SII-SWORD/CoKE huggingface dataset:
Pfam PF19394: Family of unknown function (DUF5969) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000604) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
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 PF03400: IS1 transposase (family)
Transposase proteins are necessary for efficient DNA transposition. This family represents bacterial IS1 transposases.
Pfam PF15359: Carnitine deficiency-associated protein 3 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 128 and 251 amino acids in length. CDV3 is also known as TPP36 - tyrosine-phosphorylated protein 36. The function is not known.
Pfam PF05149: Paraflagellar rod protein (family)
This family consists of several eukaryotic paraflagellar rod component proteins. The eukaryotic flagellum represents one of the most complex macromolecular structures found in any organism and contains more than 250 proteins. In addition to its locomotive role, the flagellum is probably involved in nutrient uptake since receptors for host low-density lipoproteins are localised on the flagellar membrane as well as on the flagellar pocket membrane.
Pfam PF01557: Fumarylacetoacetate (FAA) hydrolase C-terminal (domain)
This entry consists of fumarylacetoacetate (FAA) hydrolase,  or fumarylacetoacetate hydrolase (FAH) and it also includes  HHDD isomerase/OPET decarboxylase from E. coli strain W.    FAA is the last enzyme in the tyrosine catabolic pathway, it hydrolyses fumarylacetoacetate into fumarate and acetoacetate which then join the  citric acid cycle. Mutations in FAA cause type I tyrosinemia in humans this is an inherited disorder mainly affecting the liver leading to  liver cirrhosis, hepatocellular carcinoma, renal tubular damages and  neurologic crises amongst other symptoms. The enzymatic defect causes the toxic accumulation of phenylalanine/tyrosine catabolites. The E. coli W enzyme HHDD isomerase/OPET decarboxylase contains two copies of this domain and functions in fourth and fifth steps of the homoprotocatechuate pathway; here it decarboxylates OPET to HHDD and isomerises this to OHED.  The final products of this pathway are pyruvic acid and succinic  semialdehyde. This family also includes various hydratases and 4-oxalocrotonate decarboxylases which are involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds. 2-hydroxypentadienoic acid hydratase encoded by mhpD in E. coli [swissprot:P77608] is involved in the phenylpropionic acid pathway of E. coli and catalyses the conversion of 2-hydroxy pentadienoate to 4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor. OHED hydratase encoded by hpcG in E. coli [swissprot:P42270] is involved  in the homoprotocatechuic acid (HPC) catabolism. XylI in P. putida [swissprot:P49155] is a 4-Oxalocrotonate decarboxylase.
Pfam PF19417: RNase LS, bacterial toxin N-terminal (domain)
RnlA_toxin is an RNase LS and a putative toxin of a bacterial toxin-antitoxin pair. Toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of cell growth and rapidly degrades T4 late mRNAs to prevent their expression, and this is neutralised by the activity of the unstable antitoxin RnlB. This entry represents the N-terminal domain composed of four-stranded twisted antiparallel beta-sheet and two alpha-helices.
Pfam PF24242: Domain of unknown function (DUF7449) (domain)
This entry represents a small family of uncharacterised proteins found in pseudomonas phage.  The protein contains a compact domain composed of two alpha helices followed by four beta strands that form a beta sheet.
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 PF18438: Glycosyl hydrolases family 38 C-terminal domain 1 (domain)
The enzymatic hydrolysis of alpha-mannosides is catalyzed by glycoside hydrolases (GH), termed alpha-mannosidases. Streptococcal (Sp) GH38 alpha-mannosidase active on N-glycans and possibly O-glycans. SpGH38 structure can be considered as five domains: an N-terminal alpha/beta-domain, a three-helix bundle and three predominantly beta-sheet domains. This is the first of the three beta-sheet domains found in GH38, termed Beta-1. Structural analysis indicate that the beta-1 domain bows outward from the protein core, is involved in dimer interactions whilst also forming a lid 'above' and somewhat into the active centre of its dimer.
Pfam PF02677: Epoxyqueuosine reductase QueH (family)
The reduction of epoxyqueuosine (oQ) is the last step in the synthesis of the tRNA modification queuosine (Q). members of this family were predicted to encode for an alternative epoxyqueuosine reductase. Furthermore, it has been suggested that family members are a non-orthologous replacement of queG, responsible for oQ to Q conversion. QueH contains conserved cysteines that could be involved in the coordination of a Fe/S center in a similar fashion to what has been identified in QueG. No cobalamin was identified associated with recombinant QueH protein, indicating that the reduction activity is independent from cobalamin.
Pfam PF21713: Cyclic GMP-AMP synthase, C-terminal domain (domain)
This domain is found  Cyclic GMP-AMP synthase from Vibrio cholerae (DncV), a prokaryotic cGAS-like enzyme that synthesises cyclic GMP- AMP (c-GAMP) and stimulates intestinal colonization. DncV adopts a structure and topology that are typical of the nucleotidyltransferase superfamily. It is organised into two domains: an N-terminal domain that contains the catalytic loop ([pfam:PF21654]) and a C- terminal helix bundle that consists of eight helices and one pair of anti-parallel beta-sheets (this entry).
Pfam PF00857: Isochorismatase domain (domain)
This is a domain found in hydrolase enzymes. This domain is responsible for the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate. It shows a typical helix-sheet-helix sandwich structural architecture, with a central beta--sheet made of six parallel strands, three alpha -helices on one side and two on the other.
Pfam PF21512: Inositol-tetrakisphosphate 1-kinase, preATP-grasp domain (domain)
Inositol-tetrakisphosphate 1-kinase (ITPK1)  can phosphorylate various inositol polyphosphate such as Ins(3,4,5,6)P4 or Ins(1,3,4)P3. Phosphorylates Ins(3,4,5,6)P4 at position 1 to form Ins(1,3,4,5,6)P5 which may play a regulatory function. It may also act as an isomerase. This entry represents the preATP-grasp domain.
Pfam PF10042: Uncharacterized conserved protein (DUF2278) (family)
Members of this family of hypothetical bacterial proteins have no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF07345: ATPase inhibitor subunit zeta (domain)
This entry represents zeta-subunits, which are found in alpha-proteobacterial F1F0-ATPase regulatory proteins. The zeta subunit is a potent inhibitor of the alpha-proteobacterial F1FO-ATPase. The inhibitory region resides in the first 14 N-terminal residues of the protein, which protrude from the 4-alpha-helix bundle structure of the isolated zeta subunit.
Pfam PF10681: Chaperone for protein-folding within the ER, fungal (family)
This conserved fungal family is an essential molecular chaperone in the endoplasmic reticulum. Molecular chaperones transiently interact with unfolded proteins to inhibit their self-aggregation and to support their folding and/or assembly. Rot1 is a general chaperone with some substrate specificity, its substrates being the structurally unrelated Kre5 Kre6 Big1 Atg22, which are type I, type II, and polytopic membrane proteins. The dependencies of each for Rot1 do not share similarities. However, their folding does require BiP, and one of these proteins was simultaneously associated with both Rot1 and BiP. In addition, Rot1 may cooperate with BiP/Kar2 in the folding of Kre6.
Pfam PF02205: WH2 motif (conserved_site)
The WH2 motif (for Wiskott Aldrich syndrome homology region 2) has been shown in WASP [swissprot:P42768] and Scar1 (mammalian homologue) to be the region that interacts with actin.
Pfam PF12188: Signal transducer and activator of transcription 2 C terminal (domain)
This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with [pfam:PF02865], [pfam:PF00017], [pfam:PF01017], [pfam:PF02864]. There is a conserved DLP sequence motif. STATs are involved in transcriptional regulation and are the only regulators known to be modulated by tyrosine phosphorylation. STAT2 forms a trimeric complex with STAT1 and IRF-9 (Interferon Regulatory Factor 9), on activation of the cell by interferon, which is called ISGF3 (Interferon-stimulated gene factor 3). The C terminal domain of STAT2 contains a nuclear export signal (NES) which allows export of STAT2 into the cytoplasm along with any complexed molecules.
Pfam PF02031: Streptomyces extracellular neutral proteinase (M7) family (domain)
This group of metallopeptidases belong to the MEROPS peptidase family M7 (snapalysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA.

With a molecular weight of around 16kDa, Streptomyces extracellular neutral protease is one of the smallest known proteases ; it is capable of hydrolysing milk proteins . The enzyme is synthesised as a proenzyme with a signal peptide, a propeptide and an active domain that contains the conserved HEXXH motif characteristic of metalloproteases. Although family M7 shows active site sequence similarity to other members, it differs in one major respect: the third zinc ligand appears to be an aspartate residue rather than the usual histidine.
Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role. Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .
Pfam PF20819: T4 RNA ligase 1, C-terminal domain (domain)
This domain is found at the C-terminal end of T4 RNA ligase 1 (Rnl1) from Bacteriophage T4 and similar proteins from tailed bacteriophages. Rnl1 is involved in countering a host defense mechanism by repairing tRNA. The C-terminal domain shows an all alpha-helical fold and has a charge distribution and architecture for helix-nucleic acid groove interaction compatible with tRNA binding. It confers specificity for the repair of tRNAs with breaks in the anticodon loop.
Pfam PF21776: TetR/AcrR family transcriptional repressors, C-terminal domain (domain)
TetR/AcrR family transcriptional repressors regulate a wide range of cellular activities, including multidrug resistance, virulence and pathogenicity of bacteria. Members of this family are two domain proteins consisting of N-terminal HTH DNA-binding domain and C-terminal ligand recognition domain. This entry represents the C-terminal domain that besides the ligand recognition, is involved in dimerisation. In contrast to the N-terminal domain, this domain is more diverse allowing different regulators in the TetR/AcrR family to accommodate specific sets of inducing ligands.
Pfam PF10151: TMEM214, C-terminal, caspase 4 activator (family)
This is the N-terminal domain of transmembrane family 214, from eukaryotes. The family is localised on the endoplasmic reticulum where it recruits procaspase 4 to the ER and subsequently allows this to be cleaved to caspase 4 so leading to apoptosis.
Pfam PF05630: Necrosis inducing protein (NPP1) (family)
This family consists of several NPP1 like necrosis inducing proteins from oomycetes, fungi and bacteria. Infiltration of NPP1 into leaves of Arabidopsis thaliana plants result in transcript accumulation of pathogenesis-related (PR) genes, production of ROS and ethylene, callose apposition, and HR-like cell death.
Pfam PF12774: Hydrolytic ATP binding site of dynein motor region (domain)
This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities: AAA1-AAA6). This is the first site (out of four nucleotide binding sites in the dynein motor) where the movement depends on ATP hydrolysis. When this site is nucleotide free or bound to ADP, the microtubule binding domain (MTBD) binds to the microtubule and the linker adopts the straight post-power-stroke conformation. Upon ATP binding and hydrolysis, the MTBD detaches from the microtubule and the linker is primed into the pre-power-stroke conformation. Dynein's AAA+ domains are each divided into an alpha/beta large subdomain designated with an L and and alpha small subdomains designated with an S. This is the AAA1 large (AAA1L) subdomain with the accompanying small subdomain (AAA1S). AAA1L, AAA1S and AAA2L enclose ADP.vanadate (ADP.Vi, ATP-hydrolysis transition state analogue). The AAA1L sensor-I loop, which varies in position depending on dynein's nucleotide state, swings in to contact AAA2L forming the important AAA1 nucleotide-binding site.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF00388: Phosphatidylinositol-specific phospholipase C, X domain (family)
This associates with [pfam:PF00387] to form a single structural unit.
Wikipedia: Phosphoinositide phospholipase C is a family of eukaryotic intracellular enzymes that play an important role in signal transduction processes. These enzymes belong to a larger superfamily of Phospholipase C. Other families of phospholipase C enzymes have been identified in bacteria and trypanosomes. Phospholipases C are phosphodiesterases.
Pfam PF05206: Methyltransferase TRM13 (family)
This is a family of eukaryotic proteins which are responsible for 2'-O-methylation of tRNA at position 4.  TRM13 shows no sequence similarity to other known methyltransferases.
Pfam PF20046: Family of unknown function (DUF6448) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 187 and 219 amino acids in length and may  contain a LysM domain.
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 PF21715: CggR N-terminal DNA binding domain (domain)
The central glycolytic genes repressor (CggR) controls the transcription of the gapA operon encoding five key glycolytic enzymes in Bacillus subtilis. CggR recognizes a unique DNA target sequence comprising two direct repeats and fructose-1,6-bisphosphate (FBP) is the inducer that negatively controls this interaction. This entry represents the N-terminal DNA-binding domain.
Pfam PF21865: Talin 1-like, rod segment domain (domain)
This domain is found repeated in human Talin-1 (TLN1) and similar proteins mainly found in animals. Talin is an essential component in focal adhesions (FAs), intracellular protein assemblies that serve as tension-sensing anchoring points to link cells to the extracellular environment. This protein plays a key regulatory role in FA dynamics, similar to the activation and inactivation of integrins. It consists of a globular head, a long rod made of 62 helices forming 13 helical bundle (rod segment, RS) domains, and a dimerisation (DD) motif at the C terminus. This entry represents four of these domains, RS 5, 6, 9 and 11.
Pfam PF03112: Uncharacterized protein family (ORF7) DUF (family)
Several members of this family are Borrelia burgdorferi plasmid proteins of uncharacterized 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 PF10487: Nucleoporin Nup188, N-terminal (repeat)
Nup188 is one of the many peptides that make up the nucleoporin complex (NPC), and is found across eukaryotes. The Nup188 subcomplex (Nic96p-Nup188p-Nup192p-Pom152p) is one of at least six that make up the NPC, and as such is symmetrically localised on both faces of the NPC at the nuclear end, being integrally bound to the C-terminal of Pom34p. This protein folds into an extended stack of helices where the N-terminal forms a closed ring (subdivided into subdomains I-III in) and the C-terminal forms a more regular, superhelical structure. This entry represents the N-terminal helical repeats from Nup188.
Pfam PF14937: Domain of unknown function (DUF4500) (family)
This family is found in eukaryotes. The function of this protein remains unknown. The gene which encodes for this protein is named chromosome 6 open reading frame 162 (C6orf162) and is found between the chromosomal positions 6q15-q16.1. It is thought that this protein may be an important part of membrane 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 PF07825: Excisionase-like protein (domain)
The phage-encoded excisionase protein (Xis, [swissprot:P03699]) is involved in excisive recombination by regulating the assembly of the excisive intasome and by inhibiting viral integration. It adopts an unusual 'winged'-helix structure in which two alpha helices are packed against two extended strands.  Also present in the structure is a two-stranded anti-parallel beta-sheet, whose strands are connected by a four-residue 'wing'.  During interaction with DNA, helix alpha2 is thought to insert into the major groove, while the wing contacts the adjacent minor groove or phosphodiester backbone. The C-terminal region of Xis is involved in interaction with phage-encoded integrase (Int), and a putative C-terminal alpha helix may fold upon interaction with Int and/or DNA.
Wikipedia: In molecular biology, excisionase is a bacteriophage protein encoded by the Xis gene. It is involved in excisive recombination by regulating the assembly of the excisive intasome and by inhibiting viral integration. It adopts an unusual winged-helix structure in which two alpha helices are packed against two extended strands. Also present in the structure is a two-stranded anti-parallel beta-sheet, whose strands are connected by a four-residue wing. During interaction with DNA, helix alpha2 is thought to insert into the major groove, while the wing contacts the adjacent minor groove or phosphodiester backbone. The C-terminal region of excisionase is involved in interaction with phage-encoded integrase (Int), and a putative C-terminal alpha helix may fold upon interaction with Int and/or DNA.
Pfam PF24276: Family of unknown function (DUF7469) (family)
Members of this family are uncharacterised proteins found in cyanobacteria that grow with a filamentous morphology.
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 PF14129: Domain of unknown function (DUF4296) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 90 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 PF05739: SNARE domain (domain)
Most if not all vesicular membrane fusion events in eukaryotic cells are believed to be mediated by a conserved fusion machinery, the SNARE [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors] machinery. The SNARE domain is thought to act as a protein-protein interaction module in the assembly of a SNARE protein complex. It is composed of about 70 amino acids arranged in an alpha-helical structure.
Pfam PF21999: DNA polymerase-iota, thumb domain (domain)
This is the thumb domain found in DNA polymerase iota and related proteins. This domain makes contacts with the minor groove of DNA.