GapMind for catabolism of small carbon sources

 

Protein CA265_RS19780 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: FitnessBrowser__Pedo557:CA265_RS19780

Length: 513 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 27 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism amaB hi L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 61% 100% 600.9 Aldehyde dehydrogenase family 7 member B4; Antiquitin-1; Turgor-responsive ALDH; EC 1.2.1.3 49% 499.2
4-hydroxybenzoate catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
2'-deoxyinosine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
2-deoxy-D-ribose catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
ethanol catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
L-threonine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
thymidine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
L-tryptophan catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
L-arabinose catabolism xacF lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
D-galacturonate catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
D-glucuronate catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
D-xylose catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-arginine catabolism gabD lo aldehyde dehydrogenase-like protein yneI (characterized) 30% 97% 211.5 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
L-citrulline catabolism gabD lo aldehyde dehydrogenase-like protein yneI (characterized) 30% 97% 211.5 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
putrescine catabolism gabD lo aldehyde dehydrogenase-like protein yneI (characterized) 30% 97% 211.5 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized) 31% 97% 209.9 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 90% 195.3 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 90% 195.3 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized) 33% 70% 177.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-tryptophan catabolism praB lo 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized) 33% 70% 177.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1

Sequence Analysis Tools

View CA265_RS19780 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTTDIQSILNKLGINASNAAYSTGSNWGGELNVNTLESFSPVDGKLIASAKIATADDYDA
VVLKAQEAFTAWRSVPAPKRGEIVRQFGDALRENKDALGTLVSYEMGKSLQEGFGEVQEM
IDICDFAVGLSRQLYGLTMHSERPSHRMYEQWHPLGIVGIISAFNFPVAVWSWNTALALV
CGNVCIWKPSEKTPLTAIACQHIIAKVFKDNDIAEGVCNLILGDREVGERMTNDGRIPLI
SATGSTRMGKAVGAAVGARLGKSLLELGGNNAIIISEHADLDMSLIGAVFGAVGTAGQRC
TSTRRLIIHESVYDAFTAKLVKAYGQLRIGDPLDQNNHVGPLIDTDAVAAYLDSIAKCKA
EGGNFVVEGGVLSGDAYTSGCYVKPCIAEVQNDFKIVQHETFAPILYLIKYKTLDEAIAL
QNGVPQGLSSAIMTLNLREAEQFLSAKGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRE
SGSDAWRAYMRRQTNTINYSNTLPLAQGIKFDL

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