GapMind for catabolism of small carbon sources

 

Protein 7025959 in Shewanella sp. ANA-3

Annotation: Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)

Length: 496 amino acids

Source: ANA3 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-isoleucine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 62% 98% 636.3
myo-inositol catabolism mmsA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 62% 98% 636.3
propionate catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 62% 98% 636.3
L-threonine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 62% 98% 636.3
L-valine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 62% 98% 636.3
L-valine catabolism mmsA med methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 61% 100% 632.5 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
L-valine catabolism mmsA med mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27) (TIGR01722) 100% 686.1 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 97% 283.1 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 97% 283.1 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 97% 283.1 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 97% 283.1 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 94% 270 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 94% 270 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 94% 270 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 95% 229.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 95% 229.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 95% 229.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 95% 229.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 32% 92% 225.7 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
L-arginine catabolism gabD 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) 30% 97% 218 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
L-citrulline catabolism gabD 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) 30% 97% 218 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3
putrescine catabolism gabD 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) 30% 97% 218 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 62% 636.3

Sequence Analysis Tools

View 7025959 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MLTMTHYVNGEHTAASTRSQEIFEPATGECRGQVSLASRDEVSAAIAIAKSAFDTWSQVT
PLNRARVLFKFKALVEQHMDELAQLITLEHGKVLDDARGELIRGLEVVEFACGIPHLLKG
EHTEQVGGGVDAWSVNQALGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIMKPSEKDPSA
VMRIAELLTQAGLPAGVFNVVNGDKEAVDTLLSHEDIQAVSFVGSTPIAEYIYSTASKHG
KRVQALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGDVGDKLVDKL
LPQIQQLKVGNGLTPEMEMGPLISRQHLAKVTEFVDAGVKEGATLVVDGRQLTVADHQQG
YFLGACLFDNVTPEMRIYREEIFGPVLSIVRVKDYASALALINQHEFGNGTAIFTQSGEA
ARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITARW
PVGKQTQAEFVMPTMK

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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, the preprint on GapMind for carbon sources, 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