ribosome maturation factor RimM is an accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region
Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]; Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing is part of the Pathway/BioSystem: 16S rRNA modification
Pssm-ID: 440569 [Multi-domain] Cd Length: 173 Bit Score: 176.07 E-value: 6.27e-57
16S rRNA processing protein RimM; This family consists of the bacterial protein RimM (YfjA, ...
4-168
3.43e-46
16S rRNA processing protein RimM; This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide. [Transcription, RNA processing]
Pssm-ID: 274061 [Multi-domain] Cd Length: 165 Bit Score: 148.51 E-value: 3.43e-46
RimM N-terminal domain; The RimM protein is essential for efficient processing of 16S rRNA. ...
7-90
1.82e-23
RimM N-terminal domain; The RimM protein is essential for efficient processing of 16S rRNA. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes. This N-terminal domain is found associated with a PRC-barrel domain.
Pssm-ID: 460327 Cd Length: 84 Bit Score: 88.00 E-value: 1.82e-23
Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]; Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing is part of the Pathway/BioSystem: 16S rRNA modification
Pssm-ID: 440569 [Multi-domain] Cd Length: 173 Bit Score: 176.07 E-value: 6.27e-57
16S rRNA processing protein RimM; This family consists of the bacterial protein RimM (YfjA, ...
4-168
3.43e-46
16S rRNA processing protein RimM; This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide. [Transcription, RNA processing]
Pssm-ID: 274061 [Multi-domain] Cd Length: 165 Bit Score: 148.51 E-value: 3.43e-46
RimM N-terminal domain; The RimM protein is essential for efficient processing of 16S rRNA. ...
7-90
1.82e-23
RimM N-terminal domain; The RimM protein is essential for efficient processing of 16S rRNA. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes. This N-terminal domain is found associated with a PRC-barrel domain.
Pssm-ID: 460327 Cd Length: 84 Bit Score: 88.00 E-value: 1.82e-23
PRC-barrel domain; The PRC-barrel is an all beta barrel domain found in photosystem reaction ...
97-169
1.75e-06
PRC-barrel domain; The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the carboxyl terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain.
Pssm-ID: 398765 Cd Length: 78 Bit Score: 43.82 E-value: 1.75e-06
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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of your query sequence and the protein sequences used to curate the domain model,
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The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
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Domains are color coded according to superfamilies
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Others (non-specific hits) and
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if a domain or superfamily has been annotated with functional sites (conserved features),
they are mapped to the query sequence and indicated through sets of triangles
with the same color and shade of the domain or superfamily that provides the annotation. Mouse over the colored bars or triangles to see descriptions of the domains and features.
click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
mapped to the query sequence.
Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
(illustrated example)
and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the
advanced search options)
the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
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