GapMind for catabolism of small carbon sources

 

Protein AO356_26340 in Pseudomonas fluorescens FW300-N2C3

Annotation: AO356_26340 AMP-binding protein

Length: 554 amino acids

Source: pseudo5_N2C3_1 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism acs lo Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 35% 85% 292 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 69% 779.2
L-lactate catabolism acs lo Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 35% 85% 292 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 69% 779.2
acetate catabolism acs lo Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 35% 85% 292 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 69% 779.2
2'-deoxyinosine catabolism acs lo Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 35% 85% 292 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 69% 779.2
2-deoxy-D-ribose catabolism acs lo Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 35% 85% 292 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 69% 779.2
ethanol catabolism acs lo Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 35% 85% 292 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 69% 779.2
L-threonine catabolism acs lo Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 35% 85% 292 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 69% 779.2
thymidine catabolism acs lo Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 35% 85% 292 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 69% 779.2
L-tryptophan catabolism acs lo Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 35% 85% 292 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 69% 779.2
propionate catabolism prpE lo Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized) 35% 86% 284.3 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 69% 779.2
4-hydroxybenzoate catabolism hcl lo Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized) 31% 100% 199.1 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 69% 779.2

Sequence Analysis Tools

View AO356_26340 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

MRDYSSATSQFDYQHTVNTALHGSLEALNACVECCDRHALPGRIALFWEGRDGSEATWTY
RDLQDNAARFANFLRAQGVGKGDKVAGLLPRTAELLIVVLATWRIGAVYQPLFTAFGPKA
IEHRLGSSGARIVVTDAVNRPKLNEVAGCPTIVTVGGEKGQGIVRGDYSFWAEVANQSSQ
CEPLMLTGEDPFLLMFTSGTTGPAKALSVPLKAIVAFQSYTRDAVDLRPEDAFWNVADPG
WAYGIYFGVTGPLAMGHPITFYDGPFTLESTCRVINKYGITNLTGSPTAYRLLIAGGEQF
ARSIKGKLRIVSSAGEPLNPEVIRWFADNLNVVIHDHYGQTELGMVLCNHHGLEHPVHLG
AAGFASPGHRIVVLDEEQRELGVGQPGILAVDRSQSPMCWFAGYEGAPTKAFVGDYYLSG
DTVELNPDGSISFVGRSDDVITTSGYRVGPFDVESALIEHPAVVETAVIGKPDPERTELV
KAFVVLSSQYRASPELAEELRLHVRKRLAAHAYPREIEFVSDLPKTPSGKLQRFILRNQE
IAKAQEAAAQNVSA

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, 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