30S ribosomal protein S12 methylthiotransferase accessory factor YcaO; YcaO acts as a partner ...
4-578
0e+00
30S ribosomal protein S12 methylthiotransferase accessory factor YcaO; YcaO acts as a partner for RimO to achieve the modification of ribosomal protein S12. Homologs of YcaO are involved a wide variety of RiPP (ribosomally translated, post-translationally modified peptide) natural product biosynthesis pathways. Some members of this family have an additional N-terminal OsmC-like domain.
:
Pssm-ID: 468680 [Multi-domain] Cd Length: 571 Bit Score: 1009.43 E-value: 0e+00
30S ribosomal protein S12 methylthiotransferase accessory factor YcaO; YcaO acts as a partner ...
4-578
0e+00
30S ribosomal protein S12 methylthiotransferase accessory factor YcaO; YcaO acts as a partner for RimO to achieve the modification of ribosomal protein S12. Homologs of YcaO are involved a wide variety of RiPP (ribosomally translated, post-translationally modified peptide) natural product biosynthesis pathways. Some members of this family have an additional N-terminal OsmC-like domain.
Pssm-ID: 468680 [Multi-domain] Cd Length: 571 Bit Score: 1009.43 E-value: 0e+00
YcaO domain protein; This family consists of remarkably well-conserved proteins from gamma and ...
3-576
0e+00
YcaO domain protein; This family consists of remarkably well-conserved proteins from gamma and beta Proteobacteria, heavily skewed towards organisms of marine environments. Its gene neighborhood is not conserved. This family has an OsmC-like N-terminal domain. It shares a YcaO domain, frequently associated with ATP-dependent cyclodehydration for peptide modification. The function is unknown. Fifteen of the first sixteen members of this family are from selenouridine-positive genomes, but this correlation may not be meaningful.
Pssm-ID: 132588 [Multi-domain] Cd Length: 718 Bit Score: 620.31 E-value: 0e+00
YcaO cyclodehydratase C-terminal domain; This is the proline-rich C-terminal domain found in ...
407-582
1.85e-81
YcaO cyclodehydratase C-terminal domain; This is the proline-rich C-terminal domain found in ribosomal protein S12 methylthiotransferase accessory factor YcaO. It has been shown to be involved in both C protein recognition and cyclodehydration. The C-terminal domain resembles a tetratricopeptide repeat that mediates dimerization.
Pssm-ID: 465734 Cd Length: 172 Bit Score: 252.82 E-value: 1.85e-81
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
175-299
1.47e-03
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Pssm-ID: 380654 [Multi-domain] Cd Length: 313 Bit Score: 41.14 E-value: 1.47e-03
30S ribosomal protein S12 methylthiotransferase accessory factor YcaO; YcaO acts as a partner ...
4-578
0e+00
30S ribosomal protein S12 methylthiotransferase accessory factor YcaO; YcaO acts as a partner for RimO to achieve the modification of ribosomal protein S12. Homologs of YcaO are involved a wide variety of RiPP (ribosomally translated, post-translationally modified peptide) natural product biosynthesis pathways. Some members of this family have an additional N-terminal OsmC-like domain.
Pssm-ID: 468680 [Multi-domain] Cd Length: 571 Bit Score: 1009.43 E-value: 0e+00
YcaO domain protein; This family consists of remarkably well-conserved proteins from gamma and ...
3-576
0e+00
YcaO domain protein; This family consists of remarkably well-conserved proteins from gamma and beta Proteobacteria, heavily skewed towards organisms of marine environments. Its gene neighborhood is not conserved. This family has an OsmC-like N-terminal domain. It shares a YcaO domain, frequently associated with ATP-dependent cyclodehydration for peptide modification. The function is unknown. Fifteen of the first sixteen members of this family are from selenouridine-positive genomes, but this correlation may not be meaningful.
Pssm-ID: 132588 [Multi-domain] Cd Length: 718 Bit Score: 620.31 E-value: 0e+00
YcaO-type kinase domain; This protein family includes YcaO and homologs that can phosphorylate ...
11-404
2.35e-160
YcaO-type kinase domain; This protein family includes YcaO and homologs that can phosphorylate a peptide amide backbone (rather than side chains), as during heterocycle-forming modifications during maturation of the TOMM class (Thiazole/Oxazole-Modified Microcins) of bacteriocins. However, YcaO domain proteins also occur in contexts that do not suggest peptide modification. [Hypothetical proteins, Conserved]
Pssm-ID: 273224 Cd Length: 377 Bit Score: 463.16 E-value: 2.35e-160
YcaO cyclodehydratase C-terminal domain; This is the proline-rich C-terminal domain found in ...
407-582
1.85e-81
YcaO cyclodehydratase C-terminal domain; This is the proline-rich C-terminal domain found in ribosomal protein S12 methylthiotransferase accessory factor YcaO. It has been shown to be involved in both C protein recognition and cyclodehydration. The C-terminal domain resembles a tetratricopeptide repeat that mediates dimerization.
Pssm-ID: 465734 Cd Length: 172 Bit Score: 252.82 E-value: 1.85e-81
YcaO cyclodehydratase, ATP-ad Mg2+-binding; YcaO is an ATP- an Mg2+-binding protein involved ...
74-391
1.50e-71
YcaO cyclodehydratase, ATP-ad Mg2+-binding; YcaO is an ATP- an Mg2+-binding protein involved in the peptidic biosynthesis of azoline. There three motifs involved in the binding are, in UniProtKB:P75838, 71-79: Sx3ExxER, 184-203: Sx6Ex3Qx3ExxER, and 286-290: RxxxE. Three slightly different functional families are represented in this family, proteins involved in TOMM (thiazole/oxazole-modified microcin) biogenesis, non-TOMM proteins such as UniProtKB:P75838, and TfuA-associated non-TOMM proteins involved in trifolitoxin biosynthesis. UniProtKB:P75838 hydrolyses ATP to AMP and pyrophosphate.
Pssm-ID: 426884 Cd Length: 318 Bit Score: 232.56 E-value: 1.50e-71
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
175-299
1.47e-03
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Pssm-ID: 380654 [Multi-domain] Cd Length: 313 Bit Score: 41.14 E-value: 1.47e-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.
Click on the triangle to view details about the feature, including a multiple sequence alignment
of your query sequence and the protein sequences used to curate the domain model,
where hash marks (#) above the aligned sequences show the location of the conserved feature residues.
The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
Click on the triangle for interactive 3D structure viewing options.
Functional characterization of the conserved domain architecture found on the query.
Click here to see more details.
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
(labeled illustration) or all hits
(labeled illustration).
Domains are color coded according to superfamilies
to which they have been assigned. Hits with scores that pass a domain-specific threshold
(specific hits) are drawn in bright colors.
Others (non-specific hits) and
superfamily placeholders are drawn in pastel colors.
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
(CDART).
Modify your query to search against a different database and/or use advanced search options
