SII-SWORD/CoKE huggingface dataset:
Small ribosomal subunit protein mS35, mitochondrial, conserved domain (Ribosomal_mS35_mit)
Type: Domain

This entry represents a conserved region of approx. 125 residues of one of the small ribosomal subunit protein mS35 of the mitochondrial ribosome. In Saccharomyces cerevisiae (baker's yeast) it was known as mitochondrial ribosomal protein S24 whereas in humans was S35.

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 .
RNA polymerase I-specific transcription initiation factor RRN6-like (RNA_pol_I-sp_TIF_RRN6-like)
Type: Family

RNA polymerase I-specific transcription-initiation factor Rrn6 is a component of a multisubunit core transcription factor, essential for the initiation of rDNA transcription by Pol I . The DNA-bound core factor (CF) resembles a right hand holding the DNA molecule between the fingers and the palm, with the thumb pointing toward Pol I. The palm is composed of the N-terminal regions of Rrn11 and Rrn6, the thumb is composed of the C-terminal of Rrn11 while the fingers and knuckles are composed of Rrn7 and the C-terminal half of Rrn6, respectively . This entry represents the β-propeller domain of Rrn6 which is part of the palm (or module I in ) of the CF which interacts with Rrn11 . These proteins are found in fungi.
Protein of unknown function DUF2039 (DUF2039)
Type: Family

This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
SREBP regulating gene protein (SPRING1)
Type: Family

SPRING1 is a glycosylated Golgi-resident membrane protein involved in SREBP signaling and cholesterol metabolism. It modulates the proper localization of SCAP (SREBP cleavage-activating protein) to the endoplasmic reticulum, thereby controlling the level of functional SCAP .
Nonsense-mediated mRNA decay factor SMG8-like (SMG8-like)
Type: Family

This entry represents human SMG8 and similar eukaryotic proteins. SMG8 is a subunit of the Smg-1 complex that suppress Smg-1 kinase activity in the isolated Smg-1 complex, and is involved in nonsense-mediated mRNA decay (NMD) in both mammals and nematodes . NMD is a surveillance mechanism that detects and degrades mRNAs containing premature translation termination codons.
Cell cycle regulator Mat89Bb (Cell_cycle_regulator_Mat89Bb)
Type: Family

This entry represents the cell cycle regulator Mat89b (also known as protein asunder), which plays an evolutionarily conserved role as a crucial regulator of both cell cycle and development . It is a component of INT (Integrator) complex, being involved in the 3'-end processing of the U7 snRNA, and also the spliceosomal snRNAs U1 and U5 . Mat89Bb is also required for the correct dynein-dynactin perinuclear localization . Mat89Bb is a PNG kinase substrate that is essential for S-M cycles of early Drosophila embryogenesis, Xenopus embryonic cell cycles and morphogenesis, and cell division in cultured mammalian cells.
Menorin-like domain (Menorin_dom)
Type: Domain

This entry represents a domain found at the N-terminal end of Menorin from C. elegans and covering the whole length of the protein, sometimes in tandem, in its mammal homologues FAM151A and FAM151B.

Menorin is involved in generation of neurons and regulation of dendrite extension .

Proteins FAM151A and FAM151B are mammalian homologues of C. elegans menorin, which is involved in generation of neurons and regulation of dendrite extension . FAM151B has been shown to be essential for retinal function . Sequence analysis and the fact that these proteins have a TIM-barrel fold similar to that in phospholipase D and glycerophosphodiester phosphodiesterase (GDPD) families, indicate that they belong to PLC-like phosphodiesterase superfamily, although their substrates and function remain unknown.
Short coiled-coil protein (SCOC)
Type: Family

This entry represents short coiled-coil protein (SCOC). In human, SCOC is required for autophagosome formation during amino acid starvation. It forms a starvation-sensitive trimeric complex with UVRAG (UV radiation resistance associated gene) and FEZ1 and may regulate ULK1 and Beclin 1 complex activities .
NEMP family (NEMP_fam)
Type: Family

This entry includes a group of nuclear envelope integral membrane proteins from animals and plants. NEMPs contribute to nuclear envelope stiffness in germ cells and it is required for male and female fertility . NEMP1 from Xenopus laevis is a RanGTP-binding protein and is involved in eye development .
CCDC85 family (CCDC85)
Type: Family

This entry includes human CCDC85A/B/C and C. elegans Picc-1 protein. Picc-1 serves as a linker protein which helps to recruit the Rho GTPase-activating protein, pac-1, to adherens junctions . Human CCDC85B suppresses the beta-catenin activity in a p53-dependent manner .
Histone PARylation factor 1 (HPF1)
Type: Family

Histone PARylation factor 1 (HPF1, previously known as C4orf27) is a key regulator of ADP-ribosylation signaling in response to DNA damage. It has been demonstrated that HPF1 forms a complex with PARP-1 (poly(ADP-ribose) polymerase 1) and is recruited to DNA lesions in a PARP-1-dependent manner, but independently of PARP-1 catalytic ADP-ribosylation activity. HPF1 has also been shown limit DNA damage-induced hyper-automodification of PARP-1 by promoting PARP-1-dependent in trans ADP-ribosylation of histones . This protein is essential for Ser-ADPr (ADPr on serine residues), which represents the major fraction of ADPr synthesised after DNA damage . HPF1, which shows an α-β structure with two tightly-associated domains connected via an elaborate linker, forms a composite active site with PARP-1 .
Methylmalonic aciduria and homocystinuria type D protein (MMADHC)
Type: Family

This entry represents methylmalonic aciduria and homocystinuria type D protein (also known as cobalamin trafficking protein CblD) and homologues. These proteins are involved in cobalamin (vitamin B12) metabolism and trafficking CblD plays a role in regulating the biosynthesis and the proportion of two coenzymes, methylcob(III)alamin (MeCbl) and 5'-deoxyadenosylcobalamin (AdoCbl) . It also promotes the oxidation of cob(II)alamin bound to MMACHC .
Lipid droplet-associated hydrolase (LDAH)
Type: Family

This entry includes a group of lipid droplet-associated hydrolases (LDAHs) from eukaryotes. Human LDAH plays a role in cholesterol homeostasis . This entry also includes budding yeast Lipid droplet-associated triacylglycerol lipase YPR147C, which shows both triacylglycerol (TAG) lipase and ester hydrolase activities .
Mediator complex, subunit Med8, fungi/metazoa (Mediatior_Med8_fun/met)
Type: Family

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two α helices putatively necessary for binding to other subunits within the core of the Mediator complex. The N terminus of Med8 binds to the essential core Head part of Mediator and the C terminus hinges to Med18 on the non-essential part of the Head that also includes Med20 .
TVP18/Calcium channel flower (TVP18/Ca-channel_flower)
Type: Family

This is a family of small (less than 200 residue long) proteins that are conserved from fungi to humans. Family members include the TVP18 Golgi membrane proteins that are involved in vesicular trafficking and the calcium channel flower proteins, which form calcium channels that regulate synaptic endocytosis .
Clusterin-associated protein-1 (Clusterin-associated_protein-1)
Type: Family

This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell .
PDZ-binding protein, CRIPT (PDZ-binding_CRIPT)
Type: Family

The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners .
Small ribosomal subunit protein mS29 (Ribosomal_mS29)
Type: Family

This entry represents the family of small ribosomal subunit mitochondrial protein mS29 which was originally described as death-associated-protein-3 (DAP-3). This protein was also known as MRPS29 in mammals and RSM23 in yeast. These proteins carry a P-loop DNA-binding motif, and induce apoptosis . mS29 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis.

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 .
Protein-lysine N-methyltransferase Efm5/EEF1AKMT1 (Efm5/EEF1AKMT1)
Type: Family

Budding yeast Efm5 is a S-adenosylmethionine-dependent lysine methyltransferase involved in the trimethylation of eEF1A at lysine 79 . This entry also includes N(6)-adenine-specific DNA methyltransferase 2 (also known as N6MT2 and EEF1A lysine methyltransferase 1) from mammals.
E2F-associated phosphoprotein (E2F-assoc_phosphoprotein)
Type: Family

This entry represents E2F binding proteins. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. E2F-associated phosphoprotein (EAPP)interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis .
KxDL domain (KxDL_dom)
Type: Domain

This entry represents a conserved region of 80 residues which defines a family of coiled-coil proteins known as Biogenesis of lysosome-related organelles complex 1 subunit KXD1 in yeast and KXDL1 in animals . This domain contains the characteristic KxDL motif towards the C terminus. Members of this entry are components of the biogenesis of lysosome-related organelles complex-1 (BLOC-1) involved in endosomal cargo sorting. They may play a role in lysosomes movement and localization at the cell periphery .
Lipoma HMGIC fusion partner-like protein (LHFPL)
Type: Family

This is a group of proteins expressed from a series of genes referred to as Lipoma HMGIC fusion partner-like. The proteins carry four highly conserved transmembrane domains. In certain instances, as in LHFPL5, mutations cause deafness in humans or hypospadias . LHFPL1 is transcribed in six liver tumour cell lines .
Large ribosomal subunit protein mL51 (Ribosomal_mL51)
Type: Family

This entry represents the large ribosomal subunit protein mL51 from animals, previously known as MRP-L51. This family of small proteins from the intact 55 S mitochondrial ribosome has otherwise been referred to as bMRP-64 . The exact function of this family is not known.
Small ribosomal subunit protein mS22 (Ribosomal_mS22)
Type: Family

This entry represents the small ribosomal subunit protein mS22, previously known as MRP-S22. Mammalian mitochondria carry out the synthesis of 13 polypeptides that are essential for oxidative phosphorylation and, hence, for the synthesis of the majority of the ATP used by eukaryotic organisms. The number of proteins produced by prokaryotes is smaller, reflected in the lower number of ribosomal proteins present in them .

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 bS1m (Ribosomal_bS1m)
Type: Family

This is a family of short mitochondrial ribosomal proteins from animals, including the small ribosomal subunit protein bS1m, previously known as MRP-S35 .

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 .
Myeloid leukemia factor (Myeloid_leukemia_factor)
Type: Family

Myeloid leukemia factor is involved in lineage commitment of primary hemopoietic progenitors by restricting erythroid formation and enhancing myeloid formation .
NADH-ubiquinone oxidoreductase, subunit 10 (NADH_UbQ_OxRdtase_su10)
Type: Family

NADH-ubiquinone oxidoreductase subunit 10 of (NDUFB10) is a member of a family of conserved proteins of up to 180 residues. It is one of the 41 protein subunits within the hydrophobic fraction of the NADH:ubiquinone oxidoreductase (complex I), a multiprotein complex located in the inner mitochondrial membrane whose main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. NDUFB10 is encoded in the nucleus .
GDP-fucose protein O-fucosyltransferase (GDP-Fuc_O-FucTrfase)
Type: Family

This is a family of conserved proteins representing the enzyme responsible for adding O-fucose to EGF (epidermal growth factor-like) repeats. Six highly conserved cysteines are present as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and Caenorhabditis elegans. Both features are characteristic of several glycosyltransferase families. The enzyme is a membrane-bound protein released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese .
Gamma-secretase aspartyl protease complex, presenilin enhancer-2 subunit (Gamma_Secretase_Asp_P_PEN2)
Type: Family

This entry is a short, 101 peptide protein, which is the smallest subunit of the gamma-secretase aspartyl protease complex. It catalyses the intra-membrane cleavage of a subset of type I transmembrane proteins. The other active constituents of the complex are presenilin (PS) nicastrin and anterior pharynx defective-1 (APH-1) protein. Presenilin enhancer-2 (PEN-2) adopts a hairpin orientation in the membrane with its N- and C-terminal domains facing the luminal/extracellular space. The C-terminal domain maintains PS stability within the complex .
Casein kinase substrate, phosphoprotein PP28 (Casein_kinase_sb_PP28)
Type: Domain

This domain is a region of 70 residues conserved in proteins from plants to humans and contains a serine/arginine rich motif. In rats the full protein is a casein kinase substrate, and this region contains phosphorylation sites for both cAMP-dependent protein kinase and casein kinase II .
Phosphofurin acidic cluster sorting protein 1/2, C-terminal (PACS1/2_C)
Type: Domain

This entry represents the C-terminal region of animal PACS1/2.

PACS1 is a cytosolic sorting protein that directs the localisation of membrane proteins in the trans-Golgi network (TGN)/endosomal system. PACS1 connects the clathrin adaptor AP-1 to acidic cluster sorting motifs contained in the cytoplasmic domain of cargo proteins such as furin, the cation-independent mannose-6-phosphate receptor and in viral proteins such as human immunodeficiency virus type 1 Nef .

PACS2 controls the endoplasmic reticulum (ER)-mitochondria communication, including the apposition of mitochondria with the ER and ER homeostasis. In response to apoptotic inducer, it translocates the proapoptotic member Bid to mitochondria .