GapMind for catabolism of small carbon sources

 

Protein WP_011384974.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS13050 aldehyde dehydrogenase family protein

Length: 479 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 35 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 49% 98% 436.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 49% 98% 436.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 49% 98% 436.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
ethanol catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 49% 98% 436.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-threonine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 49% 98% 436.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
thymidine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 49% 98% 436.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 49% 98% 436.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 95% 325.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 95% 325.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 95% 325.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 39% 96% 306.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 39% 96% 306.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 39% 96% 306.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 96% 305.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 96% 305.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 96% 305.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 96% 305.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 98% 295 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 98% 295 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 93% 281.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
4-hydroxybenzoate catabolism praB lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 35% 97% 277.3 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 35% 97% 277.3 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-tryptophan catabolism praB lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 35% 97% 277.3 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 35% 96% 270.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 35% 96% 270.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 35% 96% 270.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 35% 96% 270.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 95% 209.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 95% 209.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 95% 209.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 95% 209.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 95% 209.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 96% 207.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 93% 199.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 93% 199.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 549.3

Sequence Analysis Tools

View WP_011384974.1 at NCBI

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

MGDCLDFYVDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPAWA
ATPLAERLEILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKTALSLA
KTYAFERRQGTTLVVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPSEFAPYS
ARILAEIIHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVMREGAAT
IKKVSLELGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHRLDEAEGL
AAELCAQIKVGDPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVCGGPERPEGLDKG
YFVRPTVFSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLSGYVYAGDLDE
ARAVARRLRTGMVHLNGALSHPGGPFGGIRQSGVGREWGEAGFEEFLESKTLFGSEPKE

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