SII-SWORD/CoKE huggingface dataset:
Sodium channel and clathrin linker 1 (SCLT1)
Type: Family

Sodium channel and clathrin linker 1 (SCLT1/CAP-1A) is an adapter protein that links clathrin and sodium channel Na(v)1.8. It may regulate Na(v)1.8 channel density at the cell surface . SCLT1 is a component of the distal appendages (DAPs) of centrioles, which are thought to anchor cilia to the plasma membrane . SCLT1 mutations are associated with the ciliopathy known as oral-facial-digital syndrome (OFD) .
DDB1- and CUL4-associated factor 15 (DCAF15)
Type: Family

DCAFs, Ddb1- and Cul4-associated factors, are substrate receptors for the Cul4-Ddb1 Ubiquitin Ligase. There are 18 different factors, the majority of which are WD40-repeat-proteins . This family represents the DDB1- and CUL4-associated factor 15 (DCAF15), which is the substrate-recognition component of the DCX(DCAF15) complex, a cullin-4-RING E3 ubiquitin-protein ligase complex that mediates ubiquitination and degradation of target proteins , and acts as a regulator of the natural killer (NK) cells effector functions . Aryl sulfonamide anticancer agents appear to promote binding of DCAF15 to the RNA-recognition motif (RRM) of RBM39, which suggests that derivatives of the aryl-sulfonamides may be used to target other RRM-containing proteins .
Proline-rich protein 29-like (PRR29-like)
Type: Family

This entry represents a group of proteins including proline-rich protein 29 (PRR29) and the uncharacterised protein C21orf58. The function of this family is unknown.
Protein FAM118 (FAM118)
Type: Family

This entry represents FAM118, including FAM118A and FAM118B.

FAM118A has been identified as a gene expressed in glioblastoma stem cells, but not expressed in neural stem cells . Its function is unkown.

Cajal bodies are specialized compartments in the nucleus that are involved in the biogenesis of small nuclear ribonucleoproteins (snRNPs). FAM118B is a component of Cajal bodies that plays an important role in Cajal body formation, snRNP biogenesis and cell viability .
Malonyl-CoA decarboxylase (Malonyl_CoA_deC)
Type: Family

Malonyl-CoA, in addition to being an intermediate in the
de novo
synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that regulates the transfer of long-chain fatty acyl-CoA into mitochondria, where they are oxidised. After exercise, malonyl-CoA decarboxylase participates with acetyl-CoA carboxylase in regulating the concentration of malonyl-CoA in liver and adipose tissue, as well as in muscle. Malonyl-CoA decarboxylase is regulated by AMP-activated protein kinase (AMPK) .
Stb2/Stb6 (Stb2/Stb6)
Type: Family

This entry includes Stb2/Stb6 from fungi. They interact with Sin3 . Their function is not clear.
At3g056750-like (At3g05675-like)
Type: Family

This entry represents a group of BTB/POZ domain-containing proteins mostly from plants, including At3g05675, At2g13690, At1g63850, At5g60050 and At3g50780 from Arabidopsis thaliana.

At3g05675 and related proteins may act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins .
Uncharacterized protein YOR389W-like (YOR389W-like)
Type: Family

Proteins in this family are currently uncharacterised, including YOR389W, YPL277C and YPL278C from budding yeasts.
Huntingtin-interacting protein K, UBA-like domain (HYPK_UBA)
Type: Domain

HYPK, also called Huntingtin yeast partner K or Huntingtin yeast two-hybrid protein K, is an intrinsically unstructured Huntingtin (HTT)-interacting protein with chaperone-like activity. It is involved in regulating cell growth, cell cycle, unfolded protein response, and cell death . Proteins matched by this entry contain an N-terminal ubiquitin-associated (UBA) region that shows high sequence similarity with that of eukaryotic nascent polypeptide-associated complex proteins (NAC), which is one of the cytosolic chaperones that contact the nascent polypeptide chains as they emerge from the ribosome and assist in post-translational processes .
Centrobin (Centrobin)
Type: Family

Centrobin is a centrosomal protein required for centriole duplication . It is also required for nucleation and stabilization of microtubules . In Drosophila, centrobin is a negative regulator of ciliogenesis in specialized sensory neurons , whereas in vertebrates it acts as a positive regulator of ciliogenesis .
UV-B-induced protein At3g17800-like (At3g17800-like)
Type: Family

This entry represents a group of plant proteins, including At3g17800 from Arabidopsis .
Centrosomal protein of 55kDa (CEP55)
Type: Family

Cep55 is a centrosome protein that plays a role in mitotic exit and cytokinesis . It is a regulator of the PI3K/AKT pathway and has been linked to cancers .
Uncharacterized protein C6orf163 (C6orf163)
Type: Family

This family consists of human C6orf163 and homologues. Its function is not known.
Protein LAZY1 (LAZY1)
Type: Family

The LAZY1 family contains plant-specific proteins involved in gravitropism by regulation of auxin flow . The direction of gravity is perceived by plants mainly by gravity-sensing cells (statocytes), which detect the sedimentation of starch-accumulating high-density amyloplasts. This results in a chemical signal that is transmitted to responding tissues (auxin transport), where the signal induces the differential growth of the lower and upper surfaces of gravity-responsive organs.
Coiled-coil domain-containing protein 13 (CCDC13)
Type: Family

This family represents eukaryotic Coiled-coil domain-containing protein 13 (CCDC13). Human CCDC13 is a satellite protein required for ciliogenesis and genome stability .
Precursor of CEP13/CEP14 (CEP13/CEP14)
Type: Family

This entry includes the precursors of CEP13 and CEP14. These are found only in plants and although uncharacterised are thought to be extracellular signalling peptides that regulate primary root growth rate and nitrogen-demand signalling from comparison with CEP1 (

) . The cep13 gene is induced by gibberelic acid and repressed by nitrogen and CEP13 accumulates in the roots in response to osmotic stress and depletion of nitrogen and ammonium chloride . CEP13 is repressed in shoots by nitrogen starvation . CEP14 is only slightly repressed in roots by carbon dioxide and induced in shoots by osmotic stress .
Probable NAD(P)H dehydrogenase subunit CRR3, chloroplastic (CRR3)
Type: Family

Protein CRR3 is probably a subunit of the NAD(P)H dehydrogenase found in the chloroplasts of plants. It is required for the accumulation of the hydrogenase in chloroplasts of
Arabidopsis
.
PCNA-interacting partner (PARPBP)
Type: Family

PCNA-interacting partner (also known as PARI) is an antirecombinase. It interacts with PCNA and inhibits homologous recombination . It also modulates stalled fork processing, which is required for stable genome inheritance under both endogenous and exogenous replication stress .
Ovate protein family (Ovate)
Type: Family

This entry includes a group of plant transcriptional repressors, known as Ovate proteins. In Arabidopsis, there are 18 Ovate family members . They function as transcriptional repressors that regulate growth and development in plants .
Uncharacterized protein At5g64816-like (At5g64816-like)
Type: Family

This family of uncharacterised proteins includes Arabidopsis thaliana At5g64816, a thionin-like protein of unknown function.
Uncharacterized protein C5orf52 (C5orf52)
Type: Family

This uncharacterised family consists of human C5orf52 and homologues.
Protein maintenance of PSII under high light 1 (MPH1)
Type: Family

MPH1 is a photosystem II (PSII) associated protein that participates in the maintenance of normal PSII activity under photoinhibitory stress, protecting PSII against photooxidative damage .
Rop guanine nucleotide exchange factor (RopGEF)
Type: Family

In plants, the small GTP-binding proteins called Rops work as signalling switches that control growth, development and plant responses to various environmental stimuli. Rop (Rho of plants) proteins, Rac-like, and atRac in Arabidopsis thaliana belong to the Rho family of Ras-related GTP-binding proteins that turn on signalling pathways by switching from a GDP-bound inactive to a GTP-bound active conformation. Activation depends on guanine nucleotide exchange factors (GEFs) that catalyse the otherwise slow GDP dissociation for subsequent GTP binding. The plant-specific RopGEFs represent a unique family of exchange factors that display no homology to any known RhoGEFs from animals and fungi. They comprise a highly conserved catalytic domain termed PRONE (plant-specific Rop nucleotide exchanger) with exclusive substrate specificity for members of the Rop family. The PRONE domain has been shown to be necessary and sufficient to promote nucleotide release from Rop .
Beta-carotene isomerase D27-like (D27-like)
Type: Family

Beta-carotene isomerase D27 (also known as Protein DWARF-27) from plants is involved in strigolactones biosynthesis. It is a beta-carotene isomerase that converts all-trans-beta-carotene into 9-cis-beta-carotene, which is cleaved by CCD7 into a 9-cis-configured aldehyde . This is an iron-containing protein that localises in chloroplasts and is expressed mainly in vascular cells of shoots and roots . This entry also includes some uncharacterised proteins from bacteria.
Plastid division protein PDV1/PDV2 (PDV1/PDV2)
Type: Family

This entry represents a group of plant proteins, including PDV1 and PDV2. They mediate recruitment of the dynamin-related protein ARC5 to the plastid division site .
Noncompact myelin-associated protein (NCMAP)
Type: Family

Noncompact myelin-associated protein, also known as MP11, plays a role in myelin formation. It is a membrane protein that inhibits myelination when it is either over- or underexpressed. MP11 expression is restricted to the placenta and peripheral nervous system, where it is expressed by Schwann cells and localized to paranodes and Schmidt-Lanterman incisures (SLIs) of non-compact myelin. .
At4g14100-like (At4g14100-like)
Type: Family

This entry represents a group of plant proteins, including At4g14100 from Arabidopsis. Their function is not clear.
Transmembrane protein 52 (TMEM52)
Type: Family

This family includes Transmembrane protein 52 (TMEM52) and Transmembrane protein 52B (TMEM52B). The function of the family is unknown.
PLD-regulated protein1-like (PLDrp1-like)
Type: Family

This entry includes a group of plant proteins, including At5g39570 (also known as PLD-regulated protein1, PLDrp1) from Arabidopsis. PLDrp1 has been found to bind phosphatidic acid and act downstream of PLDalpha .
Outer envelope membrane protein 7-like (OEP7-like)
Type: Family

This entry represents a group of plant proteins, including OEP7 (AT3G52420) from Arabidopsis. OEP7 is a chloroplast outer envelope protein .
Methyl-CpG-binding domain-containing protein 13-like (MBD13-like)
Type: Family

This entry represents a group of plant proteins, including MBD13 (At5g52230) from Arabidopsis. MBD13 contains the methyl-CpG-binding domain .
F-box only protein 47 (FBXO47)
Type: Family

The function of FBXO47 is not clear. It may play a role in carcinogenesis .
At3g27210-like (At3g27210-like)
Type: Family

This entry represents a group of plant proteins, including At3g27210 from Arabidopsis. Their function is not clear.
Protein POLR1D, isoform 2-like (POLR1D-like)
Type: Family

This entry represents a group of animal proteins, including protein POLR1D, isoform 2 from humans. The function of this isoform is not clear. However, mutations of the POLR1D gene have been linked to Treacher Collins syndrome, a mandibulofacial dysostosis caused by mutations in genes involved in ribosome biogenesis and synthesis .
Tektin-like protein 1 (TEKTL1)
Type: Family

This entry represents homologues of Tektin-like protein 1 (TEKTL1 also known as Ccdc105). TEKTL1 is a conserved tektin-like sperm microtubule inner protein (MIP) that decorate the lumen of axonemal doublet microtubules (DMTs) and stabilise the structure. The tertiary structure of TEKTL1 is similar to that of tektins . However, the mechanism by which TEKTL1 and tektins assemble into filaments differs slightly. TEKTL1 shares many structural features with tektins, including the overall helix-turn-helix fold and head-to-tail association into filaments, but does not
seem to assemble into the large oligomeric bundles associated with tektins. In both sea urchin and bovine sperm, TEKTL1 binds to the outer inter-protofilament cleft of A11/A12, where it may help stabilise the outer junction .
BEN domain-containing protein 4 (BEND4)
Type: Family

This entry represents a family of chordate-specific proteins known as BEN domain-containing protein 4 (BEND4). The function of BEND4 is not clear.
Outer envelope pore protein 37-like (OEP37-like)
Type: Family

This entry represents a group of plant proteins, including OEP37 from Arabidopsis. OEP37 may constitute a novel peptide-sensitive ion channel in the outer envelope of plastids .
Protein TOPAZ1 (TOPAZ1)
Type: Family

TOPAZ1 is a germ cell specific protein highly conserved in vertebrates . It is essential for male meiotic progression . TOPAZ1 is an abbreviation for testis and ovary-specific PAZ domain-containing protein 1, although TOPAZ1 does not contain a PAZ domain.
Putative C->U-editing enzyme APOBEC-4 (APOBEC4)
Type: Family

APOBEC4 belongs to the AID/APOBEC family. In mammals, APOBEC4 is expressed primarily in testis .

The AID/APOBEC family are deaminases that function in RNA/DNA editing. The AID/APOBEC family contains several subfamilies: AID, APOBEC1, APOBEC2, APOBEC3, APOBEC4 and APOBEC5 . APOBEC1, the founder member of the family, catalyzes cytidine to uridine (C ->U) deamination .
Casein kinase II subunit alpha'-interacting protein (CSNKA2IP)
Type: Family

CSNKA2IP, also known as CKT2, may play a role in chromatin regulation of male germ cells .
Protein PriA/CPL1 (PriA/CPL1_fungi)
Type: Family

This family represents a group of fungal proteins, including PriA from Lentinula edodes and CPL1 from Cryptococcus neoformans. PriA was identified as a gene that may play a role during the beginning of fruiting . CPL1 is a virulence factor which promotes fungal virulence by enhancing type 2 inflammation in the mouse host[[cite35896747]].
Late embryogenesis abundant protein, LEA_5 subgroup (LEA_5)
Type: Family

LEA (late embryogenesis abundant) proteins were first identified in land plants. Plant LEA proteins have been found to accumulate to high levels during the last stage of seed formation (when a natural desiccation of the seed tissues takes place) and during periods of water deficit in vegetative organs. Later, LEA homologues have also been found in various species . They have been classified into several subgroups in Pfam and according to Bray and Dure .

This entry represents Pfam LEA_5, or D-19 from Dure, or group 1 from Bray. Proteins in this entry includes EM1 (At3g51810) and EM6 (At2g40170) from Arabidopsis . This entry also includes some bacterial hydrophilins. Some proteins in this entry also contain the KGG motif (

).
Protein plastid transcriptionally active 7 (PTAC7)
Type: Family

Transcriptionally active chromosome (TAC) is a fraction of protein/DNA complexes with RNA polymerase activity in the plastid. It consists of the multisubunit plastid-encoded polymerase (PEP) and several non-rpo subunits. PTAC7/TAC7 is a TAC component. It has a role in regulating PEP-dependent chloroplast gene expression and chloroplast development .
Prp19 (Prp19)
Type: Family

This family includes animal Pre-mRNA-processing factor 19 (Prp19) and its homologues.

Prp19, also known as DNA repair protein Pso4 (psoralen-sensitive mutant 4), is a ubiquitously expressed multifunctional E3 ubiquitin ligase with pleiotropic activities in DNA damage signalling, repair, and replicative senescence. It functions as a critical component of DNA repair and DNA damage checkpoint complexes. It senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, and regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex .

Prp19 is essential for spliceosome assembly and stability. It is a core component of the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome and participates in its assembly, its remodelling and is required for its activity. During assembly of the spliceosome, it mediates Lys-63-linked polyubiquitination of the U4 spliceosomal protein PRPF3. Ubiquitination of PRPF3 allows its recognition by the U5 component PRPF8 and stabilises the U4/U5/U6 tri-snRNP spliceosomal complex .

Prp19 contains an N-terminal E3 ubiquitin ligase U-box domain with E2 recruitment function that facilitates dimerisation and is essential for its auto-ubiquitination activity in vitro or when overexpressed , a coiled-coil Prp19 homology region that mediates its tetramerisation and interaction with CDC5L and SPF27 and a C-terminal seven-bladed WD40 β-propeller that forms an asymmetrical barrel-shaped structure important for substrate recognition and recruitment .
Protein PEP-related development arrested 1 (PRDA1)
Type: Family

PRDA1 is a chloroplast nucleoid protein that is involved in the regulation of plastid gene expression and is required for early chloroplast development. It may positively regulate plastid-encoded RNA polymerase (PEP) activity through its interaction with two other proteins known to be essential for PEP-related chloroplast development, MRL7 and FSD2 .
Transmembrane protein 158 (TMEM158)
Type: Family

Transmembrane protein 158 (TMEM158) is upregulated during Ras-induced senescence and has been associated with various cancers .
Uncharacterized protein C17orf107 (C17orf107)
Type: Family

This family of uncharacterised proteins from mammals includes human C17orf107 and homologues.
Alpha-L-arabinofuranosidase B (ABFB)
Type: Family

ABFB is an alpha-L-arabinofuranosidase involved in the degradation of arabinoxylan, a major component of plant hemicellulose . It catalyses the hydrolysis of alpha-1,2-, alpha-1,3- and alpha-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan and L-arabinan .
Translation machinery-associated protein 17 (TMA17)
Type: Family

Demands on the proteasome increase during environmental stresses. TMA17 (ADC17) is a stress responsive gene that functions as a proteasome assembly chaperone. It interacts with the amino terminus of Rpt6 to assist formation of the Rpt6-Rpt3 ATPase pair, an early step in proteasome assembly .
DSC E3 ubiquitin ligase complex subunit 4-like (Dsc4-like)
Type: Family

This entry represents a group of fungal proteins, including Dsc4 from fission yeasts. Dsc4 is a component of the DSC E3 ubiquitin ligase complex, which is required for the sre1 transcriptional activator proteolytic cleavage to release the soluble transcription factor from the membrane in low oxygen or sterol conditions. The complex also plays an important role in the multivesicular body (MVB) pathway and functions in a post-endoplasmic reticulum pathway for protein degradation .
Centriolar satellite-associated tubulin polyglutamylase complex regulator 1 (CSTPP1)
Type: Family

Centriolar satellite-associated tubulin polyglutamylase complex regulator 1 (CSTPP1, previously referred to as C11orf49) is a regulator of the tubulin polyglutamylase complex (TPGC) that controls cytoskeletal organization, nuclear shape, and cilium disassembly by balancing microtubule and actin assembly . Disruption of CSTPP1-TPGC leads to developmental defects.
Flap endonuclease (FEN)
Type: Family

This entry represents a family of proteins that includes flap endonucleases from bacteria and viruses. Flap endonucleases (FENs) catalyse the exonucleolytic hydrolysis of blunt-ended duplex DNA substrates and the endonucleolytic cleavage of 5'-bifurcated nucleic acids at the junction formed between single and double-stranded DNA .

Escherichia phage T5 encodes the flap endonuclease D15, which catalyzes both the 5'-exonucleolytic and structure-specific endonucleolytic hydrolysis of DNA branched nucleic acid molecules . In bacteriophage T4, disruption of the rnh gene (which encodes a FEN, known historically as T4 RNase H) results in slower, less accurate DNA replication. Bacteriophage T4 has both 5' nuclease and flap endonuclease activities .
Polysaccharide lyase 8 (Lyase_8)
Type: Family

This entry includes a group of lyase enzymes capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues. This family also includes xanthan lyase from Bacillus .
Cyclin-dependent protein kinase inhibitor SMR11/SMR16 (SMR11/SMR16)
Type: Family

The SIAMESE-RELATED (SMR) family of cyclin-dependent kinase inhibitors regulate the transition from the mitotic cell cycle to endoreplication in plants . The specific cyclin-dependent kinase complexes which are inhibited, and the functions of most SMRs remain unknown.

Seventeen putative SMR genes have been identified in the Arabidopsis genome 17. The most divergent group consists of SMR11 and SMR16, which are represented by this entry.
Inner membrane protein YiaA-like (YiaA-like)
Type: Family

This entry represents a group of proteins including the inner membrane protein YiaA. The function of YiaA is not clear.
DNA mismatch repair protein MutL/Mlh/Pms-like (MutL/Mlh/Pms-like)
Type: Family

Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex . This entry represents a family of evolutionarily related DNA mismatch repair proteins, including MutL, Mlh1, Mlh2 and Mlh3, and Pms 1 and 2. Bacterial MutL proteins are homodimers, while their eukaryotic homologues form heterodimers consisting of the MutL homologue Mlh1 and either Pms1, Pms2 or Mlh3 . MutL homologues share a conserved ATP binding site .
Protein Casparian strip integrity factor 1/2 (CIF1/2)
Type: Family

This entry represents a group of plant proteins, including Protein Casparian strip integrity factor 1/2 (CIF1/2) from Arabidopsis. They are required for contiguous Casparian strip formation in Arabidopsis roots .
Thionin-like protein (THNL)
Type: Family

This entry represents a group of plant proteins, including TAP1 from Antirrhinum majus and THNL1/2 from Arabidopsis. THNL1/2 belongs to the plant thionin (PR-13) family and may be involved in plant defense .
Protein snakeskin (Ssk)
Type: Family

This entry represents a group of insect proteins, including protein snakeskin (Ssk) from Drosophila melanogaster. It is required for assembly of smooth septate junctions (sSJs), together with mesh and Tsp2A .
Zinc finger protein 428 (ZNF428)
Type: Family

The function of ZNF428 is not clear.
Protein MJ0935 (MJ0935)
Type: Family

This entry represents uncharacterised proteins from archaea, including protein MJ0935 from
Methanocaldococcus jannaschii
. These proteins are related to the eukaryote integral membrane proteins EMC3 and TMCO1-like. The structure has been solved for protein MJ0480 also from
M. jannaschii
, which has four transmembrane helices. It has been suggested that archaeal proteins may function as insertases of the archaeal plasma membrane . They may interact with their substrates in a groove-like structure at an amphiphilic protein-lipid interface and allow the transmembrane segments of the substrate to slide into the lipid bilayer .