GapMind for catabolism of small carbon sources

 

Protein PP_5063 in Pseudomonas putida KT2440

Annotation: PP_5063 betaine aldehyde dehydrogenase, NAD-dependent

Length: 490 amino acids

Source: Putida in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 490 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-citrulline catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 490 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
putrescine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 490 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 97% 384.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 97% 384.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 39% 97% 336.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 35% 98% 270.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 35% 98% 270.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 35% 98% 270.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 35% 98% 270.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 35% 98% 270.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 35% 98% 270.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 251.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 251.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 251.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 251.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 251.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7
L-lysine catabolism amaB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 32% 83% 222.2 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 83% 809.7

Sequence Analysis Tools

View PP_5063 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MARFGTQKLYIDGAYVDAGSDATFEAINPATGEVLAHVQRATEADVEKAVESAERGQKVW
AAMTAMQRSRILRRAVDILRERNDELAMLETLDTGKSYSETRYVDIVTGADVLEYYAGLV
PAIEGEQIPLRESSFVYTRREPLGVTVGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEV
TSLTTLKLAEIYTEAGLPNGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTTTGKKVMAS
ASSSSLKEVTMELGGKSPLIICADADLDKAADIAMMANFYSSGQVCTNGTRVFIPAEMKA
AFEAKIAERVARIRVGNPEDENTNFGPLVSFQHMESVLGYIAKGKEEGARVLCGGERLTA
GDFAKGAFVAPTVFTDCTDDMTIVKEEIFGPVMSILTYETEEEVIRRANDTDYGLAAGVC
TNDITRAHRIIHKLEAGICWINAWGESPAEMPVGGYKQSGVGRENGVSSLAQYTRIKSVQ
VELGGYNSVF

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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