SII-SWORD/CoKE huggingface dataset:
Pfam PF02098: Tick histamine binding protein (domain)
The lipocalins are a diverse, interesting, yet poorly understood family of proteins composed, in the main, of extracellular ligand-binding proteins displaying high specificity for small hydrophobic molecules . Functions of these proteins include transport of nutrients, control of cell regulation, pheromone transport, cryptic colouration and the enzymatic synthesis of prostaglandins.

The crystal structures of several lipocalins have been solved and show a novel 8-stranded anti-parallel Î²-barrel fold well conserved within the family. Sequence similarity within the family is at a much lower level and would seem to be restricted to conserved disulphides and 3 motifs, which form a juxtaposed cluster that may act as a common cell surface receptor site . By contrast, at the more variable end of the fold are found an internal ligand binding site and a putative surface for the formation of macromolecular complexes . The anti-parallel Î²-barrel fold is also exploited by the fatty acid-binding proteins (which function similarly by binding small hydrophobic molecules), by avidin and the closely related metalloprotease inhibitors, and by triabin. Similarity at the sequence level, however, is less obvious, being confined to a single short N-terminal motif. The lipocalin family can be subdivided into kernal and outlier sets. The kernal lipocalins form the largest self-consistent group, comprising the subfamily of tick histamine-binding proteins. The outlier lipocalins form several smaller distinct subgroups: the OBPs, the von Ebner's gland proteins, alpha-1-acid glycoproteins, tick histamine binding proteins and the nitrophorins.

The tick histamine binding proteins are the most recently identified set of outlier lipocalins. The structure of one tick histamine binding protein has been solved  and has shown the proteins to have the characteristic lipocalin fold but without any appreciable sequence similarity. The tick histamine binding proteins are secreted into the saliva of the ixodid tick Rhipicephalus appendiculatus and share functional similarity with the nitrophorins, sequestering histamine at the wound site. Because the tick histamine binding proteins outcompete histamine receptors, they are able to overcome host inflammatory and immune responses. This enables the ticks to feed for extended periods, lasting from days to several weeks, and are able to gorge themselves on large blood meals increasing their body mass 100 fold. Unlike nitrophorins, the tick proteins do not bind haem (or other cofactor), but ligate histamine directly in two rigid orthogonally-arranged binding sites, at opposing ends of the lipocalin anti-parallel Î²-barrel, which have an unusually polar character.
Pfam PF05931: Staphylococcal AgrD protein (family)
This family consists of several AgrD proteins from many Staphylococcus species. The agr locus was initially described in Staphylococcus aureus as an element controlling the production of exoproteins implicated in virulence. Its pattern of action has been shown to be complex, upregulating certain extracellular toxins and enzymes expressed post-exponentially and repressing some exponential-phase surface components. AgrD encodes the precursor of the autoinducing peptide (AIP).The AIP derived from AgrD by the action of AgrB interacts with AgrC in the membrane to activate AgrA, which upregulates transcription both from promoter P2, amplifying the response, and from P3, initiating the production of a novel effector: RNAIII. In S. aureus, delta-hemolysin is the only translation product of RNA III and is not involved in the regulatory functions of the transcript, which is therefore the primary agent for modulating the expression of other operons controlled by agr.
Pfam PF13650: Aspartyl protease (domain)
This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.
Wikipedia: Aspartic proteases are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. In general, they have two highly conserved aspartates in the active site and are optimally active at acidic pH. Nearly all known aspartyl proteases are inhibited by pepstatin.
Pfam PF08017: Fibrinogen binding protein (repeat)
Proteins in this family bind to fibrinogen.  Members of this family includes the fibrinogen receptor, FbsA, ([swissprot:Q8GIU3]) which  mediates platelet aggregation.
Pfam PF11186: Protein of unknown function (DUF2972) (family)
Some members in this family of proteins with unknown function are annotated as sugar transferase proteins, however this cannot be confirmed.
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 PF23114: HRPKS sdrA-like, NAD(P)-binding Rossmann-fold domain (domain)
This domain is found in Highly reducing polyketide synthase srdA from Neurospora crassa (HRPKS sdrA) and similar fungal proteins. HRPKS sdrA is  part of the gene cluster that mediates the biosynthesis of sordarial, a salicylic aldehyde structurally related to the phytotoxin pyriculol. This domain is predicted to adopt a Rossmann-type fold with an alpha/beta configuration.
Pfam PF00670: S-adenosyl-L-homocysteine hydrolase, NAD binding domain (domain)
S-adenosyl-L-homocysteine hydrolase (3.3.1.1) (AdoHcyase) is an enzyme of the activated methyl cycle, responsible for the reversible hydration of S-adenosyl-L-homocysteine into adenosine and homocysteine. AdoHcyase is an ubiquitous enzyme which binds and requires NAD+as a cofactor. AdoHcyase is a highly conserved protein  of about 430 to 470 amino acids.
Wikipedia: Adenosylhomocysteinase (EC 3.13.2.1, S-adenosylhomocysteine synthase, S-adenosylhomocysteine hydrolase, adenosylhomocysteine hydrolase, S-adenosylhomocysteinase, SAHase, AdoHcyase) is an enzyme that catalyzes the nicotinamide adenine dinucleotide (NAD+) dependent, reversible hydrolysis of S-adenosylhomocysteine to homocysteine and adenosine.S-adenosyl-L-homocysteine + H2O ⇌ L-homocysteine + adenosine
Pfam PF04516: CP2 transcription factor (family)
This family represents a conserved region in the CP2 transcription factor family.
Pfam PF05173: Dihydrodipicolinate reductase, C-terminus (domain)
Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate.  This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain.
Pfam PF22631: Phosphoinositide phospholipase C beta1-4-like EF-hand domain (domain)
This entry represents the first EF-hand domain found in 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1-4 (PLCB1-4) from human and related proteins. PLC-beta isoforms mediate the production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) to propagate signals  for several physiological responses.
Pfam PF17417: Herpesvirus Glycoprotein B PH-like domain (domain)
This domain corresponds to the second PH-like domain in herpesvirus glycoprotein B.
Wikipedia: Herpesvirus glycoprotein B is a viral glycoprotein that is involved in the viral cell entry of Herpes simplex virus (HSV). Herpesviruses have a lipid bilayer, called the envelope, which contains twelve surface glycoproteins. For infectivity to be attained, the double stranded DNA genome of HSV must enter the host cell through means of fusion of its envelope with the cellular membrane or via endocytosis. Other viral glycoproteins involved in the process of viral cell entry include gC, gB, gD, gH, and gL, but only gC, gB, gD, and gH are required for the fusion of the HSV's envelope with the cellular membrane. It can be noted that all herpesviruses have glycoproteins gB, gH, and gL.
Pfam PF16584: Outer membrane lipoprotein carrier protein LolA (domain)
LolA_2 is a family of Bacteroidetes outer membrane lipoprotein carrier protein LolA-like proteins.  The exact function is not known.
Pfam PF17973: Bacterial Alpha-2-macroglobulin MG10 domain (domain)
Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. Bacterial A2Ms are located in the periplasm where they are believed to provide protection to the cell by trapping external proteases through a covalent interaction with an activated thioester. This domain is found on the C-terminal region in A2Ms in bacteria. Structure analysis of Salmonella enterica ser A2Ms (SA-A2Ms) show that they are composed of 13 domains, all of which fold as variants of beta sandwiches with the exception of the TED, which consists of 14 alpha helices. Most of the beta sandwich domains appear to serve a structural role and are referred to as the macroglobulin-like (MG) domains. This is the MG10 domain. MG10 is markedly different from the other MG domains in that it has more beta strands and an alpha helix. The position of MG10 is stabilized by, in addition to other hydrogen bonds, the formation of a beta sheet with MG9.
Pfam PF24784: Temptin C-terminal (domain)
This domain is found in Temptin which is a component of the complex of water-borne protein pheromones that stimulates attraction and mating behaviour. This protein modulates pheromone signaling by direct binding to attractin. This domain contains two highly conserved cysteines that are predicted to to form a disulfide bond. It is also enriched with conserved acidic residues.
Pfam PF08473: Neuronal voltage-dependent calcium channel alpha 2acd (family)
This eukaryotic domain has been found in the neuronal voltage-dependent calcium channel (VGCC) alpha 2a, 2c, and 2d subunits. It is also found in other calcium channel alpha-2 delta subunits to the C-terminus of a Cache domain ([pfam:PF02743]).
Wikipedia: Voltage-gated calcium channels (VGCCs), also known as voltage-dependent calcium channels (VDCCs), are a group of voltage-gated ion channels found in the membrane of excitable cells (e.g. muscle, glial cells, neurons) with a permeability to the calcium ion Ca2+. These channels are slightly permeable to sodium ions, so they are also called Ca2+–Na+ channels, but their permeability to calcium is about 1000-fold greater than to sodium under normal physiological conditions.
Pfam PF17890: Peptidoglycan hydrolase LytB WW-like domain (domain)
Structural analysis revealed that the catalytic domain of LytB consists of three structurally independent modules: SH3b, WW domain-like, and the glycoside hydrolase family 73 (GH73). This entry is the WW like domain found in endo-beta-N-acetylglucosaminidase LytB from Streptococcus pneumoniae. Functional analysis show that the deletion of both SH3b and WW modules almost completely abolished the activity of LytB. Furthermore, it was shown that the SH3b and WW modules are indispensable for LytB in cell separation.
Pfam PF18698: Histidine kinase sensor domain (domain)
The Bacillus subtilis ResD-ResE two-component (TC) regulatory system activates genes involved in nitrate respiration in response to oxygen limitation or nitric oxide (NO). The sensor kinase ResE activates the response regulator ResD through phosphorylation, which then binds to the regulatory region of genes involved in anaerobiosis to activate their transcription. In other words, ResE is involved in sensing signals related to the redox state of the cells. ResE is composed of an N-terminal signal input domain and a C-terminal catalytic domain. The N-terminal domain contains two transmembrane subdomains and a large extra-cytoplasmic loop. Mutational analysis indicate that cytoplasmic ResE lacking the transmembrane segments and the extra-cytoplasmic loop retains the ability to sense oxygen limitation and NO, which leads to transcriptional activation of ResDE-dependent genes. Having said that, it is also proposed that the extra-cytoplasmic region may serve as a second signal-sensing subdomain. This suggests that the extracytoplasmic region could contribute to amplification of ResE activity leading to the robust activation of genes required for anaerobic metabolism in B. subtilis. This entry represents the extracytoplasmic subdomain. Family members also include SrrB found in S. aureus that is similar to ResE of B. subtilis.
Wikipedia: In molecular biology, a two-component regulatory system serves as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions. Two-component systems typically consist of a membrane-bound histidine kinase that senses a specific environmental stimulus, and a corresponding response regulator that mediates the cellular response, mostly through differential expression of target genes. Although two-component signaling systems are found in all domains of life, they are most common by far in bacteria, particularly in Gram-negative and cyanobacteria; both histidine kinases and response regulators are among the largest gene families in bacteria. They are much less common in archaea and eukaryotes; although they do appear in yeasts, filamentous fungi, and slime molds, and are common in plants, two-component systems have been described as "conspicuously absent" from animals.
Pfam PF05637: galactosyl transferase GMA12/MNN10 family (family)
This family contains a number of glycosyltransferase enzymes that contain a DXD motif. This family includes a number of C. elegans homologues where the DXD is replaced by DXH. Some members of this family are included in glycosyltransferase family 34.
Pfam PF08370: Plant PDR ABC transporter associated (family)
This domain is found on the C-terminus of ABC-2 type transporter domains ([pfam:PF01061]).  It seems to be associated with the plant pleiotropic drug resistance (PDR) protein family of ABC transporters.  Like in yeast, plant PDR ABC transporters may also play a role in the transport of antifungal agents [1, also [pfam:PF06422]].  The PDR family is characterised by a configuration in which the ABC domain is nearer the N-terminus of the protein than the transmembrane domain.
Pfam PF11836: Phage tail tube protein, GTA-gp10 (family)
This is a family of phage tail tube proteins.
Pfam PF06565: DM10 domain (domain)
This entry represents the DM10 domain, which consists of approximately 105 residues whose function is unknown. It has been identified in nucleoside diphosphate kinases, namely Nucleoside diphosphate kinase 7 (NDK7), which contain a single copy of the DM10 domain, and in uncharacterised proteins including Rib72 from Chlamydomonas and EF-hand domain-containing protein 1/EF-hand domain-containing family member C2 (EFHC1/2) from mammals, which contain multiple copies of DM10 domains. In Chlamydomonas, and possibly mammals, DM10 domain-containing proteins are tightly bound to the flagellar doublet microtubules. This suggests that DM10 domains might act as flagellar NDK regulatory modules or as units specifically involved in axonemal targeting or assembly. This domain have a PH-like fold which includes seven beta strands, with a short 3-4 residue helix after the first strand, and a more extended alpha helical region at the C terminus.
Pfam PF12545: Filamentous haemagglutinin family outer membrane protein (family)
This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with [pfam:PF05860].
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 PF23518: WW domain (domain)
This entry represents a set of WW domains that are found in a large family of fungal RasGEF domain containing proteins. This domain is found close to the N-terminus of the proteins adjacent to an SH3 domain.
Pfam PF00682: HMGL-like (domain)
This family contains a diverse set of enzymes.  These include various aldolases and a region of pyruvate carboxylase.
Wikipedia: Pyruvate carboxylase (PC) encoded by the gene PC is an enzyme of the ligase class that catalyzes the physiologically irreversible carboxylation of pyruvate to form oxaloacetate (OAA).
Pfam PF02707: Major Outer Sheath Protein N-terminal region (family)
This is a family of spirochete major outer sheath protein N-terminal regions. These proteins are present on the bacterial cell surface.  In T. denticola the major outer sheath protein (Msp) binds immobilised laminin and  fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola.
Pfam PF09196: Domain of unknown function (DUF1953) (domain)
This domain is found in the Archaeal protein maltooligosyl trehalose synthase produced by Sulfolobus spp. Its function has not, as yet, been defined.
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 PF02363: Cysteine rich repeat (repeat)
This Cysteine repeat C-X3-C-X3-C is repeated in sequences of this family, 34 times in [swissprot:O17970]. The function of these repeats is unknown as is the function of the proteins in which they  occur.  Most of the sequences in this family are from C. elegans.
Pfam PF21629: Bleomycin resistance protein domain (domain)
This domain is found in Bleomycin resistance protein from Lachnoclostridium phytofermentans (Cphy_0674) and similar bacterial sequences. It is found usually associated with [pfam:PF12833]. It shows an alpha-beta structure.
Pfam PF11700: Vacuole effluxer Atg22 like (family)
Autophagy is a major survival survival mechanism in which eukaryotes recycle cellular nutrients during stress conditions. Atg22, Avt3 and Avt4 are partially redundant vacuolar effluxes, which mediate the efflux of leucine and other amino acids resulting from autophagy.  This family also includes other transporter proteins.
Pfam PF07140: Interferon gamma receptor (IFNGR1), D2 domain (domain)
This entry consists of mammal and viral interferon gamma receptor proteins. Molecular interactions among cytokines and cytokine receptors in eukaryotes form the basis of many cell-signalling pathways relevant to immune function. Human interferon-gamma (IFN-gamma) signals through a multimeric receptor complex consisting of two different but structurally related transmembrane chains: the high-affinity receptor-binding subunit (IFN-gammaRalpha) and a species specific accessory factor (AF-1 or IFN-gammaRbeta). The vaccinia viral interferon gamma receptor has been shown to be secreted from infected cells during early infection. The structure has been halved such that the N-terminus of this family is now represented by Tissue_fac [pfam:PF01108] (which represents the D1 domain), and this domain represents the D2 domain, both of which adopt an Ig-like fold. This domain is mediates receptor-receptor contacts.
Wikipedia: In molecular biology, the interferon gamma receptor (IFNGR1) family is a family of proteins which includes several eukaryotic and viral interferon gamma receptor proteins.
Pfam PF15816: Transmembrane protein 82 (family)
TMEM82 is a family of proteins found in eukaryotes. The function is not known.
Pfam PF21190: Bbp16 (family)
This protein family includes Bbp16 from Bordetella phage BPP-1 and similar proteins from tailed bacteriophages and prophages mainly found in Proteobacteria. Bbp16, which adopts a dimeric configuration, is essential for forming infectious phage particles. This cement protein has a jellyroll fold with two beta-sheets, each consisting of four anti-parallel strands.
Pfam PF23562: AMP-binding enzyme C-terminal domain (domain)
This is a small domain that is found C terminal to [pfam:PF00501]. It has a central beta sheet core that is flanked by alpha helices.
Pfam PF07555: beta-N-acetylglucosaminidase (family)
This family has previously been described as a hyaluronidase. However, more recently it has been shown that this family has beta-N-acetylglucosaminidase activity.
Wikipedia: Hyaluronidases are a family of enzymes that catalyse the degradation of hyaluronic acid. Karl Meyer classified these enzymes in 1971, into three distinct groups, a scheme based on the enzyme reaction products. The three main types of hyaluronidases are two classes of eukaryotic endoglycosidase hydrolases and a prokaryotic lyase-type of glycosidase.
Pfam PF21579: tRNA (uracil(54)-C(5))-methyltransferase, TRAM domain (domain)
This domain is found at the N-terminal end of tRNA (uracil(54)-C(5))- methyltransferase from Pyrococcus abyssi (PabTrmU54), which catalyses the formation of 5-methyl-uridine at position 54 (m5U54) in tRNA. This domain, a TRAM domain, adopts a five-stranded beta barrel architecture characteristic of an oligosaccharide/ oligonucleotide-binding fold (OB-fold).
Pfam PF05663: Protein of unknown function (DUF809) (family)
This family consists of several proteins of unknown function Raphanus sativus (Radish) and Brassica napus (Rape).
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 PF03678: Hexon, adenovirus major coat protein, C-terminal domain (domain)
Hexon 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.  The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices. The N and C-terminal domains adopt the same PNGase F-like fold although they are significantly different in length.
Wikipedia: In molecular biology, the hexon protein is a major coat protein found in adenoviruses. Hexon coat proteins are synthesised during late infection and form homo-trimers. The 240 copies of the hexon trimer that are produced 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. The penton complex, formed by the peripentonal hexons and penton base, lie at each of the 12 vertices. The hexon coat protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. Within a hexon trimer, the domains are arranged around a pseudo 6-fold axis. The domains have a beta-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology; each domain is heavily decorated with many insertions. Some hexon proteins contain a distinct C-terminal domain.