GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_1850 in Pseudomonas fluorescens FW300-N2E2

Annotation: Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

Length: 715 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism ech med long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) (characterized) 35% 94% 380.9
4-hydroxybenzoate catabolism fadB lo fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 35% 98% 378.6 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 35% 380.9
4-hydroxybenzoate catabolism paaH lo fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 35% 98% 378.6 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 35% 380.9
L-arginine catabolism fadB lo fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 35% 98% 378.6 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 35% 380.9
L-citrulline catabolism fadB lo fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 35% 98% 378.6 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 35% 380.9
L-lysine catabolism fadB lo fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 35% 98% 378.6 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 35% 380.9
phenylacetate catabolism fadB lo fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 35% 98% 378.6 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 35% 380.9
phenylacetate catabolism paaH lo fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 35% 98% 378.6 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 35% 380.9
L-phenylalanine catabolism fadB lo fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 35% 98% 378.6 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 35% 380.9
L-phenylalanine catabolism paaH lo fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 35% 98% 378.6 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 35% 380.9
L-proline catabolism fadB lo fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 35% 98% 378.6 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 35% 380.9
4-hydroxybenzoate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 32% 97% 301.2 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 391.0
phenylacetate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 32% 97% 301.2 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 391.0
L-phenylalanine catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 32% 97% 301.2 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 35% 391.0
4-hydroxybenzoate catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 33% 58% 202.2
L-arginine catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 33% 58% 202.2
L-citrulline catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 33% 58% 202.2
L-lysine catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 33% 58% 202.2
phenylacetate catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 33% 58% 202.2
L-phenylalanine catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 33% 58% 202.2
L-proline catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 33% 58% 202.2
L-valine catabolism ech lo 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized) 33% 58% 202.2

Sequence Analysis Tools

View Pf6N2E2_1850 at FitnessBrowser

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

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MSAFNYEKDADGIVTVTMDMPGPVNAMNQLYRETMAATVNRLEQENGLTGVVIASAKSTF
FAGGDLNELTDFKPGDEADFQAKIELTKNDLRRLERLPVPVVAAINGAALGGGFEIALAC
NYRVLLNSPAAVVGLPEVSLGLLPGGGGIVRLVHHLGLERALPLLLEGKRMKPAEALALG
LVNELIEQADALVPAAKAWIKAQVGDDGVSLQPWDHKGHKIPGGTAQQPHVAQMIAGAQA
MTAKNTRGLLPAPERILAVAVEATLLDFDAALLVETRGLTHLAASVQAKNIINTMFFQMN
EVNGGSSRPTGFDKSKVSKLGIIGAGMMGNGIAHVSAKVGIEVMLLDVSLEAAERGKANV
EKLLSKTVSQGRLSEAKKDEILALIKPTVDYADLQGVDFVVEAVFESVDLKGKVTQQAEA
QLPESAVFGTNTSTLPISLLANASKRPANFIGIHFFSPVERMPLVEIICGEQTSDAALAK
AFDFARQIGKTAIVVNDSLGFFTSRTFGSYFDEGCKLLQEGVDPLLIDNLGKQIGMPVGP
LTVLDEVSLELMRKVNETQKEMGVFATVFDNSHSDAVGNILIKEYNRPGRHYGGGFYDYP
EGGEKTIWPGLYELFVRPEVVLPVEDIKERLLFRQVIEAVKCLQEGVLRSVADGNVGSIL
GIGAPTWTGGFLQFVNGYGVERFVQRARELAQTYGERFTPPVLLLEKAAKGEELR

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 paper from 2022 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