Protein WP_003471449.1 in Gracilibacillus halophilus YIM-C55.5
Annotation: NCBI__GCF_000359605.1:WP_003471449.1
Length: 473 amino acids
Source: GCF_000359605.1 in NCBI
Candidate for 41 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-fucose catabolism | aldA | hi | lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) | 44% | 100% | 380.2 | succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) | 37% | 317.0 |
L-rhamnose catabolism | aldA | hi | lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) | 44% | 100% | 380.2 | succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) | 37% | 317.0 |
L-threonine catabolism | aldA | hi | lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) | 44% | 100% | 380.2 | succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) | 37% | 317.0 |
L-arginine catabolism | gabD | lo | succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) | 37% | 100% | 317 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-citrulline catabolism | gabD | lo | succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) | 37% | 100% | 317 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
putrescine catabolism | gabD | lo | succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) | 37% | 100% | 317 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
4-hydroxybenzoate catabolism | adh | lo | Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) | 35% | 90% | 287.3 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
2'-deoxyinosine catabolism | adh | lo | Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) | 35% | 90% | 287.3 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
2-deoxy-D-ribose catabolism | adh | lo | Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) | 35% | 90% | 287.3 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
ethanol catabolism | adh | lo | Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) | 35% | 90% | 287.3 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-threonine catabolism | adh | lo | Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) | 35% | 90% | 287.3 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
thymidine catabolism | adh | lo | Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) | 35% | 90% | 287.3 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-tryptophan catabolism | adh | lo | Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) | 35% | 90% | 287.3 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-arginine catabolism | patD | lo | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 35% | 96% | 285 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-arginine catabolism | puuC | lo | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 35% | 96% | 285 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-citrulline catabolism | patD | lo | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 35% | 96% | 285 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-citrulline catabolism | puuC | lo | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 35% | 96% | 285 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
putrescine catabolism | patD | lo | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 35% | 96% | 285 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
putrescine catabolism | puuC | lo | 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) | 35% | 96% | 285 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-arginine catabolism | davD | lo | Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) | 35% | 98% | 282.7 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-citrulline catabolism | davD | lo | Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) | 35% | 98% | 282.7 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-lysine catabolism | davD | lo | Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) | 35% | 98% | 282.7 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-proline catabolism | davD | lo | Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) | 35% | 98% | 282.7 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
4-hydroxybenzoate catabolism | praB | lo | 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) | 34% | 97% | 270.4 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-tryptophan catabolism | praB | lo | 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) | 34% | 97% | 270.4 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-arginine catabolism | putA | lo | 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) | 35% | 90% | 270 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-arginine catabolism | rocA | lo | 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) | 35% | 90% | 270 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-citrulline catabolism | putA | lo | 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) | 35% | 90% | 270 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-citrulline catabolism | rocA | lo | 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) | 35% | 90% | 270 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-proline catabolism | putA | lo | 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) | 35% | 90% | 270 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-tryptophan catabolism | nbaE | lo | 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) | 32% | 97% | 266.9 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-arginine catabolism | kauB | lo | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 35% | 94% | 265 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-phenylalanine catabolism | pad-dh | lo | Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized) | 35% | 96% | 260 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-arabinose catabolism | xacF | lo | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 35% | 97% | 258.1 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
D-galacturonate catabolism | dopDH | lo | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 35% | 97% | 258.1 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
D-glucuronate catabolism | dopDH | lo | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 35% | 97% | 258.1 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
D-xylose catabolism | dopDH | lo | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 35% | 97% | 258.1 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-valine catabolism | mmsA | lo | Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized) | 31% | 99% | 200.7 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-lysine catabolism | amaB | lo | Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) | 31% | 87% | 196.8 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-arginine catabolism | astD | lo | N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) | 31% | 94% | 185.3 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
L-citrulline catabolism | astD | lo | N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) | 31% | 94% | 185.3 | lactaldehyde dehydrogenase (EC 1.2.1.22) | 44% | 380.2 |
Sequence Analysis Tools
View WP_003471449.1 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
MERYALYINGGWVETEETIDVLDKYSQTTYATVAKASREHVDEAISSATKAYRKNQLSPY
QRFEILRNVSTLMKNNKEELAYTITKEAGKPLKQARTEIDRSAETFLLAAEEAKRIHGEG
VPVEAAPGSEHRMAFTIKVPVGVVGAISPFNFPLNLVAHKVAPALAAGNAVVLKPASKTP
LASLKLAKLLEEAGLPKGLLQVVVGSGSVVGQQMMDDERIDLYTFTGSAEVGLQLKQNTG
LNRLILELGNNSPVIVDKEADIDHAAKTLAGQSFAFAGQVCISVQRVYVHESIQERFLET
FSEQIKQLLVGDPTDATTDVGPMISVSEAERAETWIHEAVDKGAKVVLGGKREGALLEPT
ILTDVKPEMRVVCEEIFAPVVSVIAYTDLDSCIEEVNQSVYGLQGGIFTQNIDTAYYAAK
RVEVGGFMINDGSQYRVDLMPYGGVKDSGNGKEGPKYSIEEMTEERLIVMNLR
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