GapMind for catabolism of small carbon sources

 

Protein GFF4637 in Pseudomonas simiae WCS417

Annotation: PS417_23725 methylmalonate-semialdehyde dehydrogenase

Length: 505 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-valine catabolism mmsA hi Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 93% 100% 944.9 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 59% 602.4
L-valine catabolism mmsA med mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27) (TIGR01722) 100% 748.2 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 59% 602.4
L-isoleucine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 59% 92% 604.4
myo-inositol catabolism mmsA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 59% 92% 604.4
propionate catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 59% 92% 604.4
L-threonine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 59% 92% 604.4
L-valine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 59% 92% 604.4
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 72% 143.3 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 93% 944.9
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 72% 143.3 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 93% 944.9
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 72% 143.3 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 93% 944.9
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 72% 143.3 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 93% 944.9
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 72% 143.3 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 93% 944.9

Sequence Analysis Tools

View GFF4637 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

MNASADISVQQVKLLINGEWVESKTTEWQDIVNPATQEVLAKVPFATADEVNAAIDAAHR
AFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHA
CSIGTLQMGEFSENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL
KPSEQDPLSTMLLVELALEAGVPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH
VYDLAGKHGKRVQSMMGAKNHAVVLPDANREHTLNALVGAGFGAAGQRCMATSVVVLVGA
SKQWLPDLKALAQKLKVNAGSEAGTDVGPVISKRAKARILELIESGVKEGAKLELDGRDI
KVPGFEQGNFVGPTLFSGVTPSMQIYTQEIFGPVLVVLEVATLDEAIALVNANPFGNGTG
LFTQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ
TKTVTSRWFDDDTVNDGVNTTINLR

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