GapMind for catabolism of small carbon sources

 

Protein CCNA_03293 in Caulobacter crescentus NA1000

Annotation: CCNA_03293 multifunctional fatty acid oxidation complex subunit alpha FadJ

Length: 696 amino acids

Source: Caulo in FitnessBrowser

Candidate for 25 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) 57% 98% 750 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 46% 593.2
phenylacetate catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 57% 98% 750 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 46% 593.2
L-phenylalanine catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 57% 98% 750 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 46% 593.2
4-hydroxybenzoate catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 98% 593.2 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
4-hydroxybenzoate catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 98% 593.2 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
L-arginine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 98% 593.2 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
L-citrulline catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 98% 593.2 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
L-lysine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 98% 593.2 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
phenylacetate catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 98% 593.2 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
phenylacetate catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 98% 593.2 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
L-phenylalanine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 98% 593.2 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
L-phenylalanine catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 98% 593.2 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
L-proline catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 46% 98% 593.2 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
L-isoleucine catabolism ech med enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 43% 96% 528.1 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
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) 32% 58% 174.9 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
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% 174.9 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
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% 174.9 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
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% 174.9 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
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% 174.9 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
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% 174.9 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
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% 174.9 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
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% 174.9 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
4-hydroxybenzoate catabolism badK lo BadK (characterized) 36% 96% 138.3 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
phenylacetate catabolism badK lo BadK (characterized) 36% 96% 138.3 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0
L-phenylalanine catabolism badK lo BadK (characterized) 36% 96% 138.3 6-carboxyhex-2-enoyl-CoA hydratase 57% 750.0

Sequence Analysis Tools

View CCNA_03293 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

MEAAMAAINAVTDFSVEGDIGVVTLNSPPVNALSAAVREGLQGAFDAAIADAAVKAIVLI
CDGKTFIAGADITEFGKAMTGPSLQDVQNVIENSPKPVIAAIHGTALGGGLEVALVANYR
VAVPSAKAGLPEVNIGLLPGAGGTQRLPRIVGVEKALEMVTTGQHVPAKAAHAMGLFDEL
VEEGKLREGAIAFAKAVVAENRPLKKVRDLNEKVEAARGKPEIFEAFRKANAKKFRGFMA
PENNIKCIEAAVNLPFDEGLKAERKLFMELMTGSQSAAQRYVFFAERQAAKIPDVPDDTP
TIPVKKVGVIGAGTMGGGIAMNFLNAGIPVTIIEAKQENLERGVGIIRKNYENTAKKGRL
TQDDVEKRMALLTPSMEMEALADCDMIIEAVFELMEIKKEVFTKLDKIAKPGAILATNTS
YLDVDAIAAVTSRPESVIGTHFFSPANVMRLLELVRGDKTSKDVIATCMKLSKTIGKVPV
LVGVCYGFVGNRMLAQRQREAQKLILEGAMPWDVDRVLYDFGLPMGPFAMSDLAGLDIGW
DPAKTSSSTVREVLCEMDRRGQKNGKGFYDYDENRNAKPSPVVEEVIRDFAEKRQIQRRE
ITDQEILERCLYPMVNEGAKILEEGKAIRASDIDIVWINGYGWPVYSGGPMFWGELVGLD
KVLAKMKQFHAELGDDFKPSALLERLVAEGKGFKDA

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