GapMind for catabolism of small carbon sources

 

Protein 3607155 in Dinoroseobacter shibae DFL-12

Annotation: FitnessBrowser__Dino:3607155

Length: 483 amino acids

Source: Dino in FitnessBrowser

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism xacF hi 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 57% 99% 549.7 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 38% 314.7
D-galacturonate catabolism dopDH hi 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 57% 99% 549.7 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 38% 314.7
D-glucuronate catabolism dopDH hi 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 57% 99% 549.7 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 38% 314.7
D-xylose catabolism dopDH hi 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 57% 99% 549.7 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 38% 314.7
L-arginine catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 38% 98% 314.7 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-citrulline catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 38% 98% 314.7 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
putrescine catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 38% 98% 314.7 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 306.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 306.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 306.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 306.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 264.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 264.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 264.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 264.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 264.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 264.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 91% 255 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 91% 255 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 91% 255 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 91% 255 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 91% 255 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 95% 226.9 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 95% 226.9 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 34% 85% 226.1 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 57% 549.7

Sequence Analysis Tools

View 3607155 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTDRTQLYIDGAWTEGTAQIENRNPSDTTDLIGMYAQADAGQLDTALAAARRAQPAWWAA
GIQKRHDVLMAIGTELMARSDEIGRLLSREEGKPLAEGKGEVYRAGQFFTYFAAEALRQH
GDLAESVRPGIEIDVRREAVGVVAIISPWNFPVATPAWKIAPALAFGNAVVWKPANVTPA
SAIALTEIIARQDIPKGLFNLVAGPGRDVGQRLVESAEVDAISFTGSVPVGRGIAAAAVQ
NMTKVQMEMGSKNPLIVMDDCDLDLAVAHAASSAFGGTGQKCTAASRLIVHSAVHDAFVE
KLVAAARAMKVGHALEDGTQLGPVVSESQLNQNMEYIGVGKDEGAELLCGGDRLEMATDG
YFMAPAVFAGTANDMRINREEMFAPITAVQRVDSYDEALARANDTQFGLTAGIMTTSLAR
ASHFRAHMRAGCVMVNLPTAGTDYHVPFGGRGASSFGPREQGSYAAEFYTTVKTAYVAAG
APA

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:

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