SII-SWORD/CoKE huggingface dataset:
Pfam PF03523: Macrophage scavenger receptor (family)
Scavenger receptors type I and II were the first scavenger receptors purified and are products of alternative splicing of a single gene. They are now named as class A, type I and type II (SR-AI/II) or collectively SR-A member 1. They can recognise a wide variety of ligands, from bacteria and yeast to self (native proteins) and self-modified ligands and they are involved in host defense, homeostasis, antigen presentation, pathogenesis of neurodegenerative disorders and atherosclerosis .
Pfam PF20302: HisK-N-like globin domain of the ASK signalosome (domain)
Predicted non-heme-binding version of the Globin domain identified in ASK signalosome. Displays strongest affinities to the HisK-N family of sensor domains, which inhibit histidine kinase activation required for sporulation in bacteria of the firmicutes lineage. This globin domain is predicted to represent an independent sensory element recognizing a fatty acid or a related membrane-derived molecule which regulates activity of the ASK signalosome in apoptosis.
Pfam PF10367: Vacuolar sorting protein 39 C-terminal zinc finger domain (domain)
This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. This is likely a zinc binding domain which shows some similarity to the RING fingers found at the C-terminus of pf Vps protein. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole.  In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange.  This domain is involved in localisation and in mediating the interactions of Vps39 with Vps11.
Pfam PF11408: Sgs1 RecQ helicase (family)
RecQ helicases unwind DNA in an ATP-dependent manner. Sgs1 has a HRDC (helicase and RNaseD C-terminal) domain which modulates the helicase function via auxiliary contacts to DNA.
Pfam PF09580: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ) (family)
This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Pfam PF01815: Rop protein (domain)
The Rop protein regulates plasmid DNA replication by modulating the initiation of transcription of the primer RNA precursor. Processing of the precursor, RNAII, is inhibited by hydrogen bonding of RNAII to its complementary sequence in RNAI. Rop increases the affinity of RNAI for RNAII and thus decreases the rate of replication initiation events. The 3D structure of Rop has been determined by X-ray crystallography and refined to 1.7A resolution. The 63 amino acid protein is a homodimer, each monomer consisting almost entirely of two Î±-helices, the whole molecule forming a highly regular four-Î±-helix bundle . This can be approximated by a four-stranded rope, with radius 7.0 A, a left-handed helical twist, and pitch 172.5 A. A very compact packing of side chains in the helix interfaces of the Rop coiled-coil structure is presumed to account for its high stability . The overall details of the structure have been confirmed by proton NMR .
Pfam PF01463: Leucine rich repeat C-terminal domain (family)
Leucine Rich Repeats [pfam:PF00560] are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the C-terminus of tandem leucine rich repeats.
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF21145: Complement C4, MG1 domain (domain)
Complement component C4 is a non-enzymatic component of C3 and C5 convertases and essential for the propagation of the classical complement pathway. It covalently binds to immunoglobulins and immune complexes and enhances the solubilization of immune aggregates and clearance through CR1 on erythrocytes. C4 is cleaved into the fragments C4a and C4b by MASP-2 protease. C4A isotype is responsible for effective binding to form amide bonds with immune aggregates or antigens, whereas C4B isotype catalyses the transacylation of the thioester carbonyl group to form ester bonds with carbohydrate antigens. This entry represents the macroglobulin 1 (MG1) domain found at the N-terminal of C4.
Pfam PF10027: Predicted integral membrane protein (DUF2269) (family)
Members of this family of bacterial hypothetical integral membrane 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 PF12959: Protein of unknown function (DUF3848) (domain)
A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This domain frequently seen with DUF3849.
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 PF00191: Annexin (domain)
This family of annexins also includes giardin that has been shown to function as an annexin.
Wikipedia: Annexin is a common name for a group of cellular proteins. They are mostly found in eukaryotic organisms.
Pfam PF08360: QacR-like protein, C-terminal region (domain)
This family features the C-terminal region of a number of proteins that bear similarity to the QacR protein ([swissprot:P23217]), a transcriptional regulator of the TetR family. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA ([swissprot:P23215]), a multidrug efflux pump. The C-terminal region contains the multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites.
Pfam PF02874: ATP synthase alpha/beta family, beta-barrel domain (domain)
This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.
Wikipedia: The alpha and beta subunits are found in the F1, V1, and A1 complexes of F-, V- and A-ATPases, respectively, as well as flagellar (T3SS) ATPase and the termination factor Rho. The subunits make up a ring that contains the ATP-hydrolyzing catalytic core. The F-ATPases, V-ATPases and A-ATPases are composed of two linked complexes: the F1, V1 or A1 complex containsthat synthesizes/hydrolyses ATP, and the Fo, Vo or Ao complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis.
Pfam PF13234: Mtr4-like, beta-barrel domain (domain)
Exosome RNA helicase Mtr4 is a essential RNA helicase, and is an exosome-activating cofactor. It functions together with the nuclear exosome being involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclear RNA surveillance pathways involving the so-called TRAMP complex. It contains an arch domain, required for proper 5.8S rRNA processing, and appears to function independently of canonical helicase activity. The arch domain comprises an helical stalk/elbow that flanks a KOW module which adopts a beta-barrel fold. This entry represents the beta-barrel of MTR4 and related Ski2-like helicases. Ski2 from yeast has an overall similar structure to MTR4 proteins. However, it does not have the KOW motif and it is not included in this entry.
Pfam PF09665: Type II restriction endonuclease (RE_Alw26IDE) (family)
Members of this entry are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterised specificities of the three members are GGTCTC, CGTCTC and the shared subsequence GTCTC.
Pfam PF23776: Protein of unknown function (DUF7170) (family)
The DUF7170 domain family consists of several uncharacterized phage proteins of around 50 amino acids in length. The family is found in a variety of phages that infect bacterial hosts such as Escherichia, Salmonella, Klebsiella, Vibrio, Citrobacter, Shigella, Pseudomonas and Aeromonas. A few longer proteins of around 60-90 amino acids are also included.
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 PF24078: PIC/HAP1/IgA0 second beta-solenoid repeat region (repeat)
This entry represents the second solenoid-repeat region found in some serine peptidase autotransporters from bacteria, including IgA0, HAP1, Pic, SepA and EspC. These proteins have been associated to virulent strains. Pic and other bacterial autotransporters confer serum resistance but do not degrade immunoglobulin, as in the case of IgA0. This region counts with insertions between beta-solenoid repeats which have been suggested to be involved in forming a unique structure for recognition and binding of protein substrate.
Pfam PF10799: Biofilm formation protein (YliH/bssR) (family)
YliH is induced in biofilms and is involved in repression of motility in the biofilms. YliH is also known as bssR (regulator of biofilm through signal secreton).
Pfam PF19721: Family of unknown function (DUF6215) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001856) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the caniferolide A biosynthetic gene cluster from Streptomyces  caniferus. This family appears to be predominantly found in  Actinobacteria.
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 PF13088: BNR repeat-like domain (repeat)
This family of proteins contains BNR-like repeats suggesting these proteins may act as sialidases.
Wikipedia: Bacterial neuraminidase is type of neuraminidase and a virulence factor for many bacteria including Bacteroides fragilis and Pseudomonas aeruginosa.
Its function is to cleave a sialic acid residue off ganglioside-GM1 turning it into asialo-GM1 to which type 4 pili bind preferentially.
Pfam PF11442: Protein of unknown function (DUF2826) (family)
This is a family of uncharacterised proteins that is highly conserved in Trypanosoma cruzi.
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 PF17291: N-terminal domain of M60-like peptidases (domain)
This accessory domain has a jelly roll topology.
Pfam PF14476: Petal formation-expressed (family)
The members of this plant family from Arabidopsis thaliana appear to be proteins found in the chloroplast, expressed in the pollen tube during the petal differentiation and expansion stage. The function is not known.
Pfam PF19199: Phage major coat protein, Gp8 (family)
Class I phage major coat protein Gp8 or B.  The coat protein  is largely alpha-helix with a slight curve.
Pfam PF05860: TPS secretion domain (repeat)
Filamentous hemagglutinin (FHA), the major 230-kDa adhesin of the whooping cough agent Bordetella pertussis, is one of the most efficiently secreted proteins in Gram-negative bacteria. FHA is secreted by means of the two-partner secretion (TPS) pathway. A TPS system is composed of two separate proteins, with TpsA the secreted protein and TpsB its associated specific outer-membrane transporter. All TPS-secreted proteins contain a distinctive N-proximal module essential for secretion, the TPS domain. The TPS domain folds into a beta-helix. This domain is found in a wide variety of secreted proteins from bacterial pathogens.
Wikipedia: In molecular biology, the haemagglutination activity domain is a conserved protein domain found near the N terminus of a number of large, repetitive bacterial proteins, including many proteins of over 2500 amino acids. A number of the members of this family have been designated adhesins, filamentous haemagglutinins, haem/haemopexin-binding protein, etc. Members generally have a signal sequence, then an intervening region, then the region described in this entry. Following this region, proteins typically have regions rich in repeats but may show no homology between the repeats of one member and the repeats of another. This domain is suggested to be a carbohydrate-dependent haemagglutination activity site.
Pfam PF05986: ADAM-TS Spacer 1 (domain)
This domain represents the Spacer-1 region from the ADAM-TS and ADAM-TS-like proteins. ADAM-TS (A Disintegrin and Metalloproteinase with Thrombospondin Motifs) is closely related to the ADAM family (A Disintegrin and Metalloproteinase) and is a subfamily of the metalloprotease family, sharing a high degree of sequence similarity and conserved domain organisation among its members. Members of the ADAM-TS family have been implicated in a range of diseases. ADAM-TS-like proteins lack a metalloprotease domain. They resides in the ECM and have regulatory roles. Examples of ADAM-TS-like proteins are papilin and punctin.
Pfam PF18631: Cucumopine synthase C-terminal helical bundle domain (domain)
McbB from Marinactinospora thermotolerans is an enzyme that catalyzes the Pictet-Spengler (PS) reaction of L-tryptophan and oxaloacetaldehyde to produce the betaC scaffold of marinacarbolines. This is the C-terminal domain composed of 5 bundled alpha helices. It is weakly similar to the signal transduction histidine-protein kinase BarA from E. coli and the DNA endonuclease I-MsoI from Monomastix sp.
Pfam PF12642: Conjugative transposon protein TcpC (family)
This family of proteins are annotated as conjugative transposon protein TcpC. The transfer clostridial plasmid (tcp) locus is part of some conjugative antibiotic resistance and virulence plasmids. TcpC was one of five genes whose products had low-level sequence identity to Tn916 proteins, having similarity to ORF13 homologues from Tn916, Tn5397, and CW459tet. This family of proteins is found in bacteria. Proteins in this family are typically between 302 and 351 amino acids in length.
Pfam PF23012: Syntrophin C-terminal PH domain (domain)
This entry represents the C-terminal PH domain found in syntrophin proteins. The syntrophin family are intracellular membrane-associated proteins that interact with both ion channels and signalling proteins. As such, syntrophins appear to be important for linking ion channels to intracellular signalling pathways. Syntrophins are concentrated at postsynaptic sites at the neuromuscular junction and may be involved in clustering acetylcholine receptors. In muscle and non-muscle tissues, syntrophin is associated with dystrophin, utrophin, and two homologues of the dystrophin carboxy-terminal region.
Pfam PF13866: SAP30 zinc-finger (domain)
SAP30 is a subunit of the histone deacetylase complex, and this domain is a zinc-finger. Solution of the structure shows a novel fold comprising two beta-strands and two alpha-helices with the zinc organising centre showing remote resemblance to the treble clef motif. In silico analysis of the structure revealed a highly conserved surface dominated by basic residues. NMR-based analysis of potential ligands for the SAP30 zn-finger motif indicated a strong preference for nucleic acid substrates. The zinc-finger of SAP3 probably functions as a double-stranded DNA-binding motif, thereby expanding the known functions of both SAP30 and the mammalian Sin3 co-repressor complex.
Pfam PF10406: Transcription factor TFIID complex subunit 8 C-term (domain)
This is the C-terminal, Delta, part of the TAF8 protein. The N-terminal is generally the histone fold domain, Bromo_TP ([pfam:PF07524]). TAF8 is one of the key subunits of the transcription factor for pol II, TFIID. TAF8 is one of the several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery.
Pfam PF14994: Testis-specific gene 13 protein (family)
This family of uncharacterised proteins are found in chordates. In humans this gene is found to be expressed specifically in the testes.
Pfam PF14781: Ciliary BBSome complex subunit 2, N-terminal (repeat)
The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme. The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialised for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction. BBS2 is one of the three Bardet-Biedl syndrome subunits that is required for leptin receptor signalling in the hypothalamus, and BBS2 and 4 are also required for the localisation of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia.
Pfam PF23079: Nucleolar protein 4, helical (domain)
This domain is found in human Nucleolar protein 4 (NOL4) and similar animal sequences. This domain is predicted to form an helical bundle.
Pfam PF22738: NACHT N-terminal Helical domain 7 (domain)
This entry represents the helical domain found at the N-terminus of bacterial NACHT conflict systems. This position is frequently occupied by an effector domain.
Pfam PF08887: GAD-like domain (domain)
This domain is functionally uncharacterised, but it appears to be distantly related to the GAD domain [pfam:PF02938].
Pfam PF09326: NADH-ubiquinone oxidoreductase subunit G, C-terminal (family)
Members of this family of are found at the C-terminus of NADH dehydrogenases subunit G or NADH-ubiquinone oxidoreductase subunit G. [ec:1.6.99.5].
Pfam PF04575: Surface lipoprotein assembly modifier (family)
Surface lipoprotein assembly modifier (Slam) is a surface lipoprotein that may have a role in virulence. In Neisseria, it is required for the surface display of lipidated virulence factors. Proteins in this family contain an eight-stranded beta-barrel domain.
Pfam PF16099: Recq-mediated genome instability protein 1, C-terminal OB-fold (family)
RMI1_C is a C-terminal oligo-nucleotide binding domain of Recq-mediated genome instability proteins. This domain interacts with RMI2-OB folds to make up the RMI core complex. The RMI core interface is crucial for BLM, Bloom syndrome, dissolvasome assembly and may have additional cellular roles as a docking hub for other proteins.
Pfam PF00888: Cullin family (repeat)
Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express several cullins (Cul1, 2, 3, 4A, 4B, 5, 7 and 9), each forming part of a multi-subunit ubiquitin complex . Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) , play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins .
This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an Î±+Î² domain, and a winged helix-like domain.
Wikipedia: Cullins are a family of hydrophobic scaffold proteins which provide support for ubiquitin ligases (E3). All eukaryotes appear to have cullins. They combine with RING proteins to form Cullin-RING ubiquitin ligases (CRLs) that are highly diverse and play a role in myriad cellular processes, most notably protein degradation by ubiquitination.
Pfam PF24048: NXF1/2/3/5 leucine-rich repeat domain (repeat)
This entry represents the leucine-rich repeat domain found in nuclear RNA export factor 1, 2, 3 and 5 (NXF1, NXF2, NXF3 and NXF5, respectively) from animals and their yeast orthologues mRNA export factor 67 (MEX67). These proteins are involved in the nuclear export of mRNA from the nucleus to the cytoplasm. NXFs are used by type D retroviruses to export their unspliced genomic RNA to the cytoplasm through this LRR domain, which binds to constitutive transport element of retroviral RNAs. Additionally, cellular mRNA transport is affected when this domain is mutated. In the case of MEX67, this domain is found within a region of the protein that allows MEX67 to act as an accessory factor in Rae1p-dependent mRNA export and is devoid of RNA-binding.