Annotation: 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase
Length: 281 amino acids
Source: acidovorax_3H11 in FitnessBrowser
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| L-fucose catabolism | KDF-hydrolase | hi | 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized) | 60% | 98% | 348.6 | 2,4-dihydroxy-5-methyl-6-oxohexa-2,4-dienoate isomerase | 36% | 168.7 |
| L-rhamnose catabolism | LRA6 | hi | 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized) | 60% | 98% | 348.6 | 2,4-dihydroxy-5-methyl-6-oxohexa-2,4-dienoate isomerase | 36% | 168.7 |
| D-xylose catabolism | HDOP-hydrol | med | FAA hydrolase family protein (characterized, see rationale) | 56% | 99% | 331.3 | Ureidoglycolate lyase; UGL; Ureidoglycolase; Ureidoglycolatase; Ureidoglycolate hydrolase; EC 4.3.2.3 | 58% | 342.4 |
View Ac3H11_4136 at FitnessBrowser
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Predict protein localization: PSORTb (Gram negative bacteria)
Predict transmembrane helices and signal peptides: Phobius
Check the SEED with FIGfam search
Fitness BLAST: loading...
MKLIRYGQPGAERPGLLDATGTLRDLSMLLPDIGPAQLNPRTLSALAAIDASRLPPVYGT PRLGSPVGGVGKIVCVGLNYADHAREAGLQPPAEPVLFMKAVTALSGPHDDVRIPAGAVK TDWEVELGIVIGTRARNVAKAQALEHVAGYVLANDVSERAWQMERGGQWDKGKSHDTFAP IGPWLVTADEVGDPHAIDLWLEVNGRRVQNGSTRNFIFDVPTVVSYISEFMTLESGDLVL TGTPAGVGLGQKPAPWFLKPGDVMRLGATGLGEQVQKCVGG
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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