type IV conjugative transfer system coupling protein TraD; The TraD protein performs an ...
8-413
0e+00
type IV conjugative transfer system coupling protein TraD; The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).
Pssm-ID: 131806 Cd Length: 566 Bit Score: 570.11 E-value: 0e+00
Type IV secretion-system coupling protein DNA-binding domain; The plasmid conjugative coupling ...
174-412
3.95e-76
Type IV secretion-system coupling protein DNA-binding domain; The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export.
Pssm-ID: 431268 [Multi-domain] Cd Length: 386 Bit Score: 241.43 E-value: 3.95e-76
TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are ...
187-224
2.15e-04
TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion (T4S) systems, versatile bacterial secretion systems mediating transport of protein and/or DNA. They are present in gram-negative and gram-positive bacteria, as well as archaea. They form hexameric rings and belong to the RecA-like NTPases superfamily, which also includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases.
Pssm-ID: 410871 [Multi-domain] Cd Length: 144 Bit Score: 41.05 E-value: 2.15e-04
type IV conjugative transfer system coupling protein TraD; The TraD protein performs an ...
8-413
0e+00
type IV conjugative transfer system coupling protein TraD; The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).
Pssm-ID: 131806 Cd Length: 566 Bit Score: 570.11 E-value: 0e+00
Type IV secretion-system coupling protein DNA-binding domain; The plasmid conjugative coupling ...
174-412
3.95e-76
Type IV secretion-system coupling protein DNA-binding domain; The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export.
Pssm-ID: 431268 [Multi-domain] Cd Length: 386 Bit Score: 241.43 E-value: 3.95e-76
F sex factor protein N terminal; This domain family is found in bacteria, and is typically ...
32-128
6.03e-45
F sex factor protein N terminal; This domain family is found in bacteria, and is typically between 96 and 107 amino acids in length. The family is found in association with pfam10412. TraD is a cytoplasmic membrane protein with possible DNA binding domains. It is part of the bacterial F sex factor complex.
Pssm-ID: 432671 [Multi-domain] Cd Length: 97 Bit Score: 151.05 E-value: 6.03e-45
TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are ...
187-224
2.15e-04
TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion (T4S) systems, versatile bacterial secretion systems mediating transport of protein and/or DNA. They are present in gram-negative and gram-positive bacteria, as well as archaea. They form hexameric rings and belong to the RecA-like NTPases superfamily, which also includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases.
Pssm-ID: 410871 [Multi-domain] Cd Length: 144 Bit Score: 41.05 E-value: 2.15e-04
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
