain.
Pfam PF23693: YmgM (family)
This protein family includes Protein YmgM from Escherichia coli, a 67-residue long sequence.
Pfam PF24820: Diguanylate cyclase-like sensor domain (domain)
This entry represents a sensor domain found at the N-terminal of the putative diguanylate cyclase from Shewanella oneidensis, whose structure was solved (PDBe:3mfx).
Pfam PF22612: Glycoside Hydrolase Family 113 (family)
This family includes Endo-beta-1,4-mannanase from Alicyclobacillus acidocaldarius and similar bacterial sequences that belong to the Glycoside Hydrolase Family 113 (GH113). It shows a (beta/alpha)8 -barrel fold.
Pfam PF04570: zinc-finger of the FCS-type, C2-C2 (domain)
zf-FLZ is a FCS-like zinc-finger domain found in higher plants. It is bryophitic in origin. It carries a zf-FCS-like C2-C2 zinc finger, consisting of a consensus cysteine-signature sequence with conserved phenyl alanine and serine residue associated with a third cysteine. It acts as a protein-protein interaction module.
Pfam PF19042: Nuclear cap binding complex subunit CBP110 (family)
This entry represents the CBP110 component of the trypanasome nuclear cap binding complex. Trypanosomes have a different cap 4 structure for mRNAs. CBP110 is part of the complex that recognises this cap.
Pfam PF03194: LUC7 N_terminus (family)
This family contains the N terminal region of several LUC7 protein homologues and only contains eukaryotic proteins. LUC7 has been shown to be a U1 snRNA associated protein with a role in splice site recognition. The family also contains human and mouse LUC7 like (LUC7L) proteins and human cisplatin resistance-associated overexpressed protein (CROP).
Pfam PF13123: Protein of unknown function (DUF3978) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length.
Pfam PF17235: STD1/MTH1 (family)
This family of proteins includes the known homologues STD1 (also known as MSN3) and MTH1. Both STD1 and MTH1 are involved in modulating the expression of glucose-regulated genes in yeast, but have been shown to function by slightly different methods. It has been suggested that both STD1 and MTH1 are required to repress the hexose transporter genes in low glucose conditions. STD1 has also been shown to stimulate SNF1 kinase through interaction with the catalytic domain of SNF1, antagonising auto-inhibition and promoting an active conformation of the kinase.
Pfam PF00686: Starch binding domain (family)
This entry represents CBM20, which binds starch. The crystal structure of CBM20 has been solved . It consists of seven Î²-strands forming an open-sided distorted Î²-barrel. Several aromatic residues, especially the well-conserved Trp and Tyr residues, participate in granular starch binding.
A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins.

CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose . However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology.

Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see .
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.