GapMind for catabolism of small carbon sources

 

Protein 7024269 in Shewanella sp. ANA-3

Annotation: Shewana3_1461 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Length: 709 amino acids

Source: ANA3 in FitnessBrowser

Candidate for 33 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism fadB hi fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 58% 99% 817.4 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) 44% 570.9
4-hydroxybenzoate catabolism paaH hi fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 58% 99% 817.4 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) 44% 570.9
L-arginine catabolism fadB hi fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 58% 99% 817.4 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) 44% 570.9
L-citrulline catabolism fadB hi fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 58% 99% 817.4 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) 44% 570.9
L-isoleucine catabolism ech hi fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 58% 99% 817.4
L-lysine catabolism fadB hi fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 58% 99% 817.4 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) 44% 570.9
phenylacetate catabolism fadB hi fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 58% 99% 817.4 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) 44% 570.9
phenylacetate catabolism paaH hi fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 58% 99% 817.4 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) 44% 570.9
L-phenylalanine catabolism fadB hi fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 58% 99% 817.4 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) 44% 570.9
L-phenylalanine catabolism paaH hi fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 58% 99% 817.4 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) 44% 570.9
L-proline catabolism fadB hi fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 58% 99% 817.4 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) 44% 570.9
L-isoleucine catabolism fadA med long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 44% 93% 570.9 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
4-hydroxybenzoate catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 36% 84% 139
L-arginine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 36% 84% 139
L-citrulline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 36% 84% 139
L-lysine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 36% 84% 139
phenylacetate catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 36% 84% 139
L-phenylalanine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 36% 84% 139
L-proline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 36% 84% 139
L-valine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 36% 84% 139
4-hydroxybenzoate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 36% 98% 391.7 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
phenylacetate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 36% 98% 391.7 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
L-phenylalanine catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 36% 98% 391.7 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 91% 144.1 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 91% 144.1 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 91% 144.1 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 91% 144.1 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 33% 79% 118.2 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
4-hydroxybenzoate catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 31% 92% 116.3 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
phenylacetate catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 31% 92% 116.3 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
L-phenylalanine catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 31% 92% 116.3 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 32% 74% 79 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 32% 74% 79 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 58% 817.4

Sequence Analysis Tools

View 7024269 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

MEKTFNLTRREDGIAILMMDVPGETMNTLKAEFGPEISEILSEIKRDSSIRGLVLISGKK
DSFVAGADISMLDACQTAGDAKALSQQGHVVFNELEALNIPVVAAIHGACLGGGLELALA
CHQRVCSDDGKTMLGVPEVQLGLLPGGGGTQRLPRLVGITTALDMMLTGKQIRPKQALKM
GLVNDVVPQTILLQTAVEMALAGKRTAKPVKKSLVNQLLEGTGFGRNIIFDQAAKQVVKK
TQGNYPAPAKIIDCVRQGMAKGMQKGLEVEASHFAELVVSKESEALRSIFFATTEMKKET
GAEGATPRKVKKAVILGGGLMGGGIASVTTTKAKIPARVKDINEKGLSNALSYAYKLLDK
GVKRRHMTPAVRDNLMALMTTTTEYKGVKDADIVVEAVFEDLALKHQMVKDIERECGEHT
IFASNTSSLPIGQIAQAASRPENVIGLHYFSPVEKMPLVEVIAHAKTSPETIATTVAFAR
KQGKTPIVVQDGAGFYVNRILALYMNEAAQLLLEGQSIEHLDKALVKFGFPVGPITLLDE
VGIDVGAKIAPILEKELGERFKAPAAFDKLLSDDRKGRKNGKGFYQYAAGNKASSKKKAV
DESVYAVLGIKPGMDKDLSAVAERCVVQMLNEAVRCLDDGIIASPRDGDIGAIFGIGFPP
FLGGPFHYIDTLGADNLVNILERYQAQYGDRFEPCPRLKAMAAEKARFF

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