SCC2/Nipped-B family protein similar to Saccharomyces cerevisiae sister chromatid cohesion protein 2 (SCC2) that plays a structural role in chromatin and is involved in sister chromatid cohesion
Sister chromatid cohesion protein 2 and homologs; This family includes Sister chromatid ...
759-1966
0e+00
Sister chromatid cohesion protein 2 and homologs; This family includes Sister chromatid cohesion protein 2 (Scc2) and its homolog (Scc2 homolog, also called Nipped-B-like protein or NIPBL). Scc2/NIPBL and Scc4 form a complex that is responsible for loading the cohesin protein onto sister chromatids during mitosis and meiosis. Cohesin is a ring-shaped protein complex that encircles the sister chromatids and helps to hold them together until they are ready to be separated during cell division. In addition to its role in chromosome segregation, cohesin also plays important roles in other cellular processes such as transcription, chromosome condensation, and DNA repair.
:
Pssm-ID: 467937 [Multi-domain] Cd Length: 1197 Bit Score: 1398.96 E-value: 0e+00
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
73-662
1.28e-11
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.
The actual alignment was detected with superfamily member pfam03154:
Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 70.57 E-value: 1.28e-11
Sister chromatid cohesion protein 2 and homologs; This family includes Sister chromatid ...
759-1966
0e+00
Sister chromatid cohesion protein 2 and homologs; This family includes Sister chromatid cohesion protein 2 (Scc2) and its homolog (Scc2 homolog, also called Nipped-B-like protein or NIPBL). Scc2/NIPBL and Scc4 form a complex that is responsible for loading the cohesin protein onto sister chromatids during mitosis and meiosis. Cohesin is a ring-shaped protein complex that encircles the sister chromatids and helps to hold them together until they are ready to be separated during cell division. In addition to its role in chromosome segregation, cohesin also plays important roles in other cellular processes such as transcription, chromosome condensation, and DNA repair.
Pssm-ID: 467937 [Multi-domain] Cd Length: 1197 Bit Score: 1398.96 E-value: 0e+00
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
73-662
1.28e-11
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.
Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 70.57 E-value: 1.28e-11
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
115-257
9.44e-07
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.
Pssm-ID: 197891 [Multi-domain] Cd Length: 165 Bit Score: 50.94 E-value: 9.44e-07
N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as ...
142-260
1.33e-04
N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as Krueppel-like factor 1 or Erythroid Kruppel-like Factor/EKLF) was the first Kruppel-like factor discovered. It was found to be vitally important for embryonic erythropoiesis in promoting the switch from fetal hemoglobin (Hemoglobin F) to adult hemoglobin (Hemoglobin A) gene expression by binding to highly conserved CACCC domains. EKLF ablation in mouse embryos produces a lethal anemic phenotype, causing death by embryonic day 14, and natural mutations lead to beta+ thalassemia in humans. However, expression of embryonic hemoglobin and fetal hemoglobin genes is normal in EKLF-deficient mice, suggesting other factors may be involved. KLF1 functions as a transcriptional activator. It belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF1, which is related to the N-terminal domains of KLF2 and KLF4.
Pssm-ID: 409227 [Multi-domain] Cd Length: 278 Bit Score: 46.19 E-value: 1.33e-04
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
108-278
6.41e-04
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.
Pssm-ID: 130689 [Multi-domain] Cd Length: 562 Bit Score: 44.80 E-value: 6.41e-04
Sister chromatid cohesion protein 2 and homologs; This family includes Sister chromatid ...
759-1966
0e+00
Sister chromatid cohesion protein 2 and homologs; This family includes Sister chromatid cohesion protein 2 (Scc2) and its homolog (Scc2 homolog, also called Nipped-B-like protein or NIPBL). Scc2/NIPBL and Scc4 form a complex that is responsible for loading the cohesin protein onto sister chromatids during mitosis and meiosis. Cohesin is a ring-shaped protein complex that encircles the sister chromatids and helps to hold them together until they are ready to be separated during cell division. In addition to its role in chromosome segregation, cohesin also plays important roles in other cellular processes such as transcription, chromosome condensation, and DNA repair.
Pssm-ID: 467937 [Multi-domain] Cd Length: 1197 Bit Score: 1398.96 E-value: 0e+00
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
73-662
1.28e-11
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.
Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 70.57 E-value: 1.28e-11
HEAT repeat associated with sister chromatid cohesion; This HEAT repeat is found most ...
1292-1333
1.17e-09
HEAT repeat associated with sister chromatid cohesion; This HEAT repeat is found most frequently in sister chromatid cohesion proteins such as Nipped-B. HEAT repeats are found tandemly repeated in many proteins, and they appear to serve as flexible scaffolding on which other components can assemble.
Pssm-ID: 403845 [Multi-domain] Cd Length: 42 Bit Score: 55.54 E-value: 1.17e-09
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
115-257
9.44e-07
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.
Pssm-ID: 197891 [Multi-domain] Cd Length: 165 Bit Score: 50.94 E-value: 9.44e-07
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
104-295
6.10e-06
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.
Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 51.55 E-value: 6.10e-06
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
120-362
1.29e-05
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.
Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 50.39 E-value: 1.29e-05
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
93-265
7.45e-05
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.
Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 48.08 E-value: 7.45e-05
N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as ...
142-260
1.33e-04
N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as Krueppel-like factor 1 or Erythroid Kruppel-like Factor/EKLF) was the first Kruppel-like factor discovered. It was found to be vitally important for embryonic erythropoiesis in promoting the switch from fetal hemoglobin (Hemoglobin F) to adult hemoglobin (Hemoglobin A) gene expression by binding to highly conserved CACCC domains. EKLF ablation in mouse embryos produces a lethal anemic phenotype, causing death by embryonic day 14, and natural mutations lead to beta+ thalassemia in humans. However, expression of embryonic hemoglobin and fetal hemoglobin genes is normal in EKLF-deficient mice, suggesting other factors may be involved. KLF1 functions as a transcriptional activator. It belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF1, which is related to the N-terminal domains of KLF2 and KLF4.
Pssm-ID: 409227 [Multi-domain] Cd Length: 278 Bit Score: 46.19 E-value: 1.33e-04
Sister chromatid cohesion protein PDS5; Pds5 plays a crucial role in sister chromatid cohesion. ...
1284-1382
3.53e-04
Sister chromatid cohesion protein PDS5; Pds5 plays a crucial role in sister chromatid cohesion. Together with WapI and Scc3, it is involved in the release of the cohesin complex from chromosomes during S phase. The core of the cohesin complex consists of a coiled-coiled heterodimer of Smc1 and Smc30, together with Scc1 (also called kleisin). Pds5 interacts with Scc1 via a conserved patch on the surface of its heat repeats. Pds5 also promotes the acetylation of Smc3 that protects cohesin from releasing activity in G2 phase.
Pssm-ID: 410996 [Multi-domain] Cd Length: 630 Bit Score: 45.98 E-value: 3.53e-04
Sister chromatid cohesion protein PDS5 protein; This entry represents the Sister chromatid ...
1283-1370
4.47e-04
Sister chromatid cohesion protein PDS5 protein; This entry represents the Sister chromatid cohesion protein PDS5. The large PDS5 molecule is exclusively alpha helical, composed of a large number of HEAT-like repeats and helical extensions/additions that deviate from the HEAT repeat pattern.
Pssm-ID: 466319 [Multi-domain] Cd Length: 1051 Bit Score: 45.66 E-value: 4.47e-04
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
108-278
6.41e-04
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.
Pssm-ID: 130689 [Multi-domain] Cd Length: 562 Bit Score: 44.80 E-value: 6.41e-04
AF-4 proto-oncoprotein N-terminal region; This family consists of AF4 (Proto-oncogene AF4) and ...
110-363
5.63e-03
AF-4 proto-oncoprotein N-terminal region; This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homolog Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila.
Pssm-ID: 461550 [Multi-domain] Cd Length: 514 Bit Score: 41.65 E-value: 5.63e-03
Sister chromatid cohesion protein PDS5 protein; This entry represents the Sister chromatid ...
1316-1373
8.15e-03
Sister chromatid cohesion protein PDS5 protein; This entry represents the Sister chromatid cohesion protein PDS5. The large PDS5 molecule is exclusively alpha helical, composed of a large number of HEAT-like repeats and helical extensions/additions that deviate from the HEAT repeat pattern.
Pssm-ID: 466319 [Multi-domain] Cd Length: 1051 Bit Score: 41.42 E-value: 8.15e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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