GapMind for catabolism of small carbon sources

 

Protein GFF4232 in Pseudomonas stutzeri RCH2

Annotation: Psest_4305 NAD-dependent aldehyde dehydrogenases

Length: 497 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 16 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 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 84% 100% 854.4 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 59% 583.6
L-arginine catabolism puuC hi gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 84% 100% 854.4 aldehyde dehydrogenase 57% 559.7
L-citrulline catabolism puuC hi gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 84% 100% 854.4 aldehyde dehydrogenase 57% 559.7
putrescine catabolism puuC hi gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 84% 100% 854.4 aldehyde dehydrogenase 57% 559.7
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 59% 99% 583.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 59% 99% 583.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 59% 99% 583.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 59% 99% 583.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 59% 99% 583.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 59% 99% 583.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 45% 92% 414.1 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 100% 371.3 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 100% 371.3 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 39% 97% 322.8 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 34% 94% 210.3 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 34% 94% 210.3 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 84% 854.4

Sequence Analysis Tools

View GFF4232 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

MPTLTLADWQQRARDLHIEGRAFIQGEYCAAADGGQFDCISPVDGRVLAQVASCEQADAE
RAVASARAAFDAGSWSRLAPAKRKAVLIRFADLLEANREELALLETLDMGKPIGDSLAVD
IPGAARALRWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVAAIVPWNFPLMMACWKLGP
ALATGNSVVLKPSEKSPLTAIRIAQLAIDAGIPAGVLNVLPGYGHTVGKALALHMDVDTL
VFTGSTRVAKQLMIYAGESNMKRVWLEAGGKSPNIVFADAPDLQAAAQAAAGAIAFNQGE
VCTAGSRLLVERSIRERFLPMVVEALKGWKPGNPLDPATNVGALVDTQQLNTVLGYIDAG
RQAGAQVLIGGQRTLEETGGLYVEPTIFDGVDNAMRIAQEEIFGPVLSVITFDSAEEAVA
IANDTPYGLAAAVWTADLSKAHRTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKS
LHAFDKYTELKATWIQL

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