outer membrane protein assembly factor BamD is part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
outer membrane assembly lipoprotein YfiO; Members of this protein family include YfiO, a ...
23-246
1.58e-96
outer membrane assembly lipoprotein YfiO; Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795). [Protein fate, Protein and peptide secretion and trafficking]
:
Pssm-ID: 274513 [Multi-domain] Cd Length: 235 Bit Score: 282.52 E-value: 1.58e-96
outer membrane assembly lipoprotein YfiO; Members of this protein family include YfiO, a ...
23-246
1.58e-96
outer membrane assembly lipoprotein YfiO; Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795). [Protein fate, Protein and peptide secretion and trafficking]
Pssm-ID: 274513 [Multi-domain] Cd Length: 235 Bit Score: 282.52 E-value: 1.58e-96
BamD lipoprotein, a component of the beta-barrel assembly machinery; BamD, also called YfiO, ...
44-244
5.12e-66
BamD lipoprotein, a component of the beta-barrel assembly machinery; BamD, also called YfiO, is part of the beta-barrel assembly machinery (BAM), which is essential for the folding and insertion of outer membrane proteins (OMPs) in the OM of Gram-negative bacteria. Transmembrane OMPs carry out important functions including nutrient and waste management, cell adhesion, and structural roles. The BAM complex is composed of the beta-barrel OMP BamA (also called Omp85/YaeT) and four lipoproteins BamBCDE. BamD is the only BAM lipoprotein required for viability. Both BamA and BamD are broadly distributed in Gram-negative bacteria, and may constitute the core of the BAM complex. BamD contains five Tetratricopeptide repeats (TPRs). The three TPRs at the N-terminus may participate in interaction with substrates, while the two TPRs in the C-terminus may be involved in binding with other BAM components.
Pssm-ID: 276939 [Multi-domain] Cd Length: 213 Bit Score: 204.41 E-value: 5.12e-66
Outer membrane lipoprotein; This outer membrane lipoprotein carries a TPR-like region towards ...
41-237
5.81e-47
Outer membrane lipoprotein; This outer membrane lipoprotein carries a TPR-like region towards its N-terminal. YfiO in E.coli is one of three outer membrane lipoproteins that form a multicomponent YaeT complex in the outer membrane of Gram-negative bacteria that is involved in the targeting and folding of beta-barrel outer membrane proteins. YfiO is the only essential lipoprotein component of the complex. It is required for the proper assembly and/or targeting of outer membrane proteins to the outer membrane. Through its interactions with NlpB it maintains the functional integrity of the YaeT complex.
Pssm-ID: 433282 [Multi-domain] Cd Length: 200 Bit Score: 155.18 E-value: 5.81e-47
outer membrane assembly lipoprotein YfiO; Members of this protein family include YfiO, a ...
23-246
1.58e-96
outer membrane assembly lipoprotein YfiO; Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795). [Protein fate, Protein and peptide secretion and trafficking]
Pssm-ID: 274513 [Multi-domain] Cd Length: 235 Bit Score: 282.52 E-value: 1.58e-96
BamD lipoprotein, a component of the beta-barrel assembly machinery; BamD, also called YfiO, ...
44-244
5.12e-66
BamD lipoprotein, a component of the beta-barrel assembly machinery; BamD, also called YfiO, is part of the beta-barrel assembly machinery (BAM), which is essential for the folding and insertion of outer membrane proteins (OMPs) in the OM of Gram-negative bacteria. Transmembrane OMPs carry out important functions including nutrient and waste management, cell adhesion, and structural roles. The BAM complex is composed of the beta-barrel OMP BamA (also called Omp85/YaeT) and four lipoproteins BamBCDE. BamD is the only BAM lipoprotein required for viability. Both BamA and BamD are broadly distributed in Gram-negative bacteria, and may constitute the core of the BAM complex. BamD contains five Tetratricopeptide repeats (TPRs). The three TPRs at the N-terminus may participate in interaction with substrates, while the two TPRs in the C-terminus may be involved in binding with other BAM components.
Pssm-ID: 276939 [Multi-domain] Cd Length: 213 Bit Score: 204.41 E-value: 5.12e-66
Outer membrane lipoprotein; This outer membrane lipoprotein carries a TPR-like region towards ...
41-237
5.81e-47
Outer membrane lipoprotein; This outer membrane lipoprotein carries a TPR-like region towards its N-terminal. YfiO in E.coli is one of three outer membrane lipoproteins that form a multicomponent YaeT complex in the outer membrane of Gram-negative bacteria that is involved in the targeting and folding of beta-barrel outer membrane proteins. YfiO is the only essential lipoprotein component of the complex. It is required for the proper assembly and/or targeting of outer membrane proteins to the outer membrane. Through its interactions with NlpB it maintains the functional integrity of the YaeT complex.
Pssm-ID: 433282 [Multi-domain] Cd Length: 200 Bit Score: 155.18 E-value: 5.81e-47
tol-pal system protein YbgF; Members of this protein family are the product of one of seven ...
45-169
4.45e-12
tol-pal system protein YbgF; Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Pssm-ID: 188247 [Multi-domain] Cd Length: 117 Bit Score: 61.53 E-value: 4.45e-12
tol-pal system protein YbgF; Members of this protein family are the product of one of seven ...
128-248
1.23e-06
tol-pal system protein YbgF; Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Pssm-ID: 188247 [Multi-domain] Cd Length: 117 Bit Score: 46.12 E-value: 1.23e-06
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
42-247
2.15e-03
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Pssm-ID: 274350 [Multi-domain] Cd Length: 899 Bit Score: 39.30 E-value: 2.15e-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.
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
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(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).
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