RNA-binding protein containing an RNA recognition motif (RRM) similar to apoptotic chromatin condensation inducer in the nucleus (acinus), a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation
RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus ...
969-1055
2.36e-48
RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins; This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity.
:
Pssm-ID: 409866 [Multi-domain] Cd Length: 90 Bit Score: 166.61 E-value: 2.36e-48
RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which ...
1164-1198
1.33e-14
RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which the ASAP complex is built. The apoptosis and splicing-associated protein complex, ASAP, is made up of three proteins, SAP18 (Sin3-associated protein of 18 kDa), RNA-binding protein S1 (RNPS1) and apoptotic chromatin inducer in the nucleus (Acinus). The ASAP complex appears to be an assembly of proteins at the interface between transcription, splicing and NMD, acting as a hub in the network of protein-interactions that regulate gene-expression.
:
Pssm-ID: 465085 Cd Length: 91 Bit Score: 70.53 E-value: 1.33e-14
pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model ...
373-507
9.17e-03
pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model describes a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and per cent identity (UPGMA) trees. Members of this set include two or three copies of the lipoyl-binding domain. E. coli AceF is a member of this model, while mitochondrial and some other bacterial forms belong to a separate model. [Energy metabolism, Pyruvate dehydrogenase]
The actual alignment was detected with superfamily member TIGR01348:
Pssm-ID: 273566 [Multi-domain] Cd Length: 546 Bit Score: 40.24 E-value: 9.17e-03
RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus ...
969-1055
2.36e-48
RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins; This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity.
Pssm-ID: 409866 [Multi-domain] Cd Length: 90 Bit Score: 166.61 E-value: 2.36e-48
RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which ...
1164-1198
1.33e-14
RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which the ASAP complex is built. The apoptosis and splicing-associated protein complex, ASAP, is made up of three proteins, SAP18 (Sin3-associated protein of 18 kDa), RNA-binding protein S1 (RNPS1) and apoptotic chromatin inducer in the nucleus (Acinus). The ASAP complex appears to be an assembly of proteins at the interface between transcription, splicing and NMD, acting as a hub in the network of protein-interactions that regulate gene-expression.
Pssm-ID: 465085 Cd Length: 91 Bit Score: 70.53 E-value: 1.33e-14
pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model ...
373-507
9.17e-03
pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model describes a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and per cent identity (UPGMA) trees. Members of this set include two or three copies of the lipoyl-binding domain. E. coli AceF is a member of this model, while mitochondrial and some other bacterial forms belong to a separate model. [Energy metabolism, Pyruvate dehydrogenase]
Pssm-ID: 273566 [Multi-domain] Cd Length: 546 Bit Score: 40.24 E-value: 9.17e-03
RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus ...
969-1055
2.36e-48
RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins; This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity.
Pssm-ID: 409866 [Multi-domain] Cd Length: 90 Bit Score: 166.61 E-value: 2.36e-48
RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which ...
1164-1198
1.33e-14
RNSP1-SAP18 binding (RSB) motif; The RSB motif on the Acinus protein is the core around which the ASAP complex is built. The apoptosis and splicing-associated protein complex, ASAP, is made up of three proteins, SAP18 (Sin3-associated protein of 18 kDa), RNA-binding protein S1 (RNPS1) and apoptotic chromatin inducer in the nucleus (Acinus). The ASAP complex appears to be an assembly of proteins at the interface between transcription, splicing and NMD, acting as a hub in the network of protein-interactions that regulate gene-expression.
Pssm-ID: 465085 Cd Length: 91 Bit Score: 70.53 E-value: 1.33e-14
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
972-1031
3.79e-04
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 39.96 E-value: 3.79e-04
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
969-1047
8.05e-04
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.
Pssm-ID: 409865 [Multi-domain] Cd Length: 80 Bit Score: 39.49 E-value: 8.05e-04
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
972-1032
3.44e-03
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.
Pssm-ID: 409873 [Multi-domain] Cd Length: 79 Bit Score: 37.61 E-value: 3.44e-03
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
86-376
8.91e-03
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 40.34 E-value: 8.91e-03
pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model ...
373-507
9.17e-03
pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model describes a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and per cent identity (UPGMA) trees. Members of this set include two or three copies of the lipoyl-binding domain. E. coli AceF is a member of this model, while mitochondrial and some other bacterial forms belong to a separate model. [Energy metabolism, Pyruvate dehydrogenase]
Pssm-ID: 273566 [Multi-domain] Cd Length: 546 Bit Score: 40.24 E-value: 9.17e-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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