GapMind for catabolism of small carbon sources

 

Protein 17148 in Escherichia coli BW25113

Annotation: b3073 putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent (RefSeq)

Length: 459 amino acids

Source: Keio in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism patA hi putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 100% 100% 909.4 Aminotransferase PigE; EC 2.6.1.- 40% 272.7
L-arginine catabolism patA hi ygjG: putrescine aminotransferase (EC 2.6.1.82) (TIGR03372) 100% 977.1 Aminotransferase PigE; EC 2.6.1.- 40% 272.7
L-citrulline catabolism patA hi putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 100% 100% 909.4 Aminotransferase PigE; EC 2.6.1.- 40% 272.7
L-citrulline catabolism patA hi ygjG: putrescine aminotransferase (EC 2.6.1.82) (TIGR03372) 100% 977.1 Aminotransferase PigE; EC 2.6.1.- 40% 272.7
putrescine catabolism patA hi putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 100% 100% 909.4 Aminotransferase PigE; EC 2.6.1.- 40% 272.7
putrescine catabolism patA hi ygjG: putrescine aminotransferase (EC 2.6.1.82) (TIGR03372) 100% 977.1 Aminotransferase PigE; EC 2.6.1.- 40% 272.7
L-lysine catabolism patA hi putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 100% 100% 909.4 Aminotransferase PigE; EC 2.6.1.- 40% 272.7
L-arginine catabolism rocD lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 39% 91% 258.8 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4
L-citrulline catabolism rocD lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 39% 91% 258.8 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4
L-arginine catabolism astC lo Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized) 35% 92% 212.2 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4
L-citrulline catabolism astC lo Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized) 35% 92% 212.2 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4
L-arginine catabolism davT lo 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized) 35% 99% 209.1 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4
L-arginine catabolism gabT lo 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized) 35% 99% 209.1 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4
L-citrulline catabolism davT lo 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized) 35% 99% 209.1 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4
L-citrulline catabolism gabT lo 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized) 35% 99% 209.1 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4
L-lysine catabolism davT lo 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized) 35% 99% 209.1 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4
L-proline catabolism davT lo 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized) 35% 99% 209.1 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4
putrescine catabolism gabT lo 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized) 35% 99% 209.1 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4
L-lysine catabolism lat lo L-lysine 6-transaminase (EC 2.6.1.36) (characterized) 30% 90% 139 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) 100% 909.4

Sequence Analysis Tools

View 17148 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNRLPSSASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAG
GDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQE
LLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAF
HGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPI
QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK
ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE
QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLN
NAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVSVEEA

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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