GapMind for catabolism of small carbon sources

 

Protein 5210423 in Shewanella loihica PV-4

Annotation: Shew_2864 3-hydroxyacyl-CoA dehydrogenase, NAD-binding (RefSeq)

Length: 708 amino acids

Source: PV4 in FitnessBrowser

Candidate for 32 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) 49% 98% 637.5 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 44% 552.4
phenylacetate catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 49% 98% 637.5 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 44% 552.4
L-phenylalanine catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 49% 98% 637.5 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 44% 552.4
4-hydroxybenzoate catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 43% 98% 552.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
4-hydroxybenzoate catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 43% 98% 552.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
L-arginine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 43% 98% 552.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
L-citrulline catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 43% 98% 552.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
L-lysine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 43% 98% 552.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
phenylacetate catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 43% 98% 552.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
phenylacetate catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 43% 98% 552.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
L-phenylalanine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 43% 98% 552.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
L-phenylalanine catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 43% 98% 552.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
L-proline catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 43% 98% 552.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
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) 40% 98% 464.2 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
4-hydroxybenzoate catabolism paaF med 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 40% 72% 119.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
phenylacetate catabolism paaF med 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 40% 72% 119.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
L-phenylalanine catabolism paaF med 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 40% 72% 119.4 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
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% 181 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
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% 181 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
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% 181 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
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% 181 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
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% 181 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
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% 181 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
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% 181 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
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% 181 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 46% 59% 120.9 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 46% 59% 120.9 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 46% 59% 120.9 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 46% 59% 120.9 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 34% 72% 100.9 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 34% 72% 100.9 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 34% 72% 100.9 6-carboxyhex-2-enoyl-CoA hydratase 49% 637.5

Sequence Analysis Tools

View 5210423 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

MTNATLYQIHGRTAVIILNQPPVNSLGLALRTHLLADLKRAEADESVDAIVLASSGKLFC
GGADISEFSSDDALAEPNLPQVCDALEASPKLVVAAVNGLALGGGCELTLACDYRIALPA
AKLGLPEVNLGILPGAGGTQRLPRIGGVQLALEMITSGRPLGAAAMLDAGVIDNLYQDGG
NFIQAAVDFAQELVAQHKPKRSCFEMSVDTSNISSEIFNEFRAAIARRSRGYYAPERCIQ
AVEAACELPLAEGLKREHQLFMECLDTPQARAQQHLFFAERGVAKIPGINPKTTATREIR
KVAVIGSGTMGGGIAMNFINVGIPTQILDLNGEALERGLGVIRKNYEYTLKKGKLSQAQL
DERMALLSGTTDYADIADVDLVIEAVFEKMEIKKQVFKTLDATCKPGAILATNTSTLDVD
EIAAETSRPQDVLGLHFFSPANVMRLLEIVRANKTAPDALLTTVQLAQRIKKVPVVSGVC
WGFIGNRATDSYLRESMSLILEGASPAQIDKVHTEFGMPMGLPSMVDLAGIDVGILTRED
RKAFTTDLDPSHFAILHKLYAKQRYGQKTGRGLYIYEGRDKQEDPEVLELAAEAAKEFGV
TRRSPEQISDQEILERTIYPIINEGARILEEGIALRASDIDIVLAYGFGFPIFRGGPMQY
ADEIGLERVLTALNKYRDTLDKGELWFKPAPLLERLVKEGKTFAQYQA

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