SII-SWORD/CoKE huggingface dataset:
Pfam PF16810: RXLR phytopathogen effector protein, Avirulence activity (family)
RXLR is a family of phytopathogen avirulence or effector proteins. RXLR proteins are defined by a secretion signal peptide - not in this family - followed by a conserved N-terminal domain with the sequence motif RXLR (Arg-Xaa-Leu-Arg) consensus sequence. The RXLR part is required for translocation inside plant cells, although it appears to be dispensable for the biochemical activity of the effectors when expressed directly inside host cells.  The effector activity resides in the C-terminal part of the family, which activate effector-triggered immunity in plants that carry a corresponding resistance (R) protein. The C-terminal region exhibits a fold appears to be able to evolve to outwit the host as the latter tries to acquire new immunity.
Pfam PF14319: Transposase zinc-binding domain (family)
This domain is likely to be a zinc-binding domain. It is found at the N-terminus of transposases belonging to the IS91 family.
Pfam PF06786: Uncharacterised protein family (UPF0253) (family)
This is a group of proteins of unknown function.
Pfam PF18534: Helical bundle domain (domain)
Lpg0393 is a Legionella pneumophila effector protein. Structure analysis reveals that it has two domains, the N-terminal domain is a Vps9-like domain, which is structurally most similar to the catalytic core of human Rabex-5 that activates the endosomal Rab proteins Rab5, Rab21 and Rab22. The C-terminal domain is a helical bundle domain. The C-terminal helical bundle of Lpg0393 corresponds to the N-terminal helical bundle of Rabex-5, it lacks an obvious region that corresponds to the membrane-binding motif of Rabex-5. One possibility may be that Lpg0393 localization to endosomes depends on an unknown Legionella effector.
Pfam PF22361: IglE, N-terminal domain (domain)
This entry represents the N-terminal domain of the intracellular growth locus E (IglE) protein from Francisella tularensis subsp. novicida. The lipoprotein IglE has been identified as a virulence factor that functions as a regulator of the Type IV system-mediated secretion.
Pfam PF05278: Arabidopsis phospholipase-like protein (PEARLI 4) (family)
This family contains several phospholipase-like proteins from Arabidopsis thaliana which are homologous to PEARLI 4.
Pfam PF18490: tRNA-binding domain (domain)
This is the N-terminal domain found in archeal type-2 serine-tRNA ligase (SerRS) ([ec:6.1.1.11]). The SerRS N-terminal domain interacts with the extra-arm stem and the outer corner of tRNA specific to Selenocysteine (tRNA-Sec).
Pfam PF02864: STAT protein, DNA binding domain (domain)
STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. This family represents the DNA binding domain of STAT, which has an ig-like fold. STAT proteins also include an SH2 domain [pfam:PF00017].
Wikipedia: Members of the signal transducer and activator of transcription (STAT) protein family are intracellular transcription factors that mediate many aspects of cellular immunity, proliferation, apoptosis and differentiation. They are primarily activated by membrane receptor-associated Janus kinases (JAK). Dysregulation of this pathway is frequently observed in primary tumors and leads to increased angiogenesis which enhances the survival of tumors and immunosuppression. Gene knockout studies have provided evidence that STAT proteins are involved in the development and function of the immune system and play a role in maintaining immune tolerance and tumor surveillance.
Pfam PF13806: Rieske-like [2Fe-2S] domain (domain)
In Proteobacteria and Actinobacteria the main nitrite reductase activity is contributed by the NADH-dependent nitrite reductase, which detoxifies the nitrite formed as the product of nitrate reduction. The NADH-nitrite reductase operon consists of 4 genes: nirB, nirD, nirC and cysG. The enzyme is formed by the two subunits nirB and nirD. NirC is a nitrite transporter and cysG is required for the synthesis of sirohaem, a cofactor of the nirB subunit . NirD displays some sequence similarities with the 2Fe-2S Rieske domain (see [prositedoc:PDOC00177]), but it does not contain the essential residues for the coordination of the iron sulphur .

The entry includes the NirD subunit. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant . The Rieske domain is a  cluster binding domain involved in electron transfer. The Rieske  cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs . In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske  cluster.
Pfam PF03522: Solute carrier family 12 (family)
This entry represents a domain found in the C-terminal of the solute carrier family 12 (SLC12) members, which are K-Cl cotransporters. The SLC12 family members are predicted to have 12 transmembrane (TM) regions in a central hydrophobic domain, together with hydrophilic N- and C-termini that are likely cytoplasmic. Comparison of their sequences with those of other ion-tranporting membrane proteins reveals that they are part of a new superfamily of cation-chloride co-transporters, which includes the Na-Cl and Na-K-2Cl co-transporters .
Wikipedia: In molecular biology, the electroneutral cation-Cl family of proteins are a family of solute carrier proteins. This family includes the products of the Human genes: SLC12A1, SLC12A1, SLC12A2, SLC12A3, SLC12A4, SLC12A5, SLC12A6, SLC12A7, SLC12A8 and SLC12A9.
Pfam PF13948: Domain of unknown function (DUF4215) (family)
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 PF00892: EamA-like transporter family (domain)
This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6. Members of this family usually carry 5+5 transmembrane domains, and this domain attempts to model five of these.
Wikipedia: EamA is a protein domain found in a wide range of proteins including the Erwinia chrysanthemi PecM protein, which is involved in pectinase, cellulase and blue pigment regulation, the Salmonella typhimurium PagO protein, and some members of the solute carrier family group 35 (SLC35) nucleoside-sugar transporters. Many members of this family have no known function and are predicted to be integral membrane proteins and many of the proteins contain two copies of the domain.
Pfam PF02162: XYPPX repeat (two copies) (repeat)
This repeat is found in a wide variety of proteins and generally consists of the motif XYPPX where X can be any amino acid. The family includes annexin VII [swissprot:P24639], the carboxy tail of certain rhodopsins [swissprot:Q17094]. This family also includes plaque matrix proteins, however this motif is embedded in a ten residue repeat in [swissprot:Q25460]. The molecular function of this repeat is unknown. It is also not clear if all the members of this family share a common evolutionary ancestor due to its short length and biased amino acid composition.
Pfam PF09607: Brinker DNA-binding domain (domain)
This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway.
Pfam PF03403: Platelet-activating factor acetylhydrolase, isoform II (domain)
Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in [pfam:PF02266], the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted.
Pfam PF20064: Family of unknown function (DUF6463) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. This family appears to be related to [pfam:PF03729].
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 PF21452: Cmr1-like, C-terminal (domain)
This entry represents the C-terminal RRM domain of CRISPR system Cmr subunit Cmr1-1 from P. furiosus.
Pfam PF13050: Protein of unknown function (DUF3911) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.
Pfam PF04852: ALOG domain (domain)
The 125-residue ALOG (Arabidopsis LSH1 and oryza G1) domain is rich in basic amino acids, especially arginine, and is highly conserved among land plants. Members of the ALOG family of proteins function as key developmental regulators. It has been proposed that the ALOG domain originated from the N-terminal DNA-binding domains of integrases belonging to the tyrosine recombinase superfamily encoded by a distinct type of DIRS1-like LTR retrotransposon found in several eukaryotes. Secondary structure predictions revealed an all-alpha helical domain with four conserved helices. Some proteins known to contain an ALOG domain are Arabidopsis thaliana LIGHT_DEPENDENT SHORT HYPOCOTYLS1 (LSH1),involved in phytochrome- dependent light signalling; Oryza G1, involved in the specification of sterile lemma identity and Plant defence proteins.
Pfam PF15281: Consortin C-terminus (domain)
Consortin is a trans-Golgi network cargo receptor involved in targeting connexins to the plasma membrane. This entry represents the C-terminal region which consists of two alpha- helices according to structure predictions.
Pfam PF17546: Beta defensin 50 (family)
Beta-defensin are small cationic antimicrobial peptides. Family members such as beta-defensin 50 (Defb50) has poor antimicrobial activity in its oxidised form, but this improves under reduced conditions.
Pfam PF18215: Histone chaperone Rtt106 N-terminal domain (domain)
This is the N-terminal domain of Rtt106 in Saccharomyces cerevisiae. Rtt106 is a histone chaperone that contributes to the deposition of newly synthesized acetylated Histone 3 Lysine 56 (H3K56ac) carrying H3-H4 complex on replicating DNA. The N-terminal domain of Rtt106 homodimerizes and interacts with H3-H4 independently of acetylation.
Pfam PF07303: Occludin homology domain (domain)
This domain represents a conserved region approximately 100 residues long within eukaryotic occludin proteins and the RNA polymerase II elongation factor ELL. Occludin is an integral membrane protein that localises to tight junctions, while ELL is an elongation factor that can increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by polymerase at multiple sites along the DNA. This shared domain is thought to mediate protein interactions.
Pfam PF01459: Eukaryotic porin (family)
This entry represents both eukaryotic mitochondrial porins and Tom40 proteins.

Eukaryotic mitochondrial porins are voltage-dependent anion-selective channels (VDAC) that behave as general diffusion pores for small hydrophilic molecules . The channels adopt an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The eukaryotic mitochondrial porins are Î²-barrel proteins, composed of between 12 to 16 Î²-strands that span the mitochondrial outer membrane. Yeast contains two members of this family (genes POR1 and POR2); vertebrates have at least three members (genes VDAC1, VDAC2 and VDAC3) . They are related to the mitochondrial import receptor subunit Tom40 proteins, sharing a common evolutionary origin and structure .

Tom40 is a mitochondrion outer membrane protein and a component of the TOM (translocator of the outer mitochondrial membrane) complex, which is essential for import of protein precursors into mitochondria . In Saccharomyces cerevisiae, TOM complex is composed of the subunits Tom70, Tom40, Tom22, Tom20, Tom7, Tom6, and Tom5 . Tom40 is an integral membrane protein and the main structural component of the protein-conducting channel formed by the TOM complex . It is stabilised by other components, such as Tom5, Tom6, and Tom7 .
Wikipedia: Voltage-dependent anion channels, or mitochondrial porins, are a class of porin ion channel located on the outer mitochondrial membrane. There is debate as to whether or not this channel is expressed in the cell surface membrane.
Pfam PF23697: YnfS (family)
This protein family includes Protein YnfS from Escherichia coli, a 29-residue long sequence encoded in the Qin prophage. It is predicted to adopt an alpha-helical configuration.
Pfam PF11073: Rift valley fever virus non structural protein (NSs) like (family)
This family contains several Phlebovirus non structural proteins which act as a major determinant of virulence by antagonising interferon beta gene expression.
Pfam PF00934: PE family (domain)
This family named after a PE motif near to the amino terminus of the domain.  The PE family of proteins all contain an amino-terminal region of about 110 amino acids.  The carboxyl terminus of this family are variable and fall into several classes.  The largest class of PE proteins is the highly repetitive PGRS class which have a high glycine content. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis.  The C-terminus of this domain contains the type VII secretion signal that has a YXXXD/E motif.
Pfam PF10388: EAL-domain associated signalling protein domain (domain)
In Bacillus species this highly conserved region of the YkuI protein lies immediately downstream of the EAL (diguanylate cyclase/phosphodiesterase domain 2) [pfam:PF00563] domain so that together they form a monomer which dimerises for its enzymatic action. The region contains three alpha helices and five beta strands and is the C-terminal half of the structure.
Pfam PF05165: GTP cyclohydrolase III (family)
GTP cyclohydrolase (GCH) III from Methanocaldococcus jannaschi catalyses the conversion of GTP to 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (FAPy). The reaction requires two bound magnesium ions for the catalysis and is activated by monovalent cations such as potassium and ammonium. The enzyme is a tetramer of identical subunits; each monomer is composed of an N- and a C-terminal domain that adopt nearly superimposible structures, suggesting that the protein has arisen by gene duplication. The family is found in archaea and bacteria.
Pfam PF01771: Viral alkaline exonuclease (family)
This family includes various alkaline exonucleases from members of the Herpesviridae and Baculoviridae. Alkaline exonuclease appears to have an important role in the replication of herpes simplex virus.
Pfam PF17985: SipA vinculin binding site (conserved_site)
This motif family includes the three vinculin binding sites found in the Shigella SipA/IpaA protein. The family also includes some proteins from Chlamydia species.
Pfam PF10171: Translocase of the Inner Mitochondrial membrane 29 (family)
This is a family of proteins conserved from nematodes to humans. The function is not known. However, family members such as the import inner membrane translocase sub-unit Tim29 (C19orf52) found in human, is shown to be required for the stability of the TIM22 complex. TIM22 complex imports and inserts multi-pass trans-membrane proteins into the mitochondrial inner membrane by formation of a twin-pore translocase with components in the outer and inner membranes. TIM29 is integrated into the inner member with the C terminus exposed to the inter-membrane space and able to contact the translocase of the outer membrane. It is required for complex stability and for the addition of the TIMM22 protein to the complex.
Pfam PF13049: Protein of unknown function (DUF3910) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length.
Pfam PF08817: WXG100 protein secretion system (Wss), protein YukD (domain)
The YukD protein family members participate in the formation of a translocon required for the secretion of WXG100 proteins ([pfam:PF06013]) in monoderm bacteria, with the WXG100 protein secretion system (Wss). Like the cytoplasmic protein EsaC in Staphylococcus aureus, YukD was hypothesized to play a role of a chaperone. YukD adopts a ubiquitin-like fold. Usually, ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins. In contrast to the situation in firmicutes, YukD-like proteins in actinobacteria are often fused to a transporter involved in the ESAT-6/ESX/Wss secretion pathway. Members of the YukD family are also associated in gene neighborhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyze ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release. This suggests that a subset of the YukD family in bacteria are conjugated and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway.
Pfam PF19487: Family of unknown function (DUF6023) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001077) is described by MIBiG as an example of the following biosynthetic classes, polyketide and terpene. This family includes a protein from the alkyl-O-dihydrogeranyl- methoxyhydroquinones biosynthetic gene cluster from Actinoplanes missouriensis 431 and 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 PF20061: Domain of unknown function (DUF6460) (domain)
This domain on unknown function is found at the C-terminal of uncharacterised proteins, found in Alphaproteobacteria. Proteins containing this domain are typically between 88 and 109 amino acids in length. There is a conserved motif GAxI/VVxP. Some members of this entry are likely integrases.
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 PF16719: SAWADEE domain (domain)
The SAWADEE domain, found in plant homeobox proteins, has a pair of tandem tudor-like folds that bind chromatin.
Pfam PF17976: RING/Ubox like zinc-binding domain (domain)
This is a RING zinc finger domain found in parkin proteins. Parkin consists of a ubiquitin-like (Ubl) domain and a 60-amino acid linker followed by this domain RING0 and three additional zinc finger domains characteristic of the RBR family. RING0 binds two coordinated zinc atoms at each extremity of the domain with a hairpin. Deletion of RING0 massively derepressed parkin activity supporting the role of RING0 in autoinhibition, point mutations in RING0 (Phe146 to Ala) or RING2 (Phe463 to Ala) both increased parkin activity. The REP (repressor element of parkin) and RING0 domains play a preeminent role in repressing parkin ligase activity through their interactions with RING1 and RING2, respectively.
Wikipedia: In molecular biology, a RING (short for Really Interesting New Gene) finger domain is a protein structural domain of zinc finger type which contains a C3HC4 amino acid motif which binds two zinc cations (seven cysteines and one histidine arranged non-consecutively). This protein domain contains 40 to 60 amino acids. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Conversely, proteins with RING finger domains are the largest type of ubiquitin ligases in the human genome.
Pfam PF15785: Serine/threonine-protein kinase smg-1 (family)
SMG1 is a family of eukaryotic proteins. In humans this family acts as an mRNA-surveillance protein. In C.elegans, SMG1, a phosphatidylinositol kinase-related protein kinase, is a key regulator of growth. Loss of SMG1 leads to hyperactive responses to injury and subsequent growth that continues out of control. It has an antagonistic role to mTOR signalling in these worms and possibly also in higher eukaryotes.
Pfam PF09883: DUF2110 central domain (domain)
This domain, found in various hypothetical archaeal proteins, has no known function. This domain is the middle of three domains found in the DUF2110 family proteins. It has an OB-like fold.
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 PF01194: RNA polymerases N / 8 kDa subunit (domain)
In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit Rpo10 (gene rpoN)  is a small protein of about 8kDa, it is evolutionary related  to a 8.3kDa component shared by all three forms of eukaryotic RNA polymerases (RPABC5, gene Rpb10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R .

This family includes both archaeal subunit N, also known as Rpo10 following the eukaryotic nomenclature , and eukaryotic Rpb10. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that bind a zinc ion .