GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS09560 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS09560 3-hydroxyacyl-CoA dehydrogenase

Length: 694 amino acids

Source: BFirm in FitnessBrowser

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 52% 98% 684.9 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 46% 597.8
phenylacetate catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 52% 98% 684.9 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 46% 597.8
L-phenylalanine catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 52% 98% 684.9 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 46% 597.8
4-hydroxybenzoate catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 97% 597.8 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
4-hydroxybenzoate catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 97% 597.8 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
L-arginine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 97% 597.8 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
L-citrulline catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 97% 597.8 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
L-lysine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 97% 597.8 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
phenylacetate catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 97% 597.8 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
phenylacetate catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 97% 597.8 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
L-phenylalanine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 97% 597.8 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
L-phenylalanine catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 97% 597.8 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
L-proline catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 97% 597.8 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
L-isoleucine catabolism ech med Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized) 44% 98% 529.3 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
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) 32% 58% 183.7 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
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) 32% 58% 183.7 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
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) 32% 58% 183.7 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
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) 32% 58% 183.7 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
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) 32% 58% 183.7 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
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) 32% 58% 183.7 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
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) 32% 58% 183.7 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
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) 32% 58% 183.7 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9
L-valine catabolism bch lo 3-hydroxy-isobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized) 32% 53% 77.8 6-carboxyhex-2-enoyl-CoA hydratase 52% 684.9

Sequence Analysis Tools

View BPHYT_RS09560 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

MAVDYTTHDGVAVITLNNPPVNGLGLSTRAGIVEGVERAQNDPAIKAIVLTGAGKAFSGG
ADITEFNTPKAGQEPTLATVIKIVEGSAKPVIAAIHSVAMGGGLELALGAHYRIAAPGAQ
IALPEVKLGILPGAGGTQRLPRAIGLEAALNMIVSGAPVMSEKLADSGLFDELAQGDLAE
AALAFARKVSAKEGPHPKVRDRKIEHPNAAGFIQFARNTVATMAKNFPAPLKCIDAVEAG
VQKGFDKGLAFERECFMALVQTPESHALRHAFFGERAASKIPDVPSDTPVRDIGQVAVIG
AGTMGGGIAMNFINAGIPVTLLETKQEALDRGLATIRKNYEATVKKGKLKPEVLGQRMAL
ITPTLSYDDLKNADLIVEAVFEELGVKEQAFKRLDEVAKQGAILASNTSTLDVDKIAAFT
KRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMNLAKKIKKTAVVSGVCDGFIGN
RMVEQYIRQALFMLEEGALPAQVDKAIEKFGFAMGPFRMSDLAGNDIGWAIRKRRYLEHP
DMHYSKIADRLCETGRFGQKTGGGWYDYKAGDRTAYPSKVVDDMIVAFSKETDTERRKIS
DEEIVERLVFALVNEGAKILEEGIASKASDIDMVYLTGYGFPLYRGGPMLYADTVGLYNV
ERAIRRYAARPNGDAWQLAPSIAELAAKNRGFNG

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