GapMind for catabolism of small carbon sources

 

Protein 15507 in Escherichia coli BW25113

Annotation: b1385 phenylacetaldehyde dehydrogenase (VIMSS)

Length: 499 amino acids

Source: Keio in FitnessBrowser

Candidate for 35 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-phenylalanine catabolism pad-dh hi phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 100% 100% 1001.1 4-hydroxyphenylacetaldehyde dehydrogenase (EC 1.2.1.53) 46% 437.6
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 99% 349 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 99% 349 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-arginine catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 99% 349 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 99% 349 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 99% 349 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-citrulline catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 99% 349 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 99% 349 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 99% 349 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
putrescine catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 99% 349 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 96% 375.2 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 96% 375.2 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 96% 375.2 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 100% 327.8 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
4-hydroxybenzoate catabolism praB lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 37% 98% 325.9 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 37% 98% 325.9 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-tryptophan catabolism praB lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 37% 98% 325.9 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 100% 316.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-arabinose catabolism xacF lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 39% 91% 287 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
D-galacturonate catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 39% 91% 287 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
D-glucuronate catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 39% 91% 287 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
D-xylose catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 39% 91% 287 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 35% 96% 261.5 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 248.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 248.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 248.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 248.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 248.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 96% 244.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 96% 244.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 96% 244.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 96% 244.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 96% 244.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 32% 93% 190.7 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 32% 93% 190.7 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 100% 1001.1

Sequence Analysis Tools

View 15507 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTEPHVAVLSQVQQFLDRQHGLYIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVD
NAVMSAWRAFVSRRWAGRLPAERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFE
VGCTLNWMRYTAGLTTKIAGKTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIG
MWKVMPALAAGCSIVIKPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSH
PHVAKISFTGSTATGKGIARTAADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFL
NQGQVCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSF
LDDAQAQQAELIRGSNGPAGEGYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEA
LQLANDTEYGLTASVWTQNLSQALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRD
FGPDWLDGWCETKSVCVRY

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:

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:

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:

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