GapMind for catabolism of small carbon sources

 

Protein 15537 in Escherichia coli BW25113

Annotation: b1415 aldehyde dehydrogenase A, NAD-linked (NCBI)

Length: 479 amino acids

Source: Keio in FitnessBrowser

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism aldA hi lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 100% 100% 947.2 NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) 62% 576.2
L-fucose catabolism aldA hi lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 100% 100% 947.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 43% 417.2
L-rhamnose catabolism aldA hi lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 100% 100% 947.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 43% 417.2
L-threonine catabolism aldA hi lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 100% 100% 947.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 43% 417.2
D-xylose catabolism aldA hi lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 100% 100% 947.2 NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) 62% 576.2
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 40% 97% 347.8 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 40% 97% 347.8 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 40% 97% 347.8 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 40% 97% 347.8 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 35% 91% 271.9 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 35% 91% 271.9 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 35% 91% 271.9 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 35% 91% 271.9 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 35% 91% 271.9 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-isoleucine catabolism iolA lo Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 31% 90% 222.2 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
myo-inositol catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 31% 90% 222.2 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
propionate catabolism iolA lo Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 31% 90% 222.2 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-threonine catabolism iolA lo Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 31% 90% 222.2 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-valine catabolism iolA lo Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 31% 90% 222.2 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 31% 90% 222.2 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2
L-lysine catabolism amaB lo Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized) 30% 90% 211.8 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 100% 947.2

Sequence Analysis Tools

View 15537 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

MSVPVQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEW
EALPAIERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWAR
RYEGEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEF
TPNNAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMAT
AAKNITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQ
FVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEG
KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNL
NVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQS

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