GapMind for catabolism of small carbon sources

 

Protein WP_011383248.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Length: 485 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 45 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 45% 97% 419.5 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 45% 97% 419.5 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
4-hydroxybenzoate catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 42% 98% 380.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
2'-deoxyinosine catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 42% 98% 380.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
2-deoxy-D-ribose catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 42% 98% 380.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
ethanol catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 42% 98% 380.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-threonine catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 42% 98% 380.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
thymidine catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 42% 98% 380.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-tryptophan catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 42% 98% 380.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-tryptophan catabolism nbaE med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 42% 98% 380.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-arginine catabolism gabD med Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 40% 90% 354.4 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-citrulline catabolism gabD med Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 40% 90% 354.4 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
putrescine catabolism gabD med Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 40% 90% 354.4 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 41% 89% 352.1 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-arginine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 41% 97% 342.8 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 342.8 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 342.8 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-citrulline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 41% 97% 342.8 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 342.8 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-lysine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 41% 97% 342.8 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-proline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 41% 97% 342.8 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 342.8 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-arginine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 39% 96% 342 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-citrulline catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 39% 96% 342 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
putrescine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 39% 96% 342 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 95% 328.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 95% 328.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 95% 328.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-arabinose catabolism xacF lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 40% 98% 322.4 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
D-galacturonate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 40% 98% 322.4 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
D-glucuronate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 40% 98% 322.4 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
D-xylose catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 40% 98% 322.4 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 259.2 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 259.2 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 259.2 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 259.2 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 259.2 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 259.2 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 91% 251.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 91% 251.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 91% 251.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 91% 251.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 91% 251.9 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 31% 95% 196.8 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 31% 95% 196.8 subunit of 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.60) 63% 645.6

Sequence Analysis Tools

View WP_011383248.1 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

MIKHLINGRQVESASTIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPASQ
RAKLLRKVGDLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGET
YPTNDHLNYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSADRL
GQLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSGGLKKYSM
ELGGKSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALAERTR
KVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGLAPHLKNGNF
VRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTENGARAI
RMAEGIEAGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVKNVCVSKGSHHI
PRWGV

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