GapMind for catabolism of small carbon sources

 

Protein 7023380 in Shewanella sp. ANA-3

Annotation: Shewana3_0610 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Length: 405 amino acids

Source: ANA3 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 hi Succinylornithine transaminase (EC 2.6.1.81) (characterized) 66% 100% 542.3 Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 62% 523.5
L-arginine catabolism astC med astC: succinylornithine transaminase family (EC 2.6.1.81) (TIGR03246) 99% 692.2 Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 62% 523.5
L-citrulline catabolism astC hi Succinylornithine transaminase (EC 2.6.1.81) (characterized) 66% 100% 542.3 Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 62% 523.5
L-citrulline catabolism astC med astC: succinylornithine transaminase family (EC 2.6.1.81) (TIGR03246) 99% 692.2 Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 62% 523.5
L-arginine catabolism rocD lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 37% 95% 258.5 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
L-citrulline catabolism rocD lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 37% 95% 258.5 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
L-arginine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 39% 92% 230.3 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
L-citrulline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 39% 92% 230.3 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
L-lysine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 39% 92% 230.3 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
L-proline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 39% 92% 230.3 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
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) 37% 91% 229.2 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
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) 37% 91% 229.2 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
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) 37% 91% 229.2 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
L-lysine catabolism lysN lo 2-aminoadipate transaminase (EC 2.6.1.39) (characterized) 34% 97% 205.3 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
L-arginine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 84% 197.2 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
L-citrulline catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 84% 197.2 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
L-lysine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 84% 197.2 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
putrescine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 84% 197.2 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3
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% 56% 135.2 Succinylornithine transaminase (EC 2.6.1.81) 66% 542.3

Sequence Analysis Tools

View 7023380 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSVDMKLNRAQFDAVMVPNYAPAAVIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHP
ALVNALKTQGEKLWHLSNVMTNEPALELATKLVNSTFAERVYFANSGAEANEAALKLARR
YALEKFGVEKDEIIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPYNDVAALEA
AVSDKTCAIMLEPLQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYAY
MGTDIVPDILTTAKALGGGFPIAAMLTTAEIAEHLKVGTHGSTYGGNPLACAIGNAVLDV
VNTPEVLNGVKHREQLLRDGLNKINEKYHVFSEIRGKGLLLGAVLNEQYQGRSRDFLVAS
VAEGLMSLMAGANVVRFAPSLVIPEADIAEGLARFERAVASIAAA

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