r. capsulatus protein database (Integrated Genomics Inc)
90
Structured Review
Integrated Genomics Inc
r. capsulatus protein database
R. Capsulatus Protein Database, supplied by Integrated Genomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/r%2E+capsulatus+protein+database/r++capsulatus+protein+database/pmc02401338-189-8-20
Average 90 stars, based on 1 article reviews
R. Capsulatus Protein Database, supplied by Integrated Genomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/r%2E+capsulatus+protein+database/r++capsulatus+protein+database/pmc02401338-189-8-20
Average 90 stars, based on 1 article reviews
r. capsulatus protein database - by Bioz Stars,
2026-09
90/100 stars
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1) Product Images from "Overproduction or Absence of the Periplasmic Protease DegP Severely Compromises Bacterial Growth in the Absence of the Dithiol: Disulfide Oxidoreductase DsbA * S⃞ "
Article Title: Overproduction or Absence of the Periplasmic Protease DegP Severely Compromises Bacterial Growth in the Absence of the Dithiol: Disulfide Oxidoreductase DsbA
Journal:
doi: 10.1074/mcp.M700433-MCP200
Figure Legend Snippet: Phenotypes of various R. capsulatus strains P, R, and C ox refer to photosynthetic growth, respiratory growth, and ability to exhibit cytochrome c oxidase activity; + and − indicate proficiency and deficiency, respectively, s and vs correspond to slow and very slow growth, respectively; and na is not applicable.
Techniques Used: Activity Assay
Figure Legend Snippet: A, 2D gel analysis of periplasmic proteins in various R. capsulatus strains. Periplasmic protein fractions prepared from the wild type (MT1131), a DsbA− mutant (MD20), and a revertant of the DsbA− mutant (MD20R3) were separated by isoelectric focusing and SDS-polyacrylamide gel electrophoresis. Gels were stained with colloidal Coomassie, scanned, and analyzed using PDQuest 2D gel analysis software (Bio-Rad) as described under “Experimental Procedures.” Each study group contained at least three independent replicas, variations in the amounts of the spots were calculated using PDQuest software (see supplemental Table 1 for magnitudes of changes), and chosen protein spots were analyzed by MALDI-TOF-MS or nLC-MS/MS as described under “Experimental Procedures.” B, comparison of the changes in the abundance of different protein spots. Normalized raw density values calculated by PDQuest analysis software were used to compare the abundance of the protein spots in different strains described in A. Spot numbers refer to those attributed by the image analysis program PDQuest. The orders of magnitude of relative abundance of each spot for wild type (WT), DsbA-null mutant (DsbA−), and its revertant (DsbA-Rev3) are indicated on the graph. Protein spots that are at, or near, the origin represent those of unchanged abundance as compared with the wild type.
Techniques Used: Two-Dimensional Gel Electrophoresis, Mutagenesis, Polyacrylamide Gel Electrophoresis, Staining, Software, Tandem Mass Spectroscopy, Comparison
Figure Legend Snippet: Summary of decreased and increased protein spots in R. capsulatus DsbA-null mutant and revertant compared with the wild-type strain MT1131 Note that all proteins listed except PgaA, which is an integral membrane protein, have a putative signal sequence recognized by the program SignalP.
Techniques Used: Mutagenesis, Membrane, Sequencing
Figure Legend Snippet: Gel-based protease activity assays (zymograms) of various R. capsulatus protein extracts. In each case, periplasmic or whole cell lysates (10 μg of total proteins) prepared from cells grown by respiration in minimal medium at 35 °C were resolved in 12.5% casein zymogram gels under non-reducing conditions. After electrophoresis, gels were incubated overnight in a renaturation buffer and stained with Coomassie Blue. WT, DsbA−, and Rev3 correspond to the wild-type MT1131, DsbA-null mutant MD20, and its revertant MD20R3, respectively. Rev4, Rev7, Rev8, Rev9, Rev10, and Rev12 indicate the lysates prepared from the revertants MD20R4, -7, -8, -9, -10, and -12, respectively, of the DsbA-null mutant MD20 of R. capsulatus as listed in Table I. The band corresponding to DegP is indicated by arrows, and molecular weight markers (MW) are shown between A and B.
Techniques Used: Activity Assay, Electrophoresis, Incubation, Staining, Mutagenesis, Molecular Weight
Figure Legend Snippet: Amino acid sequence alignment between the E. coli (Ec) DegP and its R. capsulatus homologue RRC01208. The Q-linker domain of DegP is boxed, and the trypsin-like protease, PDZ1, and PDZ2 domains are underlined. The two conserved cysteine residues in the Q-linker domain and the Asp-His-Ser catalytic triad of the trypsin-like domain are indicated with arrows and *, respectively. The point mutations found in the revertants MD20R3, -4, -7, -8, -9, -10, and -12 (Table I) of the DsbA-null mutant MD20 are indicated by R3, R4, R7, R8, R9, R10, and R12, respectively. Black and gray boxes correspond to identical and similar amino acid residues, respectively.
Techniques Used: Sequencing, Mutagenesis
Figure Legend Snippet: Homology modeling of R. capsulatus DegP-like protein using the crystal structure of E. coli DegP. Homology modeling was performed by using the SWISS-MODEL automated protein structure homology modeling server. The amino acid sequence alignment of R. capsulatus and E. coli DegP shown in Fig. 4 was loaded into the server, and the resulting .pdb files containing superimposed structures of E. coli DegP (Protein Data Bank code 1KY9) and hypothetical R. capsulatus DegP-like protein were visualized by using the Deep View/Swiss-Pdb Viewer program. Protease, PDZ1, and PDZ2 domains are colored in blue, green, and pink, respectively, and the mutations found in the revertants (MD20R3, -4, -7, -8, -9, -10, and -12 (R3, R4, R7, R8, R9, R10, and R12) described in Fig. 4) are shown in red on the structure. Note that only the protease and the PDZ1 domains could be modeled reliably.
Techniques Used: Sequencing
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![a Bifurcated electron transfer reaction conveys one electron from QH 2 oxidation to the FeS protein (FeS, yellow) [2Fe-2S] cluster and another electron to cyt b (periwinkle) hemes b L and b H . Reduced [2Fe-2S] cluster transfers the electron to cyt c 1 (green) heme c 1 via the movement of the FeS protein from near heme b L to near heme c 1 . The subsequent electron transfer step from heme b H to Q from the pool is not shown for clarity. A cyt c ( c 2 or c y ) carries electrons from heme c 1 to CIV, where electrons reach the heme-Cu (Cu -b 3 ) site, where O 2 is reduced to H 2 O, via the CcoP (P, light blue) hemes c p1 and c p2 , CcoO (O, dark green) heme c o , and CcoN (N, purple) heme b . b R. <t>capsulatus</t> petABC encodes the structural genes of the bc 1 -type CIII 2 subunits, the FeS protein ( petA , yellow), cyt b ( B , periwinkle), and cyt c 1 ( C , green), and ccoNOQP encodes those of the cbb 3 -type CIV subunits, the CcoN ( ccoN , purple), CcoO ( O , dark green), CcoQ ( Q , gray), and CcoP ( P , light blue). cycY gene (red) encodes cyt c y , and its 30-residue transmembrane helix (TMH), 69-residue linker (L), and 100-residue cyt c (cyt c ) domain are indicated. Heme cofactors of b - and c -type cyts are indicated by black and white asterisks, respectively, whereas diamond and dot designate the [2Fe-2S] cluster and Cu atom, respectively. c Plasmid-borne genetic fusions. The bipartite fusion (left) is formed by in-frame linking the 3′-end of petC to the 5′-end of ccoP and the tripartite fusion (right) by adding the linker and cyt c domain of cycY to the 3′-end of ccoP . Colors and cofactors are as in a , and the his (H) and flag (F) affinity tags (dark purple) of the bipartite and tripartite fusion subunits are shown. d Schematic depiction of bipartite (left) and tripartite (right) supercomplexes (SC). The bipartite SC encodes a CIII 2 dimer fused on each side to a His-tagged CIV. The tripartite SC also contains the Flag-tagged cyt domain of c y (red) at the end of CcoP (blue).](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_6108/pmc07876108/pmc07876108__41467_2021_21051_Fig1_HTML.jpg)
