Protein Echvi_1300 in Echinicola vietnamensis KMM 6221, DSM 17526
Annotation: Echvi_1300 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1
Length: 543 amino acids
Source: Cola in FitnessBrowser
Candidate for 17 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | putA | hi | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 49% | 94% | 515.8 | | | |
| L-arginine catabolism | putA | hi | pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01236) | | 100% | 804.1 | | | |
| L-citrulline catabolism | putA | hi | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 49% | 94% | 515.8 | | | |
| L-citrulline catabolism | putA | hi | pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01236) | | 100% | 804.1 | | | |
| L-proline catabolism | putA | hi | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 49% | 94% | 515.8 | | | |
| L-proline catabolism | putA | hi | pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01236) | | 100% | 804.1 | | | |
| L-arginine catabolism | rocA | med | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 49% | 94% | 515.8 | delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 | 50% | 515.4 |
| L-arginine catabolism | rocA | med | pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01236) | | 100% | 804.1 | delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 | 50% | 515.4 |
| L-citrulline catabolism | rocA | med | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 49% | 94% | 515.8 | delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 | 50% | 515.4 |
| L-citrulline catabolism | rocA | med | pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01236) | | 100% | 804.1 | delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 | 50% | 515.4 |
| 4-hydroxybenzoate catabolism | adh | lo | Aldehyde dehydrogenase 5, mitochondrial; EC 1.2.1.5 (characterized) | 30% | 89% | 187.2 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
| 2'-deoxyinosine catabolism | adh | lo | Aldehyde dehydrogenase 5, mitochondrial; EC 1.2.1.5 (characterized) | 30% | 89% | 187.2 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
| 2-deoxy-D-ribose catabolism | adh | lo | Aldehyde dehydrogenase 5, mitochondrial; EC 1.2.1.5 (characterized) | 30% | 89% | 187.2 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
| ethanol catabolism | adh | lo | Aldehyde dehydrogenase 5, mitochondrial; EC 1.2.1.5 (characterized) | 30% | 89% | 187.2 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
| L-threonine catabolism | adh | lo | Aldehyde dehydrogenase 5, mitochondrial; EC 1.2.1.5 (characterized) | 30% | 89% | 187.2 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
| thymidine catabolism | adh | lo | Aldehyde dehydrogenase 5, mitochondrial; EC 1.2.1.5 (characterized) | 30% | 89% | 187.2 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
| L-tryptophan catabolism | adh | lo | Aldehyde dehydrogenase 5, mitochondrial; EC 1.2.1.5 (characterized) | 30% | 89% | 187.2 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
| L-phenylalanine catabolism | pad-dh | lo | aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) | 31% | 82% | 178.3 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
| L-arabinose catabolism | xacF | lo | 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 30% | 69% | 136.3 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
| D-galacturonate catabolism | dopDH | lo | 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 30% | 69% | 136.3 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
| D-glucuronate catabolism | dopDH | lo | 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 30% | 69% | 136.3 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
| D-xylose catabolism | dopDH | lo | 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 30% | 69% | 136.3 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 49% | 515.8 |
Sequence Analysis Tools
View Echvi_1300 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
Fitness BLAST: loading...
Sequence
MLKGFFNVPEPKNEPVFDYAPGTPARAKLQAALQEARSKEVDVPMYIGSEEVRTGNKIPL
SPPHDHQHLLGHFHEGDKSHVEQAINAALGAKEAWETMEWEQRAAIFLKAADLIAGPYRY
KMNAATMLGQSKNAFQAEIDSACEIVDFLRFNVKYMTEIYKQQPPISGDGVWNRLEQRPL
EGFVFALTPFNFTAIAGNLPTAPAMMGNTVVWKPAYTQIYTANLLMQVFREAGVPDGVIN
LVYVDGPAAGEVIFEHPEFAGIHFTGSTAVFQTIWKTIGNNIEKYKSYPRIVGETGGKDF
VIAHKSADAKQLATGLVRGAFEFQGQKCSAASRAYIPSNLWEDVKKYMQEDLASIKMGGP
EDFSNFINAVIDEKSFDKIAKYIDTAKSDGLEVVAGGHYDKSKGYFVEPTVLLTKDPMYT
TMCEEIFGPVLTIYVYQEDHFEEALELVDQTSPYGLTGAIFSHDRYAAQLATQKLRNAAG
NFYINDKPTGAVVGQQPFGGARKSGTNDKAGAMINMLRWVSPRTIKETFVTPTDYRYPFL
GED
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 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