GapMind for catabolism of small carbon sources

 

Protein WP_013418243.1 in Rhodomicrobium vannielii ATCC 17100

Annotation: NCBI__GCF_000166055.1:WP_013418243.1

Length: 724 amino acids

Source: GCF_000166055.1 in NCBI

Candidate for 22 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 med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 38% 98% 437.2 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 33% 383.3
4-hydroxybenzoate catabolism paaH med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 38% 98% 437.2 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 33% 383.3
L-arginine catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 38% 98% 437.2 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 33% 383.3
L-citrulline catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 38% 98% 437.2 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 33% 383.3
L-isoleucine catabolism ech med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 38% 98% 437.2
L-lysine catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 38% 98% 437.2 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 33% 383.3
phenylacetate catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 38% 98% 437.2 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 33% 383.3
phenylacetate catabolism paaH med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 38% 98% 437.2 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 33% 383.3
L-phenylalanine catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 38% 98% 437.2 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 33% 383.3
L-phenylalanine catabolism paaH med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 38% 98% 437.2 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 33% 383.3
L-proline catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 38% 98% 437.2 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) 33% 383.3
4-hydroxybenzoate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 32% 100% 327.4 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 38% 437.2
phenylacetate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 32% 100% 327.4 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 38% 437.2
L-phenylalanine catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 32% 100% 327.4 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 38% 437.2
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) 34% 58% 190.3
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) 34% 58% 190.3
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) 34% 58% 190.3
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) 34% 58% 190.3
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) 34% 58% 190.3
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) 34% 58% 190.3
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) 34% 58% 190.3
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) 34% 58% 190.3

Sequence Analysis Tools

View WP_013418243.1 at NCBI

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

MSSISYQVDADGIATLTIDQPGKSMNVISPEFTEELSEAIERAAADSSVKGIVITSGKSS
FVAGADLIGMSGMIEHARNAPAAEALKVSSRLTEVLRRLETIGKPVATAINGTALGGGFE
IALATHYRVAADDESIKIGQPEVQVGLLPGAGGTQRIPRLIGIMASAPLLLEGKHLSPQQ
AKSSGLIHDVVPAAELLAKAKAWLLSPQAKSVQPWDERGFKVPGGAGGMHPAAAQLFMAA
NAMTRDKTLGNYPAAQAILSAVYEGTQVPIDLGLKIEAKYFLSLLRGPVAPAMIRTLFVN
KGRADKLVRRPQGVPKAKFKKIGMLGAGMMGAAIAYVAASNGIEVVLLDRDVEAAERGKG
YARKLVEKAVSRRKTTEADGQGLLARIHATADYADLADVDYIIEAVFEDRAIKADVTKKV
EAVIRPDVIFGSNTSTIPITSLAEASERPEKFIGIHFFSPAEKMPLVEIIRGKKTSDEAL
AVTLDFVQAIRKTPIVVNDGRGFFTSRFCMNYIGEGEIMLTEGIPAALVENAGKLAGMPV
GPLALADETAIDLGWKIHKAAETDLGDAYTPSAAIGVMEAMYVKNGRAGRKNGKGFYEYP
EGGPKTLWAGLADLFPVKPESEWPSIDDLKKRLLFAQALDAVRTMEDGVLTDPEDGDVGG
IFGLGFAPYTGGPLSMLDGIGIANAVAECERLAARYGERFSPPKLLRDMAAEGRTFYPAA
KAAA

This GapMind analysis is from Apr 09 2024. 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:

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