GapMind for catabolism of small carbon sources

 

Protein Synpcc7942_0943 in Synechococcus elongatus PCC 7942

Annotation: Synpcc7942_0943 acetylornithine aminotransferase

Length: 422 amino acids

Source: SynE in FitnessBrowser

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism astC med Succinylornithine transaminase (EC 2.6.1.81) (characterized) 45% 98% 326.2 acetylornithine transaminase (EC 2.6.1.11) 41% 317.8
L-citrulline catabolism astC med Succinylornithine transaminase (EC 2.6.1.81) (characterized) 45% 98% 326.2 acetylornithine transaminase (EC 2.6.1.11) 41% 317.8
L-arginine catabolism rocD lo ornithine aminotransferase (EC 2.6.1.13) (characterized) 36% 92% 267.7 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-citrulline catabolism rocD lo ornithine aminotransferase (EC 2.6.1.13) (characterized) 36% 92% 267.7 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-lysine catabolism lat lo Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized) 34% 93% 234.2 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-arginine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 36% 82% 232.6 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-citrulline catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 36% 82% 232.6 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-lysine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 36% 82% 232.6 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
putrescine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 36% 82% 232.6 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-arginine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 34% 95% 221.1 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-citrulline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 34% 95% 221.1 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-lysine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 34% 95% 221.1 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-proline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 34% 95% 221.1 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-arginine catabolism gabT lo 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 33% 93% 216.5 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-citrulline catabolism gabT lo 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 33% 93% 216.5 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
putrescine catabolism gabT lo 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 33% 93% 216.5 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2
L-lysine catabolism lysN lo 2-aminoadipate transaminase (EC 2.6.1.39) (characterized) 36% 96% 211.5 Succinylornithine transaminase (EC 2.6.1.81) 45% 326.2

Sequence Analysis Tools

View Synpcc7942_0943 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

VSPETVLAAVDAAIASPFSTDAFDACVMQTYGRFPLALERGEGCRVWDTQGRSYLDFVAG
IATCTLGHAHPELVDAISDQIRKLHHVSNLYYIPEQGQLAAWLTANSCADRVFFCNSGAE
ANEAAIKLARKHGNTVLEAENPIILTAQASFHGRTLAAVTATGQPKYHKGFQPLVQGFRY
VPYNDLAALEATLAELDAAGETVAAILLEPLQGEGGVNPGDRAYFQAVRQLCDQRRMLLI
LDEVQVGMGRSGQLWGYENLGIEPDAFTVAKGLGGGVPIGALLVKASCNILQAGEHASTF
GGNPLACRAGLAIAQVMERDQLLANVQARGEQLRAGLQELVDRYPNLLAGVRGWGLINGL
VLRNDPNVTPIALVKAAIEQGLLLVPAGAEVVRFVPPLIVSAAEIDEALAMTERALLAIA
GE

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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