Protein WP_076578675.1 in Haloterrigena daqingensis JX313
Annotation: NCBI__GCF_001971705.1:WP_076578675.1
Length: 533 amino acids
Source: GCF_001971705.1 in NCBI
Candidate for 23 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 | med | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 35% | 98% | 309.3 | Betaine aldehyde dehydrogenase; BADH; Glycine betaine aldehyde dehydrogenase; EC 1.2.1.8 | 35% | 268.1 |
| D-galacturonate catabolism | dopDH | med | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 35% | 98% | 309.3 | Betaine aldehyde dehydrogenase; BADH; Glycine betaine aldehyde dehydrogenase; EC 1.2.1.8 | 35% | 268.1 |
| D-glucuronate catabolism | dopDH | med | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 35% | 98% | 309.3 | Betaine aldehyde dehydrogenase; BADH; Glycine betaine aldehyde dehydrogenase; EC 1.2.1.8 | 35% | 268.1 |
| D-xylose catabolism | dopDH | med | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 35% | 98% | 309.3 | Betaine aldehyde dehydrogenase; BADH; Glycine betaine aldehyde dehydrogenase; EC 1.2.1.8 | 35% | 268.1 |
| L-arginine catabolism | astD | lo | N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) | 34% | 94% | 265.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-citrulline catabolism | astD | lo | N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) | 34% | 94% | 265.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-lysine catabolism | amaB | lo | L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) | 32% | 96% | 263.8 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-arginine catabolism | patD | lo | 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) | 33% | 97% | 260.8 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-citrulline catabolism | patD | lo | 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) | 33% | 97% | 260.8 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| putrescine catabolism | patD | lo | 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) | 33% | 97% | 260.8 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-isoleucine catabolism | iolA | lo | malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) | 30% | 96% | 244.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| myo-inositol catabolism | mmsA | lo | malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) | 30% | 96% | 244.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| propionate catabolism | iolA | lo | malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) | 30% | 96% | 244.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-threonine catabolism | iolA | lo | malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) | 30% | 96% | 244.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-valine catabolism | iolA | lo | malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) | 30% | 96% | 244.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-arginine catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 35% | 92% | 240.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-arginine catabolism | rocA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 35% | 92% | 240.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-citrulline catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 35% | 92% | 240.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-citrulline catabolism | rocA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 35% | 92% | 240.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-proline catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 35% | 92% | 240.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| 4-hydroxybenzoate catabolism | praB | lo | 2-aminomucoate semialdehyde dehydrogenase subunit (EC 1.2.1.32) (characterized) | 30% | 61% | 155.6 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-tryptophan catabolism | nbaE | lo | 2-aminomucoate semialdehyde dehydrogenase subunit (EC 1.2.1.32) (characterized) | 30% | 61% | 155.6 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
| L-tryptophan catabolism | praB | lo | 2-aminomucoate semialdehyde dehydrogenase subunit (EC 1.2.1.32) (characterized) | 30% | 61% | 155.6 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 35% | 305.8 |
Sequence Analysis Tools
View WP_076578675.1 at NCBI
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
MSQQATTQVHGHYIGGEWTDDSSASRSEEAERFESQNPATGESLATFERGTAEDVDAALE
AAEGAFEEWRSLSYIDRAEYLWDIYHELRERHDELGEIVSKECGKEISEGKADVTEAWHM
VEWAAGNARHPHGDVVPSEVAGKDAYMRRKPRGVVGCITPWNFPVAIPFWHMAIALVEGN
TVVWKPAEQTPWCGQVIAEMMDEAGVPDGVFNMVQGYGDAGAAITDDDRVDTVLFTGSAE
VGHEISGKVGGEAGKLAACEMGGKNGIVVTEEADLDVAVHSAIMSSFKTTGQRCVSSERL
IVHTDVYDEFKSRFVDIAEDIAVGDPLEADTFMGPVIEDDHVEKIRRHNELAVEEGADVL
VDRFELEAEEIPDGHAEGAAIAGDGERTDGFANGHWVGPFVYEIDYEPDLRCLNEECFGP
HVALIEYDGDIDRALEIHNDTPYGLAGAIVSEDYRQLNAFRDRAEIGLAYANLPCIGAEV
QLPFGGVKKSGNGYPSAREAIEAVTERTAWTINNADDIEMAQGLSADITTTDD
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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