Protein WP_011829504.1 in Methylibium petroleiphilum PM1
Annotation: NCBI__GCF_000015725.1:WP_011829504.1
Length: 499 amino acids
Source: GCF_000015725.1 in NCBI
Candidate for 42 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | kauB | hi | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 58% | 100% | 583.6 | aldehyde dehydrogenase | 59% | 569.7 |
| L-arginine catabolism | puuC | hi | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 58% | 100% | 583.6 | aldehyde dehydrogenase | 59% | 569.7 |
| L-citrulline catabolism | puuC | hi | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 58% | 100% | 583.6 | aldehyde dehydrogenase | 59% | 569.7 |
| putrescine catabolism | puuC | hi | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 58% | 100% | 583.6 | aldehyde dehydrogenase | 59% | 569.7 |
| L-arginine catabolism | gabD | med | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 53% | 98% | 513.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-arginine catabolism | patD | med | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 53% | 98% | 513.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-citrulline catabolism | gabD | med | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 53% | 98% | 513.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-citrulline catabolism | patD | med | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 53% | 98% | 513.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| putrescine catabolism | gabD | med | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 53% | 98% | 513.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| putrescine catabolism | patD | med | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 53% | 98% | 513.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| 4-hydroxybenzoate catabolism | adh | med | Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) | 44% | 88% | 401.7 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| 2'-deoxyinosine catabolism | adh | med | Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) | 44% | 88% | 401.7 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| 2-deoxy-D-ribose catabolism | adh | med | Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) | 44% | 88% | 401.7 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| ethanol catabolism | adh | med | Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) | 44% | 88% | 401.7 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-threonine catabolism | adh | med | Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) | 44% | 88% | 401.7 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| thymidine catabolism | adh | med | Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) | 44% | 88% | 401.7 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-tryptophan catabolism | adh | med | Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) | 44% | 88% | 401.7 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-phenylalanine catabolism | pad-dh | med | aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) | 45% | 91% | 397.1 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| 4-hydroxybenzoate catabolism | praB | med | 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) | 42% | 98% | 369.4 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-tryptophan catabolism | praB | med | 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) | 42% | 98% | 369.4 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-fucose catabolism | aldA | med | NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) | 42% | 95% | 349.7 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-rhamnose catabolism | aldA | med | NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) | 42% | 95% | 349.7 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-threonine catabolism | aldA | med | NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) | 42% | 95% | 349.7 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-tryptophan catabolism | nbaE | lo | aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) | 39% | 95% | 321.6 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-arabinose catabolism | xacF | lo | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 36% | 96% | 280.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| D-galacturonate catabolism | dopDH | lo | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 36% | 96% | 280.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| D-glucuronate catabolism | dopDH | lo | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 36% | 96% | 280.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| D-xylose catabolism | dopDH | lo | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 36% | 96% | 280.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-isoleucine catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 33% | 97% | 238.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| myo-inositol catabolism | mmsA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 33% | 97% | 238.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| propionate catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 33% | 97% | 238.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-threonine catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 33% | 97% | 238.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-valine catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 33% | 97% | 238.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-valine catabolism | mmsA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 33% | 97% | 238.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-arginine catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 35% | 91% | 235 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-arginine catabolism | rocA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 35% | 91% | 235 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-citrulline catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 35% | 91% | 235 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-citrulline catabolism | rocA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 35% | 91% | 235 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-proline catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 35% | 91% | 235 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-arginine catabolism | astD | lo | Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) | 33% | 94% | 206.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-citrulline catabolism | astD | lo | Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) | 33% | 94% | 206.8 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
| L-lysine catabolism | amaB | lo | L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) | 33% | 92% | 199.5 | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) | 58% | 583.6 |
Sequence Analysis Tools
View WP_011829504.1 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
MTTATIDWHARSAALTLDGRAVIGGERHPARAGESFDCISPIDGRVLGRVARGQSADIDD
AVASARAAFDDGRWSRRPPAARKRVLQAFAEKILSAKEELALLETLDMGKPIQYSLSVDV
PSTARCIAWYAEAIDKVYDEIAPTGPGALALIRREAMGVIGAIVPWNYPMIMAAWKLGPA
LAAGNSVVLKPSEKSPLTALRLAELALAAGLPPGVFNVVPGYGHEAGEALALHPQVDAIG
FTGSTRVGRKMLEYAGRSNLKRVYNELGGKSAFLVFPDFDDLDRCAATVAGSMFFNQGES
CNAPSRLLVHESIADDFARRVAAEAPQYRPADPLDAKTVMGALVDDGQLRTVMGYIDAGR
SEGATVLAGGTQARTDSGGYYVEPTVFDGVRNDMKIAREEIFGPVLSIIRFKDEAEAIRL
ANDSPYGLQASVWSSHIDRAHRVAASLRAGTVHVNQYDEDDITVPFGGFKQSGNGRDKSL
HAFDKYTELKTTWLRINAA
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