Protein RR42_RS27350 in Cupriavidus basilensis 4G11
Annotation: FitnessBrowser__Cup4G11:RR42_RS27350
Length: 486 amino acids
Source: Cup4G11 in FitnessBrowser
Candidate for 14 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arabinose catabolism | xacF | hi | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 45% | 99% | 410.6 | betaine-aldehyde dehydrogenase (EC 1.2.1.8) | 40% | 348.6 |
| D-galacturonate catabolism | dopDH | hi | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 45% | 99% | 410.6 | betaine-aldehyde dehydrogenase (EC 1.2.1.8) | 40% | 348.6 |
| D-glucuronate catabolism | dopDH | hi | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 45% | 99% | 410.6 | betaine-aldehyde dehydrogenase (EC 1.2.1.8) | 40% | 348.6 |
| D-xylose catabolism | dopDH | hi | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 45% | 99% | 410.6 | betaine-aldehyde dehydrogenase (EC 1.2.1.8) | 40% | 348.6 |
| L-fucose catabolism | aldA | med | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 41% | 98% | 379.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 45% | 410.6 |
| L-rhamnose catabolism | aldA | med | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 41% | 98% | 379.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 45% | 410.6 |
| L-threonine catabolism | aldA | med | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 41% | 98% | 379.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 45% | 410.6 |
| L-arginine catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 33% | 93% | 264.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 45% | 410.6 |
| L-arginine catabolism | rocA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 33% | 93% | 264.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 45% | 410.6 |
| L-citrulline catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 33% | 93% | 264.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 45% | 410.6 |
| L-citrulline catabolism | rocA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 33% | 93% | 264.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 45% | 410.6 |
| L-proline catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 33% | 93% | 264.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 45% | 410.6 |
| L-arginine catabolism | astD | lo | N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) | 33% | 91% | 229.9 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 45% | 410.6 |
| L-citrulline catabolism | astD | lo | N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) | 33% | 91% | 229.9 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 45% | 410.6 |
Sequence Analysis Tools
View RR42_RS27350 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MAVAKTDEFNNYINGEWSKSASGRTFDNVNPADTADIVGRFQASTADDAQAAVAAAAAAF
DAWKKTPISKRAKILNGAADYLEANAEQIAEELTREEGKALNLSKDEVLRSAQTIRFYAV
EGQSFSGETYPQDDPDMIVYSQREPLGVVTVISPWNFPVSIPARKIAPALIAGNTVVFKP
SSDAPLSGYRLAQAFVEAGIPKGVLNFITGRAGDVGAAITEAPAVRAISFTGSTAAGQHI
HRSVSLSTRTQMELGGKNPLIVMEDADLDRAVDLTIKGGLSLSGQACTGTSRVLVMASVK
AAYTEKLLAKVKTLKIGSGMTPGMDVGPLATRKQLETVLGYVEAGKSEATHLCGGDRLGG
EPYDKGFYVSPAVFTGVTQQMRIAREEIFGPVIAIIEVSSYADAIAKANDTEYGLSAAIV
TSNPRYAHDFAHDIQSGTVKINRTTTGNLINAPFGGLKQSSTSTFRESGRAGLEFYTQIK
TVYRGC
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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About GapMind
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using
ublast (a fast alternative to protein BLAST)
against a database of manually-curated proteins (most of which are experimentally characterized) or by using
HMMer with enzyme models (usually from
TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps."
For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways.
For diverse bacteria and archaea that can utilize a carbon source, there is a complete
high-confidence catabolic pathway (including a transporter) just 38% of the time, and
there is a complete medium-confidence pathway 63% of the time.
Gaps may be due to:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory