GapMind for catabolism of small carbon sources

 

Protein CA265_RS14635 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: FitnessBrowser__Pedo557:CA265_RS14635

Length: 501 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 49 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 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 67% 97% 686.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
2'-deoxyinosine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 67% 97% 686.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
2-deoxy-D-ribose catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 67% 97% 686.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
ethanol catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 67% 97% 686.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-threonine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 67% 97% 686.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
thymidine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 67% 97% 686.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-tryptophan catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 67% 97% 686.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 42% 95% 372.5 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 95% 364 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 95% 364 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 95% 364 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 361.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 361.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 361.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 361.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 94% 334.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 94% 334.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 94% 334.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 358.6 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 358.6 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-tryptophan catabolism nbaE lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 98% 350.5 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-arginine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 95% 325.5 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-citrulline catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 95% 325.5 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
putrescine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 95% 325.5 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 100% 306.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 39% 98% 297 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 39% 98% 297 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 39% 98% 297 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 39% 98% 297 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 99% 269.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 99% 269.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 257.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 257.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 257.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 257.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 240.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 240.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 240.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 240.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 240.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 240.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 90% 229.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 90% 229.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 90% 229.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 90% 229.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 90% 229.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 92% 188.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 92% 188.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 30% 77% 174.9 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 81% 847.0

Sequence Analysis Tools

View CA265_RS14635 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MENLIEKPSFKPQYDNYIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAA
HEAFKTWSKTSSTERSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHF
RYFAGVIRAEEGSLSELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCV
VLKPAESTPVSIMVLMELIGDLLPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTG
RLVMQYATENIIPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFALNQGEICTCPS
RLLIQEDIYEKFIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAE
VLTGGEINELPGELGGGYYIKPTIFKGHNKMRIFQEEIFGPVLAVTTFKTVEEAIEIAND
TLYGLGAGVWTRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMML
GHYRQTKNMLISYDKNKLGFF

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