GapMind for catabolism of small carbon sources

 

Protein WP_054255250.1 in Acidovorax caeni R-24608

Annotation: NCBI__GCF_001298675.1:WP_054255250.1

Length: 508 amino acids

Source: GCF_001298675.1 in NCBI

Candidate for 41 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) 71% 97% 741.1 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
2'-deoxyinosine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 71% 97% 741.1 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
2-deoxy-D-ribose catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 71% 97% 741.1 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
ethanol catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 71% 97% 741.1 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-threonine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 71% 97% 741.1 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
thymidine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 71% 97% 741.1 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-tryptophan catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 71% 97% 741.1 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 44% 92% 386 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 97% 380.9 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 97% 380.9 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 97% 380.9 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 353.2 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 353.2 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 94% 351.3 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 94% 351.3 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 94% 351.3 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 94% 351.3 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 38% 100% 346.3 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 99% 330.9 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 99% 330.9 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 99% 330.9 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-arginine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 323.9 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-citrulline catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 323.9 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
putrescine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 323.9 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 100% 310.5 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 35% 99% 271.2 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 35% 99% 271.2 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 35% 99% 271.2 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 35% 99% 271.2 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 257.7 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 257.7 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 100% 253.8 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 100% 253.8 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 100% 253.8 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 100% 253.8 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 225.7 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 225.7 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 225.7 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 225.7 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 225.7 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 225.7 aldehyde dehydrogenase B; EC 1.2.1.- 71% 749.2

Sequence Analysis Tools

View WP_054255250.1 at NCBI

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

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Fitness BLAST: loading...

Sequence

MDMFELKRFNLDIAYPYKQQYDNFIGGKWVAPLAGRYFDNVSPITGKAFCKVAQSDANDV
NLALDAAHAAQDKWAHTSVTERANILLKIADRMEQNLELLAIAETIDNGKPLRETMAADI
PLAIDHFRYFAGCIRAQEGGISEIDASTVAYHFHEPIGVVGQIIPWNFPLLMASWKLPPA
LAAGCCVVMKPAEQTPASIMVLMELIADLLPPGVVNVVNGFGKEAGEALATSKRITKIAF
TGSTAVGQRILHAAADNLIPSTVELGGKSPNIFFADVMEQDDEFLDKVMEGFSMFALNQG
EVCTCPSRILIQESIYDRFIERAVKRVQSMKQGHPLDKTTMVGAQVSQAQLERILGYIDV
GRQEGAQCLTGGERNRQGGDIDDGFFIKPTLLFGQNDMRVFQEEIFGPVASVTTFKTMED
AIRIANDSEYGLGAGVWSRNGTTAYQMGRAVKAGRVWTNCYHLYPAHAAFGGYKKSGIGR
ENHKSALSNYQQTKNLLVSYSPKALGFF

This GapMind analysis is from Sep 24 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