GapMind for catabolism of small carbon sources

 

Protein WP_076580767.1 in Haloterrigena daqingensis JX313

Annotation: NCBI__GCF_001971705.1:WP_076580767.1

Length: 652 amino acids

Source: GCF_001971705.1 in NCBI

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 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) (characterized) 43% 100% 528.1
4-hydroxybenzoate catabolism paaH hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) (characterized) 43% 100% 528.1
L-arginine catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) (characterized) 43% 100% 528.1
L-citrulline catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) (characterized) 43% 100% 528.1
L-lysine catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) (characterized) 43% 100% 528.1
phenylacetate catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) (characterized) 43% 100% 528.1
phenylacetate catabolism paaH hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) (characterized) 43% 100% 528.1
L-phenylalanine catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) (characterized) 43% 100% 528.1
L-phenylalanine catabolism paaH hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) (characterized) 43% 100% 528.1
L-proline catabolism fadB hi 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) (characterized) 43% 100% 528.1
4-hydroxybenzoate catabolism ech med 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) 40% 100% 456.4 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-arginine catabolism ech med 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) 40% 100% 456.4 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-citrulline catabolism ech med 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) 40% 100% 456.4 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-lysine catabolism ech med 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) 40% 100% 456.4 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
phenylacetate catabolism ech med 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) 40% 100% 456.4 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-phenylalanine catabolism ech med 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) 40% 100% 456.4 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-proline catabolism ech med 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) 40% 100% 456.4 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-valine catabolism ech med 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) 40% 100% 456.4 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-isoleucine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 41% 100% 205.7 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
propionate catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 41% 100% 205.7 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-threonine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 41% 100% 205.7 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-valine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 41% 100% 205.7 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-isoleucine catabolism ech lo Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized) 32% 56% 174.1 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 37% 83% 168.7 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
4-hydroxybenzoate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 100% 164.5 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
phenylacetate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 100% 164.5 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-phenylalanine catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 100% 164.5 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
4-hydroxybenzoate catabolism badK lo BadK (characterized) 32% 100% 148.7 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
phenylacetate catabolism badK lo BadK (characterized) 32% 100% 148.7 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-phenylalanine catabolism badK lo BadK (characterized) 32% 100% 148.7 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
phenylacetate catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 34% 96% 145.6 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-phenylalanine catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 34% 96% 145.6 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1
L-valine catabolism bch lo 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial; 3-hydroxyisobutyryl-coenzyme A hydrolase; HIB-CoA hydrolase; HIBYL-CoA-H; EC 3.1.2.4 (characterized) 30% 55% 82.8 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); 3-hydroxybutyryl-CoA dehydratase (EC 4.2.1.55) 43% 528.1

Sequence Analysis Tools

View WP_076580767.1 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

MSLDSIDRVAVLGAGNMGHGITEVTAMAGYDVTMRDIKDEFVDDGYESIAWSLEKLEEKE
LIDESADDVLSRIDTTTDLETAVSDADLVIEAAPENLDLKHDIFTDLEEFCDEDTLLATN
TSSLPISDIAEVVDTSERVLGLHFFNPPVKMDLVEVIYGNDTSDEAAEAGYEWVESIAKT
PIYVRKDVRGFVVNTIVGPFGGEPAFMVSEGEADIRQADATMSHERGYPMGPFELADLTG
IDVGYHVRKEGDSPIPPITEEKVEAEELGQKTGKGFYDYEDGDGADYQPDDAGGFDWLRV
EARMINRAAFLVGEDVAKPEEVDTGVQLGLGFPEGICRRADKIGLDEVLEKLETLHEETG
SERFEPHPYLEELVEDGKTGEDAGEGFYEYDNEDGGFDSYHNINVELADGVLAVELDRPS
RMNALSEDLLSEIDDLFSSVDTDEVRCATIEGAGDRAFSAGADVSGFSSANPTDLMDVSQ
AFETVNEFPRPVLAKIDGFCLGGGLELALACDLRVATDRSEFGAPEINLGLIPGAGGTQR
LTRILGETRAKELVFRGNHIDADRAEEWGLINRAVDREAFDDTVEEFVSDLAGGPPIALK
IAKQVMNEGQDASIDAALAMESQGFGLLTSTEDVLEGTMAFAEDREPEFEGK

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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