ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) ...
10-664
1.81e-107
ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) describes archaeal homologs of the RqcH (Ribosome-associated Quality Control H), involved in release of defective mRNAs that lack a stop codons and so are stuck on ribosomes. Conservation of a role in ribosome rescue for this archaeal family is supported by presence in a conserved gene neighborhood with homologs of Pelota/Dom34 and ABCE1/Rli1 homologs, proteins involved in splitting the ribosome into large and small subunits.
The actual alignment was detected with superfamily member NF041120:
Pssm-ID: 469043 [Multi-domain] Cd Length: 642 Bit Score: 349.58 E-value: 1.81e-107
NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, ...
964-1057
1.43e-34
NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins involved in the ribosomal quality control pathway. This context is conserved in archaea and eukaryotes, but NFACT proteins in bacteria lack the NFACT-C domain.
:
Pssm-ID: 432191 Cd Length: 104 Bit Score: 127.64 E-value: 1.43e-34
ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) ...
10-664
1.81e-107
ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) describes archaeal homologs of the RqcH (Ribosome-associated Quality Control H), involved in release of defective mRNAs that lack a stop codons and so are stuck on ribosomes. Conservation of a role in ribosome rescue for this archaeal family is supported by presence in a conserved gene neighborhood with homologs of Pelota/Dom34 and ABCE1/Rli1 homologs, proteins involved in splitting the ribosome into large and small subunits.
Pssm-ID: 469043 [Multi-domain] Cd Length: 642 Bit Score: 349.58 E-value: 1.81e-107
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) ...
10-661
2.18e-67
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) and RNA- (NFACT) binding domains [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones];
Pssm-ID: 440904 [Multi-domain] Cd Length: 578 Bit Score: 237.43 E-value: 2.18e-67
NFACT protein RNA binding domain; This domain occurs in proteins that have been annotated as ...
537-648
1.35e-47
NFACT protein RNA binding domain; This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from Swiss:O34693 where the N-terminal region is involved in this activity. It is an RNA binding domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins. This NFACT-R family is found in two eukaryotic gene contexts: fused to the NFACT-N and NFACT-C domains in the NFACT protein involved in the ribosomal quality control pathway which contributes to CAT-tailing and as a standalone domain. Additionally this domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.
Pssm-ID: 428576 [Multi-domain] Cd Length: 111 Bit Score: 165.09 E-value: 1.35e-47
NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, ...
964-1057
1.43e-34
NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins involved in the ribosomal quality control pathway. This context is conserved in archaea and eukaryotes, but NFACT proteins in bacteria lack the NFACT-C domain.
Pssm-ID: 432191 Cd Length: 104 Bit Score: 127.64 E-value: 1.43e-34
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
924-939
2.17e-03
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.
Pssm-ID: 395050 [Multi-domain] Cd Length: 18 Bit Score: 36.35 E-value: 2.17e-03
ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) ...
10-664
1.81e-107
ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) describes archaeal homologs of the RqcH (Ribosome-associated Quality Control H), involved in release of defective mRNAs that lack a stop codons and so are stuck on ribosomes. Conservation of a role in ribosome rescue for this archaeal family is supported by presence in a conserved gene neighborhood with homologs of Pelota/Dom34 and ABCE1/Rli1 homologs, proteins involved in splitting the ribosome into large and small subunits.
Pssm-ID: 469043 [Multi-domain] Cd Length: 642 Bit Score: 349.58 E-value: 1.81e-107
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) ...
10-661
2.18e-67
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) and RNA- (NFACT) binding domains [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones];
Pssm-ID: 440904 [Multi-domain] Cd Length: 578 Bit Score: 237.43 E-value: 2.18e-67
NFACT protein RNA binding domain; This domain occurs in proteins that have been annotated as ...
537-648
1.35e-47
NFACT protein RNA binding domain; This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from Swiss:O34693 where the N-terminal region is involved in this activity. It is an RNA binding domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins. This NFACT-R family is found in two eukaryotic gene contexts: fused to the NFACT-N and NFACT-C domains in the NFACT protein involved in the ribosomal quality control pathway which contributes to CAT-tailing and as a standalone domain. Additionally this domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.
Pssm-ID: 428576 [Multi-domain] Cd Length: 111 Bit Score: 165.09 E-value: 1.35e-47
NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, ...
964-1057
1.43e-34
NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins involved in the ribosomal quality control pathway. This context is conserved in archaea and eukaryotes, but NFACT proteins in bacteria lack the NFACT-C domain.
Pssm-ID: 432191 Cd Length: 104 Bit Score: 127.64 E-value: 1.43e-34
NFACT N-terminal and middle domains; This family contains the N-terminal and middle domains of ...
62-418
1.92e-25
NFACT N-terminal and middle domains; This family contains the N-terminal and middle domains of NFACT (NEMF, FbpA, Caliban, and Tae2) proteins from eukaryotes, archaea and bacteria. Many members of this family act in ribosome quality control (RQC), including RqcH, which are involved in the addition of a poly-Ala tail to defective translated proteins to tag them for degradation. This process is analogous to the ssrA/tmRNA bacterial system. However, some other NFACT family members, such as bacterial proteins FbpA in Listeria or PavA in Streptococcus, are exported (despite lack of a classical signal peptide) and behave as fibronectin-binding adhesins associated with virulence.
Pssm-ID: 428644 [Multi-domain] Cd Length: 451 Bit Score: 110.79 E-value: 1.92e-25
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
924-939
2.17e-03
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.
Pssm-ID: 395050 [Multi-domain] Cd Length: 18 Bit Score: 36.35 E-value: 2.17e-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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