SII-SWORD/CoKE huggingface dataset:
Pfam PF00407: Pathogenesis-related protein Bet v 1 family (domain)
This family is named after Bet v 1, the major birch pollen allergen. This protein belongs to family 10 of plant pathogenesis-related proteins (PR-10), cytoplasmic proteins of 15-17 kd that are wide-spread among dicotyledonous plants. In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. A classification by sequence similarity yielded several subfamilies related to PR-10: - Pathogenesis-related proteins PR-10: These proteins were identified as major tree pollen allergens in birch and related species (hazel, alder), as plant food allergens expressed in high levels in fruits, vegetables and seeds (apple, celery, hazelnut), and as pathogenesis-related proteins whose expression is induced by pathogen infection, wounding, or abiotic stress. Hyp-1 ([swissprot:Q8H1L1]), an enzyme involved in the synthesis of the bioactive naphthodianthrone hypericin in St. John's wort (Hypericum perforatum) also belongs to this family. Most of these proteins were found in dicotyledonous plants. In addition, related sequences were identified in monocots and conifers. - Cytokinin-specific binding proteins: These legume proteins bind cytokinin plant hormones. - (S)-Norcoclaurine synthases are enzymes catalysing the condensation of dopamine and 4-hydroxyphenylacetaldehyde to (S)-norcoclaurine, the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine. -Major latex proteins and ripening-related proteins are proteins of unknown biological function that were first discovered in the latex of opium poppy (Papaver somniferum) and later found to be upregulated during ripening of fruits such as strawberry and cucumber. The occurrence of Bet v 1-related proteins is confined to seed plants with the exception of a cytokinin-binding protein from the moss Physcomitrella patens ([swissprot:Q9AXI3]).
Wikipedia: Bet v I allergen is a family of protein allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens that, in most people, result in no symptoms.
Pfam PF11367: Tail completion protein gp17 (domain)
This entry includes Tail completion protein gp17 from Siphoviridae bacteriophage SPP1 [swissprot:O48448], a tail completion protein which caps the tail and interacts with the connector gp16, thereby attaching the tail to the capsid.
Pfam PF10618: Phage tail tube protein (family)
This bacterial family of proteins contains phage tail tube proteins related to the Mu phage protein [swissprot:P79679]. Bacteriophage Mu has an eicosahedral head and contractile tail. The tail is composed of an outer sheath and an inner tube.
Pfam PF18006: O-phosphoseryl-tRNA synthetase C-terminal domain (domain)
The SSHS domain is mainly found in Archaea. The domain makes up part of the anticodon binding domain at the C-terminal of O-phosphoserine--tRNA(Cys) ligase.
Pfam PF13852: Protein of unknown function (DUF4197) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 228 and 249 amino acids in length.
Pfam PF08276: PAN-like domain (domain)
Plasma kallikrein (3.4.21.34) and coagulation factor XI (3.4.21.27) are two related plasma serine proteases activated by factor XIIA and which share the same domain topology: an N-terminal region that contains four tandem repeats of about 90 amino acids and a C-terminal catalytic domain. The 90 amino-acid repeated domain contains 6 conserved cysteines. It has been shown  that three disulfide bonds link the first and sixth, second and fifth, and third and fourth cysteines. The domain can be drawn in the shape of an apple and has been accordingly called the 'apple domain'.

The apple domains of plasma prekallikrein are known to mediate its binding to high molecular weight kininogen , the apple domains of factor XI bind to factor XIIa, platelets, kininogen, factor IX and heparin .

The apple domains display some sequence similarity with the N domain of plasminogen/hepatocyte growth factor (HGF) and to some nematode and protozoan proteins . They all belong to the same domain superfamily that have been called the PAN module . The N domain of hepatocyte growth factor binds to the c-Met receptor and to the heparin molecule. The structure of the PAN module of HGF has been solved. It contains a characteristic hairpin-loop structure stabilised by two disulfide bridges, Cys-1 and 6 are not conserved in HGF PAN modules .

Apart from the cysteines, there are a number of other conserved positions in the apple domain. This entry represents the PAN domain of the plasma kalllikrein/coagulation factor XI subgroup proteins.
Pfam PF21421: Avirulence protein ATR1, WY-domain (domain)
Avirulence protein ATR1 is a secreted effector  that acts as an elicitor of hypersensitive response (HR) specifically on plants. It activates the N-terminal Toll-interleukin-1 receptor (TIR) domain of Arabidopsis NLR RPP1. This entry represents the C-terminal helical domain, referred to as the WY-domain.
Pfam PF13940: Toxin Ldr, type I toxin-antitoxin system (family)
This family includes the Ldr (long direct repeat) toxins. In Escherichia coli there are four Ldr toxins, LdrA, LdrB, LdrC and LdrD. These toxins inhibit cell growth, decrease cell viability and cause nucleoid condensation. LdrD expression is inhibited by the antisense RNA RdlD, which functions as an antitoxin.
Wikipedia: RdlD RNA is a family of small non-coding RNAs which repress the protein LdrD in a type I toxin-antitoxin system. It was discovered in Escherichia coli strain K-12 in a long direct repeat (LDR) named LDR-D. This locus encodes two products: a 35 amino acid peptide toxin (ldrD) and a 60 nucleotide RNA antitoxin. The 374nt toxin mRNA has a half-life of around 30 minutes while rdlD RNA has a half-life of only 2 minutes. This is in keeping with other type I toxin-antitoxin systems.
Pfam PF00842: Alanine racemase, C-terminal domain (domain)
Alanine racemase (5.1.1.1) plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine.

The molecular structure of alanine racemase from Bacillus stearothermophilus (Geobacillus stearothermophilus) was determined by X-ray crystallography to a resolution of 1.9 A . The alanine racemase monomer is composed of two domains, an eight-stranded Î±/Î² barrel at the N terminus, and a C-terminal domain essentially composed of Î²-strand. This entry represents the C-terminal domain.
Wikipedia: In enzymology, an alanine racemase is an enzyme that catalyzes the chemical reactionL-alanine  D-alanine
Pfam PF23330: CIZ1-like, C2H2-type zinc finger (domain)
This C2H2-type zinc finger domain is found in human Cip1 -interacting zinc finger protein (CIZ1) and similar animal proteins. CIZ1 may regulate the subcellular localisation of CIP/WAF1.
Pfam PF14601: DNA_binding protein, TFX, C-term (domain)
This is the C-terminal region of TFX-like DNA-binding proteins.
Pfam PF19592: Family of unknown function (DUF6097) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001796) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It  includes a member from the tauramamide biosynthetic gene cluster  from Brevibacillus laterosporus DSM 25 and appears to be  predominantly found in bacteria.
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 PF16831: CS6 fimbrial subunits A and B, Coli surface antigen 6 (domain)
CssAB is a family of CS6 pilins from E.coli, including both subunits A and B.  It acts as a colonisation factor for the enterotoxigenic species pf E.coli to mediate bacterial attachment to the small intestinal epithelium. Both subunits in the fibre bind to receptors on epithelial cells, and that CssB, but not CssA, specifically recognises the extracellular matrix protein fibronectin.
Pfam PF07040: Protein of unknown function (DUF1326) (family)
This family consists of several hypothetical bacterial proteins which seem to be found exclusively in Rhizobium and Ralstonia species. Members of this family are typically around 210 residues in length and contain 5 highly conserved cysteine residues at their N-terminus. 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 PF21062: Reovirus core-spike protein lambda-2 (L2), ferredoxin-like domain (domain)
Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the fourth domain, which adopts a ferredoxin-like fold consisting of four beta-strands protected by alpha-helices that probably functions as a structural support for the three enzyme domains (two methyltransferase and GTase domains).
Pfam PF06558: Secretion monitor precursor protein (SecM) (family)
This family consists of several bacterial Secretion monitor precursor (SecM) proteins. SecM is known to regulate SecA expression. The eubacterial protein secretion machinery consists of a number of soluble and membrane associated components. One critical element is SecA ATPase, which acts as a molecular motor to promote protein secretion at translocation sites that consist of SecYE, the SecA receptor, and SecG and SecDFyajC proteins, which regulate SecA membrane cycling.
Pfam PF03389: MobA/MobL family (family)
This family includes of the MobA protein from the E. coli plasmid RSF1010, and the MobL protein from the Thiobacillus ferrooxidans plasmid PTF1. These sequences are mobilisation proteins, which are essential for specific plasmid transfer.
Pfam PF19876: Family of unknown function (DUF6349) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus.
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 PF23891: Family of unknown function (DUF7243) (family)
This family of phage proteins adopt a structure composed of a pair of jelly roll fold domains with one nested within the other. This fold is suggestive of a phage head structural protein. Structure predictions suggest that these proteins can form pentameric or hexameric arrangements mediated by the outer of the two domains.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09215: Bacteriophage T4, Gp8 (domain)
Members of this family of viral baseplate structural proteins adopt a structure consisting of a three-layer beta-sandwich with two finger-like loops containing an alpha-helix at the opposite sides of the sandwich. The two peripheral, five-stranded, antiparallel beta-sheets are stacked against the middle, four-stranded, antiparallel beta-sheet. Attachment of this family of proteins to the baseplate during assembly creates a binding site for subsequent attachment of Gp6.
Pfam PF10816: Domain of unknown function (DUF2760) (domain)
This is a bacterial family of uncharacterised 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 PF02318: FYVE-type zinc finger (family)
This FYVE-type zinc finger is found at the N-terminus of effector proteins including rabphilin-3A and regulating synaptic membrane exocytosis protein 2.
Wikipedia: In molecular biology the FYVE zinc finger domain is named after the four cysteine-rich proteins: Fab 1, YOTB, Vac 1, and EEA1, in which it has been found. FYVE domains bind phosphatidylinositol 3-phosphate, in a way dependent on its metal ion coordination and basic amino acids. The FYVE domain inserts into cell membranes in a pH-dependent manner. The FYVE domain has been connected to vacuolar protein sorting and endosome function.
Pfam PF02488: Merozoite Antigen (family)
This family represents the immunodominant surface antigen of Theileria parasites including equi merozoite antigen-1 (EMA-1) and equi merozoite antigen-2 (EMA-2). The protein shows variation at a putative glycosylation site, a potential mechanism for host immune response evasion.
Pfam PF00354: Pentaxin family (domain)
Pentaxins are also known as pentraxins.
Wikipedia: Pentraxins (PTX), also known as pentaxins, are an evolutionary conserved family of proteins characterised by containing a pentraxin protein domain. Proteins of the pentraxin family are involved in acute immunological responses. They are a class of pattern recognition receptors (PRRs). They are a superfamily of multifunctional conserved proteins, some of which are components of the humoral arm of innate immunity and behave as functional ancestors of antibodies (Abs). They are known as classical acute phase proteins (APP), known for over a century.
Pfam PF08678: Rsbr N terminal (domain)
Rsbr is a regulator of the RNA polymerase sigma factor subunit sigma(B).                                The structure of the N terminal domain belongs to the globin fold superfamily.
Pfam PF00413: Matrixin (domain)
The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.
Pfam PF02177: Amyloid A4 N-terminal heparin-binding (domain)
This N-terminal domain of APP, amyloid precursor protein, is the heparin-binding domain of the protein. this region is also responsible for stimulation of neurite outgrowth. The structure reveals both a highly charged basic surface that may interact with glycosaminoglycans in the brain and an abutting hydrophobic surface that is proposed to play an important functional role such as in dimerisation or ligand-binding. Structural similarities with cysteine-rich growth factors, taken together with its known growth-promoting properties, suggest the APP N-terminal domain could function as a growth factor in vivo.
Wikipedia: A growth factor-like domain (GFLD) is a protein domain structurally related to epidermal growth factor, which has a high binding affinity for the epidermal growth factor receptor. As structural domains within larger proteins, GFLD regions commonly bind calcium ions. A subtype present in the N-terminal region of the amyloid precursor protein is a member of the heparin-binding class of GFLDs and may itself have growth factor function, particularly in promoting neuronal development.
Pfam PF16860: CHCH-CHCH-like Cx9C, IMS import disulfide relay-system, (domain)
CX9C is the first half of a twin Cx9C motif in eukaryotic proteins. The function of this motif is to import nuclear-encoded mitochondrial intermembrane-space-proteins into the IMS (intermembrane space), as these latter lack a mitochondrial targeting sequence. The Cx9C proteins have a disulfide-bonded alpha-hairpin conformation. Cx9C-containing proteins are thus putative substrates for the Mia40-dependent thiol-disulfide exchange mechanism that carries out an oxidative folding process resulting in the proteins being trapped in the IMS.
Pfam PF05518: Totivirus coat protein (family)
This family of proteins contain the coat proteins of the Totiviruses.
Pfam PF09534: Tryptophan-associated transmembrane protein (Trp_oprn_chp) (family)
Members of this family are predicted transmembrane proteins with four membrane-spanning helices. Members are found in the Actinobacteria (Mycobacterium, Corynebacterium, Streptomyces), always associated with genes for tryptophan biosynthesis.
Pfam PF13769: Virulence factor (family)
This domain is found in conserved virulence factors. It is often found in association with [pfam:PF02985] and [pfam:PF08712].
Pfam PF24826: SNU71 N-terminal (domain)
This entry represents the N-terminal domain of U1 small nuclear ribonucleoprotein component SNU71 from yeast, which is a component of the U1 snRNP particle that recognises and binds the 5'-splice site of pre-mRNA. This domain is involved in protein cross-linking and binds between Prp42 N-terminal and the Snu56 KH-like fold.
Pfam PF19040: SGNH domain (fused to AT3 domains) (domain)
This entry include SGNH domains that are found fused to membrane domains from the AT3 families [pfam:PF01757].
Pfam PF01180: Dihydroorotate dehydrogenase (domain)
This entry represents a domain found in dihydroorotate and dihydropyrimidine dehydrogenases. Dihydroorotate dehydrogenases included in this entry catalyse the conversion of dihydroorotate to orotate using quinone, fumarate and NAD+ as electron acceptor . Dihydropyrimidine dehydrogenases catalyse the conversion of 5,6-dihydrouracil to uracil and are involved in pyrimidine base degradation .
Dihydroorotate dehydrogenase (1.3.98.1) (DHOdehase) catalyses the fourth step in the de novo biosynthesis of pyrimidine, the conversion of dihydroorotate into orotate. DHOdehase is a ubiquitous FAD flavoprotein. In bacteria (gene pyrD), DHOdease is located on the inner side of the cytosolic membrane. In some yeasts, such as in Saccharomyces cerevisiae (gene URA1, subfamily 2), it is a cytosolic protein while in other eukaryotes it is found in the mitochondria .
Wikipedia: Dihydroorotate dehydrogenase (DHODH) is an enzyme that in humans is encoded by the DHODH gene on chromosome 16. The protein encoded by this gene catalyzes the fourth enzymatic step, the ubiquinone-mediated oxidation of dihydroorotate to orotate, in de novo pyrimidine biosynthesis. This protein is a mitochondrial protein located on the outer surface of the inner mitochondrial membrane (IMM). Inhibitors of this enzyme are used to treat autoimmune diseases such as rheumatoid arthritis.
Pfam PF12189: Single-strand DNA-binding protein (domain)
This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved IELE sequence motif. VirE1 is an acidic chaperone protein which binds to VirE2, a ssDNA binding protein. These proteins are virulence factors of the plant pathogens Agrobacteria. VirE1 competes for the ssDNA binding site of VirE2.
Pfam PF01355: High potential iron-sulfur protein (domain)
High potential iron-sulphur proteins (HiPIP)  are a specific class of high-redox potential 4Fe-4S ferredoxins that functions in anaerobic electron transport and which occurs commonly in purple photosynthetic bacteria and in other bacteria, such as Paracoccus denitrificans and Thiobacillus ferrooxidans .

HiPIPs seem to react by oxidation of 2+ to 3+

The HiPIPs are small proteins which show significant variation in their sequences, their sizes (from 63 to 85 amino acids), and in their oxidation- reduction potentials. As shown in the following schematic representation the iron-sulphur cluster is bound by four conserved cysteine residues.

                           [4Fe-4S cluster]
                           | |       |     |
        xxxxxxxxxxxxxxxxxxxCxCxxxxxxxCxxxxxCxxxx

'C': conserved cysteine involved in the binding of the iron-sulphur cluster.
Wikipedia: High potential iron-sulfur proteins (HIPIP) are a class of iron-sulfur proteins. They are ferredoxins that participate in electron transfer in photosynthetic bacteria as well as in Paracoccus denitrificans.
Pfam PF20853: WKTW repeat (repeat)
This repeat is found in five copies at the C-terminal of Cerebellar degeneration-related antigen 1 (CDR1) from human. It has the conserved sequence motif WKTWI.
Pfam PF14001: YdfZ protein (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved YDRNRN sequence motif. The E. coli protein has been shown to bind selenium. This protein shows structural similarity to the KOW motif.
Pfam PF17701: Family of unknown function (DUF5547) (family)
This is a family of unknown function found in mammals.
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 PF00949: Peptidase S7, Flavivirus NS3 serine protease (family)
The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine  protease, which requires NS2B ([pfam:PF01002]) as a cofactor.
Pfam PF19753: Family of unknown function (DUF6240) (family)
This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 969 and 1090 amino acids in length. Some members of this family are thought to be related to the Flagellar hook-length control protein FliK.
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 PF01303: Egg lysin (Sperm-lysin) (domain)
Egg lysin creates a hole in the envelope of the egg thereby allowing  the sperm to pass through the envelope and fuse with the egg.