SII-SWORD/CoKE huggingface dataset:
Wntless-like, transmembrane domain (WLS-like_TM)
Type: Domain

Protein wntless (WLS) regulates Wnt proteins sorting and secretion in a feedback regulatory mechanism . This reciprocal interaction plays a key role in the regulation of expression, subcellular location, binding and organelle-specific association of Wnt proteins. It also plays an important role in establishment of the anterior-posterior body axis formation during development . This protein is homologous to GPR180, TMEM145, and TMEM181, which have been described as GOST proteins (for GOLD domain seven-transmembrane helix proteins) together with TMEM87A/B, GPR107, and GPR108, as they share the same domain architecture consisting of a GOLD domain atop of a membrane-spanning seven-transmembrane helix domain .

This entry represents the seven-transmembrane domain of protein wntless (WLS) from Drosophila and its homologues.
Ropporin, dimerization/docking domain (ROP_DD)
Type: Domain

This entry includes ropporin-1A (ROP1A, also called cancer/testis antigen 91, CT91, or rhophilin-associated protein 1A), ropporin-1B (ROP1B, also called rhophilin-associated protein 1B), and ropporin-1-like protein (ROPN1L, also called ROPN1-like protein, AKAP-associated sperm protein, or ASP). ROP1A, ROP1B and ROPN1L play important roles in male fertility . They are involved in fibrous sheath integrity and sperm motility and play roles in cAMP-dependent protein kinase (PKA)-dependent signaling processes required for spermatozoa capacitation. ROP1A and ROP1B have been shown to bind AKAP3 .
This entry represents a conserved helical bundle domain that shows high sequence similarity to the dimerization/docking (D/D) domain of the regulatory subunit of PKA, which dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs). It has been suggested that ROPN1 activates RhoA signalling via rhophilin-1 (RHPN1), promoting cell migration, invasion and metastatic potential. ROPN1A/B has been identified as antigens able to induce a strong humoral immune response, being possible targets for immunotherapy in certain cancers .
RING finger protein 17-like, first Tudor domain (RNF17-like_TUDOR_rpt1)
Type: Domain

This entry represents the first Tudor domain identified in RING finger protein 17 (RNF17) and similar proteins from chordates.

TDRD4, also known as RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis . TDRD4 also acts as a potential cancer/testis antigen in breast and liver cancers . TDRD4 contains a RING finger and five Tudor domains.
Membrane protein YpdK (YpdK)
Type: Family

This entry represents a small protein YpdK (

) that was found to fractionate with the inner membrane . This protein is predicted to fold into a single transmembrane helix .
RING finger protein 17-like, second Tudor domain (RNF17-like_TUDOR_rpt2)
Type: Domain

This entry represents the second Tudor domain identified in RING finger protein 17 (RNF17) and similar proteins from chordates.

TDRD4, also known as RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis . TDRD4 also acts as a potential cancer/testis antigen in breast and liver cancers . TDRD4 contains a RING finger and five Tudor domains.
RING finger protein 17-like, third Tudor domain (RNF17-like_TUDOR_rpt3)
Type: Domain

This entry represents the third Tudor domain identified in RING finger protein 17 (RNF17) and similar proteins from chordates.

TDRD4, also known as RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis . TDRD4 also acts as a potential cancer/testis antigen in breast and liver cancers . TDRD4 contains a RING finger and five Tudor domains.
RING finger protein 17-like, fourth Tudor domain (RNF17-like_TUDOR_rpt4)
Type: Domain

This entry represents the fourth Tudor domain identified in RING finger protein 17 (RNF17) and similar proteins from chordates.

TDRD4, also known as RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis . TDRD4 also acts as a potential cancer/testis antigen in breast and liver cancers . TDRD4 contains a RING finger and five Tudor domains.
RING finger protein 17-like, fifth Tudor domain (RNF17-like_TUDOR_rpt5)
Type: Domain

This entry represents the fifth Tudor domain identified in RING finger protein 17 (RNF17) and similar proteins from chordates.

TDRD4, also known as RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis . TDRD4 also acts as a potential cancer/testis antigen in breast and liver cancers . TDRD4 contains a RING finger and five Tudor domains.
Hemotin (Hemotin)
Type: Family

This entry represents a group of proteins specific to Drosophila species, including Hemotin from Drosophila melanogaster. Hemotin is a transmembrane α-helical microprotein localised to early endosomes in hemocytes (Drosophila macrophages), where it regulates endosomal maturation during phagocytosis by repressing the cooperation of 14-3-3zeta with specific phosphatidylinositol enzymes. Hemocytes are professional phagocytes tasked with removing dying cells and microorganisms invading the body. Drosophila hemotin mutants accumulate undigested phagocytic material inside enlarged endolysosomes, resulting in reduced ability to fight bacteria and severely reduced life span .
Negative regulator of P-body association (NoBody)
Type: Family

This entry represents a group of proteins predominantly found in mammals, including human Negative regulator of P-body association, also called P-body dissociating protein or protein NoBody (non-annotated P-body dissociating polypeptide), a microprotein that interacts with mRNA decapping proteins, which remove the 5' cap from mRNAs to promote 5'-to-3' decay. It localises to P-bodies, which are mRNA-decay-associated RNA-protein granules. NoBody promotes dispersal of P-body components and is likely to play a role in the mRNA decapping process. Decapping proteins participate in mRNA turnover and nonsense-mediated decay (NMD) .
Apelin receptor early endogenous ligand (ELA)
Type: Family

This entry represents a group of proteins from vertebrates, including Apelin receptor early endogenous ligand, also called protein Elabela or protein Toddler (ELA), an endogenous peptidic ligand of the G protein-coupled receptor APJ, also called apelin receptor (APLNR). The apelin/APJ axis contributes to maintaining homeostasis in normal and pathological hearts, and is also involved in heart development, including endoderm differentiation, heart morphogenesis and coronary vascular formation. ELA plays crucial roles in heart development and disease conditions, presumably at time points or at areas of the heart different from apelin. It is a potential therapeutic peptide, showing beneficial effects on body fluid homeostasis, cardiovascular health, and renal insufficiency, as well as potential benefits for metabolism and diabetes .
Replication factor C, lid domain (RFC_lid)
Type: Domain

Replication factor C (RFC) is five-protein clamp loader complex that forms a stable ATP-dependent complex with the sliding clamp, PCNA, which binds specifically to primed DNA. RFC subunits belong to the clamp loader clade of the AAA superfamily and consist of a ATPase domain, a lid domain and a C-terminal domain . This entry represents the lid domain.
Zinc finger FYVE domain-containing protein 1, second B-box-type 1 (ZFYVE1_second_BBox1)
Type: Domain

This entry represents the second BBox-type 1 domain of ZFYVE1.

ZFYVE1, also termed double FYVE-containing protein 1 (DFCP1) is a novel tandem FYVE domain containing protein that binds phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) with high specificity over other phosphoinositides. The subcellular distribution of exogenously-expressed ZFYVE1 to Golgi, endoplasmic reticulum (ER) and vesicular is governed in part by its FYVE domains but unaffected by Wortmannin, a PI3-kinase inhibitor. It plays a role in the formation of lipid droplets (LDs), regulating their morphology, size and distribution which are storage organelles, central to lipid and energy homeostasis .

ZFYVE1 harbors two B-box domains, both of which show high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterised by a C6H2 zinc-binding consensus motif .
Zinc finger FYVE domain-containing protein 1, first B-box-type 1 domain (ZFYVE1_first_BBox1)
Type: Domain

This entry represents the first BBox type 1 domain of ZFYVE1.

ZFYVE1, also termed double FYVE-containing protein 1 (DFCP1) is a novel tandem FYVE domain containing protein that binds phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) with high specificity over other phosphoinositides. The subcellular distribution of exogenously-expressed ZFYVE1 to Golgi, endoplasmic reticulum (ER) and vesicular is governed in part by its FYVE domains but unaffected by Wortmannin, a PI3-kinase inhibitor. It plays a role in the formation of lipid droplets (LDs), regulating their morphology, size and distribution which are storage organelles, central to lipid and energy homeostasis .

ZFYVE1 harbors two B-box domains, both of which show high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterised by a C6H2 zinc-binding consensus motif .
Snurportin-1, m3G cap-binding domain (Snurportin1_C)
Type: Domain

Snurportin-1 (SPN1 or SNUPN) is a nuclear import adaptor for m3G-capped spliceosomal U small nucleoproteins (snRNPs), which are assembled in the cytoplasm. After capping and assembly, the U snRNPs are transported into the nucleus by SPN1 and importin beta; SPN1 is then returned to the cytoplasm by exportin 1 (CRM1), which also transports the non-capped U snRNPs. The U snRNPs are essential elements of the spliceosome, which catalyses the excision of introns and the ligation of exons to form a mature mRNA. SPN1 contains two domains, an N-terminal importin beta-binding (IBB) domain and a C-terminal m3G cap-binding domain, which is represented in this entry .
Fidgetin-like 1, ATPase domain (FIGNL1_ATPase)
Type: Domain

This entry represents the ATPase domain of Fidgetin-Like 1 (FIGNL1).

FIGNL1 is an ATP-dependent microtubule severing protein that plays a key role in meiotic spindle organisation . This domain correspond to the meiotic clade of AAA ATPases that includes four families: Vps4, spastin, katanin and fidgetin. These ATPases regulate diverse cellular processes, including neuronal development, cell division, and ciliogenesis . Meiotic clade AAA ATPases function as hexamers that can cycle between the active assembly and inactive monomers/dimers in a regulated process, and they appear to disassemble their polymeric substrates by translocating subunits through the central pore of their hexameric ring .
Large ribosomal subunit protein bL17, conserved site (Ribosomal_bL17_CS)
Type: Conserved_site

This entry represents a conserved site found at the N-terminal of ribosomal protein L17/bL17, one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is collinear with the sequence of L17 from Escherichia coli.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Small ribosomal subunit protein eS12, conserved site (Ribosomal_eS12_CS)
Type: Conserved_site

This entry represents a conserved site found at the N-terminal of small ribosomal subunit protein eS12, which is thought to be involved in the translation initiation step. This entry consists of eukaryotic eS12 ribosomal proteins, including those from vertebrates , Trypanosoma brucei , Caenorhabditis elegans, Drosophila and Saccharomyces cerevisiae (Baker's yeast).

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Small ribosomal subunit protein eS7, conserved site (Ribosomal_eS7_CS)
Type: Conserved_site

Eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities . This entry represents a conserved region of 14 residues which is located in the central section and is rich in charged residues found in eukaryotic eS7 proteins (also referred to as S7) .

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
TSC22/Bun, conserved site (TSC22/BUN_CS)
Type: Conserved_site

This entry represents a conserved site found in a group of eukaryotic proteins that are evolutionary related and involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation; the site represented here is located just in front of the leucine zipper. Proteins included in this entry are:

Vertebrate protein TSC22 , a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter.

Drosophila protein bunched (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis.

Caenorhabditis elegans protein tsct-1 (also known as T18D3.7), whose function is unknown.
Small ribosomal subunit protein uS8, conserved site (Ribosomal_uS8_CS)
Type: Conserved_site

This entry represents a conserved site located towards the C-terminal of small ribosomal subunit protein uS8 from bacteria, archaea and eukaryotes (in yeast, these proteins are also known as S22 and in vertebrates S15A) . In Escherichia coli, uS8 is known to bind directly to 16S ribosomal RNA.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Ribosomal protein eS26, conserved site (Ribosomal_eS26_CS)
Type: Conserved_site

This entry represents a conserved octapeptide in the central part of small ribosomal subunit protein eS26 (previously known as S26), mainly found in eukaryotes. This entry includes mammalian S26 ; Octopus S26 ; Drosophila S26 (DS31) ; plant cytoplasmic S26; and fungal S26 . S26 may be involved in the attachment of eIF3 and poly (U) . Disruption of RPS26, the gene encoding a homologue of ribosomal protein small subunit S26 in yeast (S. cerevisiae), resulted in the formation of micro-colonies, suggesting that it is important for the normal cell growth of S. cerevisiae . This entry also includes uncharacterised archaeal sequences.