Protein WP_040294591.1 in Alistipes indistinctus YIT 12060
Annotation: NCBI__GCF_000231275.1:WP_040294591.1
Length: 250 amino acids
Source: GCF_000231275.1 in NCBI
Candidate for 22 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| ethanol catabolism | etoh-dh-nad | lo | alcohol dehydrogenase (EC 1.1.1.1) (characterized) | 37% | 97% | 150.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| glycerol catabolism | dhaD | lo | NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) | 33% | 95% | 142.5 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| D-sorbitol (glucitol) catabolism | sdh | lo | L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized) | 37% | 92% | 142.5 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| L-fucose catabolism | fucDH | lo | Short-chain dehydrogenase/reductase SDR (characterized, see rationale) | 35% | 97% | 141.4 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| L-arabinose catabolism | xacB | lo | L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) | 32% | 91% | 137.9 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| D-galactose catabolism | galdh | lo | L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) | 32% | 91% | 137.9 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| lactose catabolism | galdh | lo | L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) | 32% | 91% | 137.9 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| xylitol catabolism | xdhA | lo | D-xylulose reductase (EC 1.1.1.9) (characterized) | 33% | 97% | 136.7 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| D-xylose catabolism | xdhA | lo | D-xylulose reductase (EC 1.1.1.9) (characterized) | 33% | 97% | 136.7 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| D-xylose catabolism | DKDP-dehydrog | lo | SDR family oxidoreductase (characterized, see rationale) | 31% | 100% | 119.8 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| D-sorbitol (glucitol) catabolism | srlD | lo | Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) | 30% | 96% | 115.5 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| 4-hydroxybenzoate catabolism | fadB | lo | 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) | 34% | 97% | 113.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| 4-hydroxybenzoate catabolism | paaH | lo | 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) | 34% | 97% | 113.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| L-arginine catabolism | fadB | lo | 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) | 34% | 97% | 113.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| L-citrulline catabolism | fadB | lo | 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) | 34% | 97% | 113.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| L-isoleucine catabolism | ivdG | lo | 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) | 34% | 97% | 113.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| L-lysine catabolism | fadB | lo | 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) | 34% | 97% | 113.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| phenylacetate catabolism | fadB | lo | 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) | 34% | 97% | 113.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| phenylacetate catabolism | paaH | lo | 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) | 34% | 97% | 113.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| L-phenylalanine catabolism | fadB | lo | 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) | 34% | 97% | 113.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| L-phenylalanine catabolism | paaH | lo | 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) | 34% | 97% | 113.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
| L-proline catabolism | fadB | lo | 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) | 34% | 97% | 113.6 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 39% | 186.4 |
Sequence Analysis Tools
View WP_040294591.1 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
MTTSTEKVALVTGSAMGIGLACAEAFAKAGYITVLADIKEPRSQIESLVAQGYKAVFYGC
DVSNTRTVKEMIEWIAATYGHLDAALNNAGIQTPQRPMAEITDDEFDRTVAVDLKGVWNC
MRYEILQMLRQGGGAIVNTSSQGGVTGFPGQAAYIACKHAVIGLTRTAAIDYAAKHIRIN
AVCPGVIRTPMAEELMSRNPQLEAELVRDIPAGRLGKPEEIANAVLWLCGPQASFVDGHA
LLVDGAFSIH
This GapMind analysis is from Sep 24 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