GapMind for catabolism of small carbon sources

 

Protein 14450 in Escherichia coli BW25113

Annotation: b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)

Length: 490 amino acids

Source: Keio in FitnessBrowser

Candidate for 33 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% 99% 498 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-citrulline catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 99% 498 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
putrescine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 99% 498 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 93% 392.5 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 384.4 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 384.4 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-tryptophan catabolism nbaE med 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized) 41% 99% 361.3 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 96% 360.1 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 96% 360.1 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 96% 360.1 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 96% 360.1 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 100% 334 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 100% 325.5 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 100% 325.5 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 100% 325.5 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 100% 325.5 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 98% 314.3 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 98% 314.3 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 98% 314.3 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 98% 314.3 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 96% 250.4 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 96% 250.4 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 96% 250.4 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 96% 250.4 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 96% 250.4 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 92% 248.8 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 92% 248.8 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 92% 248.8 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 92% 248.8 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 92% 248.8 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
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% 87% 210.7 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 32% 91% 204.5 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 32% 91% 204.5 NAD/NADP-dependent betaine aldehyde dehydrogenase; BADH; EC 1.2.1.8 100% 971.1

Sequence Analysis Tools

View 14450 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

MSRMAEQQLYIHGGYTSATSGRTFETINPANGNVLATVQAAGREDVDRAVKSAQQGQKIW
ASMTAMERSRILRRAVDILRERNDELAKLETLDTGKAYSETSTVDIVTGADVLEYYAGLI
PALEGSQIPLRETSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEV
TPLTALKLAEIYSEAGLPDGVFNVLPGVGAETGQYLTEHPGIAKVSFTGGVASGKKVMAN
SAASSLKEVTMELGGKSPLIVFDDADLDLAADIAMMANFFSSGQVCTNGTRVFVPAKCKA
AFEQKILARVERIRAGDVFDPQTNFGPLVSFPHRDNVLRYIAKGKEEGARVLCGGDVLKG
DGFDNGAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDYGLAAGIV
TADLNRAHRVIHQLEAGICWINTWGESPAEMPVGGYKHSGIGRENGVMTLQSYTQVKSIQ
VEMAKFQSIF

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