SII-SWORD/CoKE huggingface dataset:
FYCO1, FYVE domain (FYVE_FYCO1)
Type: Domain

This entry represents the FYVE domain of FYCO1 and similar proteins predominantly found in vertebrates.

FYVE and coiled-coil domain-containing protein 1 (FYCO1) is a multidomain autophagy adaptor protein that interacts with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7, and Phosphatidylinositol 3-phosphate (PI3P), to mediate microtubule plus-end-directed autophagosome transport . This protein is associated with congenital cataracts .
RUN domain-containing protein 3A, RUN domain (RUN_RUNDC3A)
Type: Domain

This entry represents the RUN domain of RUNDC3A and similar proteins from vertebrates.

RUN domain-containing protein 3A (RUNDC3A), also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells .
RUN domain-containing protein 3B, RUN domain (RUN_RUNDC3B)
Type: Domain

This entry represents the RUN domain of RUNDC3B and similar proteins from vertebrates.

RUN domain-containing protein 3B (RUNDC3B), also called Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates .
RUN domain-containing protein 3A/B (RUNDC3A_B)
Type: Family

This entry represents a group of proteins predominantly found in vertebrates, including RUN domain-containing protein 3A/B (RUNDC3A/B) from mammals.

RUNDC3A, also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells .

RUNDC3B, also called Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates .
AP-4 complex accessory subunit RUSC1, RUN domain (RUN_RUSC1)
Type: Domain

This entry represents the RUN domain of RUSC1 and similar proteins from vertebrates.

AP-4 complex accessory subunit RUSC1, also called RUN and SH3 domain-containing protein 1, may act as a signaling adapter that translocates to the nuclear envelope and regulates neurotrophin-induced neurite outgrowth .
AP-4 complex accessory subunit RUSC2, RUN domain (RUN_RUSC2)
Type: Domain

This entry represents the RUN domain of RUSC2 and similar proteins from vertebrates.

AP-4 complex accessory subunit RUSC2, also called RUN and SH3 domain-containing protein 2, is a novel interacting molecule for the active GTP-bound conformation of Rab1. It may function as a link between the targeting of endoplasmic reticulum derived vesicles, triggered by the Rab1 GTPase and a signalling pathway regulated by molecules containing SH3 and/or poly-proline regions .
AP-4 complex accessory subunit RUSC1/2 (RUSC1_2)
Type: Family

This entry represents a group of proteins from animals, including AP-4 complex accessory subunit RUSC1/2.

RUSC1, also called RUN and SH3 domain-containing protein 1, may acts as a signalling adapter that translocates to the nuclear envelope and regulates neurotrophin-induced neurite outgrowth .

RUSC2, also called RUN and SH3 domain-containing protein 2, is a novel interacting molecule for the active GTP-bound conformation of Rab1. It may function as a link between the targeting of endoplasmic reticulum derived vesicles, triggered by the Rab1 GTPase and a signaling pathway regulated by molecules containing SH3 and/or poly-proline regions .
Small G protein signaling modulator 1, RUN domain (RUN_SGSM1)
Type: Domain

This entry represents the RUN domain of SGSM1.

Small G protein signaling modulator 1 (SGSM1) interacts with numerous Rab family members, functioning as Rab effector for some, and as GTPase activator for others. It is a Rab9A effector and GTPase-activating protein for Rab36, and links Rab9A function to Rab36 function in the endosomal system .
Small G protein signaling modulator 2, RUN domain (RUN_SGSM2)
Type: Domain

This entry represents the RUN domain of SGSM2.

Small G protein signaling modulator 2 (SGSM2) is a GTPase-activating protein for Rab32/38, and regulates melanogenic enzyme trafficking in melanocytes. It also acts as a Rab9A effector that activates GTP hydrolysis by Rab32 and Rab33B proteins .
DNA repair protein REV1, ubiquitin-binding motif 1/2 (Rev1_UBM1/2)
Type: Conserved_site

REV1 is a DNA damage tolerance protein that contains two ubiquitin-binding motifs (UBM1 and UBM2) that acts as a translesion synthesis (TLS) DNA polymerase and may also recruit other TLS polymerases to the site of DNA damage; in that process the UBMs are essential for REV1 function, triggering TLS activation via recognition of ubiquitin moieties in PCNA, the proliferating cell nuclear antigen . From structural studies, it has been determined that REV1 UBM2 but not UBM1 is required for DNA damage tolerance . This entry represents both UBMs from REV1.
Putative sensory transducer protein YvaQ-like, ligand-binding sensor domain (YvaQ-like_sensor)
Type: Domain

This entry represents the ligand-binding sensor domain of the putative sensory transducer protein YvaQ from Bacillus subtilis and similar chemoreceptors predominantly found in proteobacteria .
DNA repair protein XRCC3-like, C-terminal (XRCC3-like_C)
Type: Domain

This entry represents the C-terminal region of XRCC3 and its eukaryotic homologues, including DNA repair protein RAD57 from Saccharomyces cerevisiae.

DNA repair protein XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells 3), a RAD51 paralogue, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. XRCC3, together with the other RAD51 paralogues, RAD51B, RAD51C, RAD51D, and XRCC2, helps recruit RAD51 to the break site. It is involved in HJ resolution and thus in processing HR intermediates late in the DNA repair process. XRCC3 plays a role in regulating mitochondrial DNA copy number under conditions of oxidative stress in the presence of RAD51 and RAD51C .
Scm-like with four MBT domains protein 1, third MBT repeat (MBT_SFMBT1_rpt3)
Type: Repeat

This entry represents the third MBT repeat of SFMBT1, which does not contain a semi-aromatic cage and may not bind methylated lysine residues.

Scm-like with four MBT domains protein 1 (SFMBT1), is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3 and functions as a chromatin reader in regulating epigenetic silencing and the myogenic gene program . It mediates the recruitment of corepressor complexes to target genes, followed by chromatin compaction and repression of transcription. SFMBT1 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognises methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine .
Scm-like with four MBT domains protein 1, second MBT repeat (MBT_SFMBT1_rpt2)
Type: Repeat

This entry represents the third MBT repeat of SFMBT1, which contains a partially conserved semi-aromatic cage.

Scm-like with four MBT domains protein 1 (SFMBT1), is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3 and functions as a chromatin reader in regulating epigenetic silencing and the myogenic gene program . It mediates the recruitment of corepressor complexes to target genes, followed by chromatin compaction and repression of transcription. SFMBT1 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognises methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine .
Scm-like with four MBT domains protein 2, first MBT repeat (MBT_SFMBT2_rpt1)
Type: Repeat

This entry represents the first MBT repeat of SFMBT2, which contains a partially conserved semi-aromatic cage.

Scm-like with four MBT domains protein 2 (SFMBT2) is a transcriptional repressor of the HOXB13 gene. It is required for trophoblast maintenance and placenta development . It also negatively regulates cell migration and invasion in prostate cancer cells . SFMBT2 has been identified as a novel regulator of SOX9 expression in human chondrocytes, in which decreased levels of SFMBT2 contribute to the catabolic phenotype of chondrocytes. SFMBT2 is negatively regulated in osteoarthritis cartilage .

SFMBT2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognises methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine.
Scm-like with four MBT domains protein 2, third MBT repeat (MBT_SFMBT2_rpt3)
Type: Repeat

This entry represents the third MBT repeat of SFMBT2, which does not contain a semi-aromatic cage and may not bind methylated lysine residues.

Scm-like with four MBT domains protein 2 (SFMBT2) is a transcriptional repressor of the HOXB13 gene. It is required for trophoblast maintenance and placenta development . It also negatively regulates cell migration and invasion in prostate cancer cells . SFMBT2 has been identified as a novel regulator of SOX9 expression in human chondrocytes, in which decreased levels of SFMBT2 contribute to the catabolic phenotype of chondrocytes. SFMBT2 is negatively regulated in osteoarthritis cartilage .

SFMBT2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognises methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine.
Scm-like with four MBT domains protein 2, fourth MBT repeat (MBT_SFMBT2_rpt4)
Type: Repeat

This entry represents the fourth MBT repeat of SFMBT2, which does not contain a semi-aromatic cage and may not bind methylated lysine residues.

Scm-like with four MBT domains protein 2 (SFMBT2) is a transcriptional repressor of the HOXB13 gene. It is required for trophoblast maintenance and placenta development . It also negatively regulates cell migration and invasion in prostate cancer cells . SFMBT2 has been identified as a novel regulator of SOX9 expression in human chondrocytes, in which decreased levels of SFMBT2 contribute to the catabolic phenotype of chondrocytes. SFMBT2 is negatively regulated in osteoarthritis cartilage .

SFMBT2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognises methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine.
Lethal(3)malignant brain tumor-like protein 2, first MBT repeat (MBT_L3MBTL2_rpt1)
Type: Repeat

This entry represents the first MBT repeat of L3MBTL2, which contains a partially conserved semi-aromatic cage.

Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2) is a putative Polycomb group (PcG) protein that binds to monomethylated and dimethylated 'Lys-20' on histone H4 and also binds histone H3 peptides which are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27' . L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage . It is an integral component of the polycomb repressive complex 1.6 (PRC1.6) and has been implicated in transcriptional repression and chromatin compaction . L3MBTL2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine.
Lethal(3)malignant brain tumor-like protein 2, second MBT repeat (MBT_L3MBTL2_rpt2)
Type: Repeat

This entry represents the second MBT repeat of L3MBTL2, which does not seem to contain a semi-aromatic cage and may not bind methylated lysine residues.

Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2) is a putative Polycomb group (PcG) protein that binds to monomethylated and dimethylated 'Lys-20' on histone H4 and also binds histone H3 peptides which are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27' . L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage . It is an integral component of the polycomb repressive complex 1.6 (PRC1.6) and has been implicated in transcriptional repression and chromatin compaction . L3MBTL2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine.
Polycomb protein Sfmbt, first MBT repeat (MBT_dSfmbt_rpt1)
Type: Repeat

This entry represents the first MBT repeat of Sfmbt from Drosophila melanogaster (dSfmbt) and similar sequences from arthropods. It contains a partially conserved semi-aromatic cage.

Polycomb protein Sfmbt from Drosophila melanogaster (dSfmbt) is a Polycomb group repressor involved in epigenetic regulation of gene expression . dSfmbt contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognises methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine.
Polycomb protein Sfmbt, second MBT repeat (MBT_dSfmbt_rpt2)
Type: Repeat

This entry represents the second MBT repeat of Sfmbt from Drosophila melanogaster (dSfmbt) and similar sequences from arthropods. It does not seem to contain a semi-aromatic cage and may not bind methylated lysine residues.

Polycomb protein Sfmbt from Drosophila melanogaster (dSfmbt) is a Polycomb group repressor involved in epigenetic regulation of gene expression . dSfmbt contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognises methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine.
Polycomb protein Sfmbt, third MBT repeat (MBT_dSfmbt_rpt3)
Type: Repeat

This entry represents the third MBT repeat of Sfmbt from Drosophila melanogaster (dSfmbt) and similar sequences from arthropods. It does not seem to contain a semi-aromatic cage and may not bind methylated lysine residues.

Polycomb protein Sfmbt from Drosophila melanogaster (dSfmbt) is a Polycomb group repressor involved in epigenetic regulation of gene expression . dSfmbt contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognises methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine.
Lethal(3)malignant brain tumor-like protein 1, first MBT repeat (MBT_L3MBTL1_rpt1)
Type: Repeat

This entry represents the first MBT repeat of L3MBTL1, which contains the semi-aromatic cage and may bind methylated lysine residues.

Lethal(3)malignant brain tumor-like protein 1 (L3MBTL1), is a Polycomb group (PcG) protein that functions as a 'reader' of a network of post-translational modifications by specifically recognizing and binding mono- and dimethyllysine residues on target proteins. It acts as a chromatin compaction factor by binding mono- and dimethylated histone H1b/HIST1H1E at 'Lys-26' (H1bK26me1 and H1bK26me2) and histone H4 at 'Lys-20' (H4K20me1 and H4K20me2), leading to condensed chromatin and repressed transcription . L3MBTL1 represses the ability of stem cells to drive hematopoietic-specific transcriptional programs by regulating the expression of SMAD5 and impairing its recruitment to target regulatory regions . L3MBTL1 contains three MBT (malignant brain tumor) repeats . The MBT repeat is a protein module that recognises methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine.
Lethal(3)malignant brain tumor-like protein 1, third MBT repeat (MBT_L3MBTL1_rpt3)
Type: Repeat

This entry represents the third MBT repeat of L3MBTL1, which contains the semi-aromatic cage and may bind methylated lysine residues.

Lethal(3)malignant brain tumor-like protein 1 (L3MBTL1), is a Polycomb group (PcG) protein that functions as a 'reader' of a network of post-translational modifications by specifically recognizing and binding mono- and dimethyllysine residues on target proteins. It acts as a chromatin compaction factor by binding mono- and dimethylated histone H1b/HIST1H1E at 'Lys-26' (H1bK26me1 and H1bK26me2) and histone H4 at 'Lys-20' (H4K20me1 and H4K20me2), leading to condensed chromatin and repressed transcription . L3MBTL1 represses the ability of stem cells to drive hematopoietic-specific transcriptional programs by regulating the expression of SMAD5 and impairing its recruitment to target regulatory regions . L3MBTL1 contains three MBT (malignant brain tumor) repeats . The MBT repeat is a protein module that recognises methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine.
Hepatoma-derived growth factor, PWWP domain (PWWP_HDGF)
Type: Domain

This entry represents the PWWP domain of HDGF and similar sequences from vertebrates. This domain is necessary for DNA binding .

Hepatoma-derived growth factor (HDGF) is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts .
Forkhead box protein S1, Forkhead domain (FH_FOXS1)
Type: Domain

This entry represents the forkhead (FH) domain of human FOXS1 and similar sequences from vertebrates. The FH domain is a winged helix DNA-binding domain.

Forkhead box protein S1 (FOXS1) is a transcriptional repressor that suppresses transcription from the FASLG, FOXO3, and FOXO4 promoters. It may have a role in the organisation of the testicular vasculature. It has also been implicated in energy turnover, motor function, and body weight . Downregulation of FOXS1 has been related to cell proliferation and metastasis . FOX transcription factors recognise the core sequence 5'-(A/C)AA(C/T)A-3'.
PTM/DIR17-like, Tudor domain (Tudor_AtPTM-like)
Type: Domain

This entry represents the Tudor domain of PTM and DIR17 from Arabidopsis thaliana.

AtPTM, also called DDT domain-containing protein 1, or PHD type transcription factor with transmembrane domains, is a membrane-bound transcription factor required for plastid-to-nucleus retrograde signalling .
Hepatocyte nuclear factor 3-gamma, forkhead domain (FH_FOXA3)
Type: Domain

This entry represents the forkhead (FH) domain of human FOXA3 and similar sequences from vertebrates. The FH domain is a winged helix DNA-binding domain .

Hepatocyte nuclear factor 3-gamma (FOXA3) acts as an essential transcriptional regulator engaged in adipogenesis and energy metabolism . FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'.
A-kinase anchor protein 1, Tudor domain (Tudor_AKAP1)
Type: Domain

This entry represents the C-terminal Tudor domain of AKAP1 proteins. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

AKAP1, also called A-kinase anchor protein 149 kDa (AKAP 149), dual specificity A-kinase-anchoring protein 1 (D-AKAP-1), protein kinase A-anchoring protein 1 (PRKA1), is found in mitochondria and in the endoplasmic reticulum-nuclear envelope, where it anchors protein kinases, phosphatases, and a phosphodiesterase. It regulates multiple cellular processes governing mitochondrial homeostasis and cell viability. AKAP1 binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane . AKAP1 is also involved in mitochondrial-mediated antiviral innate immunity .
A-kinase anchor protein 1, type I K homology domain (KH-I_AKAP1)
Type: Domain

This is the type-I KH RNA-binding domain of AKAP1.

AKAP1, also called A-kinase anchor protein 149 kDa (AKAP 149), dual specificity A-kinase-anchoring protein 1 (D-AKAP-1), protein kinase A-anchoring protein 1 (PRKA1), is found in mitochondria and in the endoplasmic reticulum-nuclear envelope, where it anchors protein kinases, phosphatases, and a phosphodiesterase. It regulates multiple cellular processes governing mitochondrial homeostasis and cell viability. AKAP1 binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane . AKAP1 is also involved in mitochondrial-mediated antiviral innate immunity .
Far upstream element-binding protein 2, second type I K homology domain (KH-I_FUBP2_rpt2)
Type: Domain

This entry represents the second type I KH domain of FUBP2.

FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA . FUBP2 contains four K-homology (KH) RNA-binding domains .
Far upstream element-binding protein 2, third type I K homology domain (KH-I_FUBP2_rpt3)
Type: Domain

This entry represents the third type I KH domain of FUBP2.

FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA . FUBP2 contains four K-homology (KH) RNA-binding domains .
Far upstream element-binding protein 2, fourth type I K homology domain (KH-I_FUBP2_rpt4)
Type: Domain

This entry represents the fourth type I KH domain of FUBP2.

FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA . FUBP2 contains four K-homology (KH) RNA-binding domains .