GapMind for catabolism of small carbon sources

 

Protein WP_101588181.1 in Brevibacterium jeotgali SJ5-8

Annotation: NCBI__GCF_900169175.1:WP_101588181.1

Length: 251 amino acids

Source: GCF_900169175.1 in NCBI

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 paaF hi 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 49% 95% 221.1 enoyl-CoA hydratase (EC 4.2.1.17); DELTA3,5-DELTA2,4-dienoyl-CoA isomerase (EC 5.3.3.21) 45% 202.6
L-isoleucine catabolism ech hi 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 49% 95% 221.1 BadK 44% 193.0
phenylacetate catabolism paaF hi 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 49% 95% 221.1 enoyl-CoA hydratase (EC 4.2.1.17); DELTA3,5-DELTA2,4-dienoyl-CoA isomerase (EC 5.3.3.21) 45% 202.6
L-phenylalanine catabolism paaF hi 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 49% 95% 221.1 enoyl-CoA hydratase (EC 4.2.1.17); DELTA3,5-DELTA2,4-dienoyl-CoA isomerase (EC 5.3.3.21) 45% 202.6
4-hydroxybenzoate catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 46% 97% 204.1 BadK 44% 193.0
L-arginine catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 46% 97% 204.1 BadK 44% 193.0
L-citrulline catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 46% 97% 204.1 BadK 44% 193.0
L-lysine catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 46% 97% 204.1 BadK 44% 193.0
phenylacetate catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 46% 97% 204.1 BadK 44% 193.0
L-phenylalanine catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 46% 97% 204.1 BadK 44% 193.0
L-proline catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 46% 97% 204.1 BadK 44% 193.0
L-valine catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 46% 97% 204.1 BadK 44% 193.0
4-hydroxybenzoate catabolism badK med BadK (characterized) 44% 96% 193 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
L-isoleucine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 97% 193 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
phenylacetate catabolism badK med BadK (characterized) 44% 96% 193 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
L-phenylalanine catabolism badK med BadK (characterized) 44% 96% 193 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
propionate catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 97% 193 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
L-threonine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 97% 193 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
L-valine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 97% 193 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 40% 98% 173.3 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 35% 94% 131.3 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 35% 94% 131.3 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 32% 96% 116.3 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 32% 96% 116.3 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 32% 96% 116.3 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 49% 221.1

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Sequence

MEDRGGVRVLTLDRPKALNALSVDLVAQLTAALTDAESTDSVRAIVLTGSDKAFCAGADI
TQIPQMQKAAPLDKLAFDGLFSTIARLNKPTIAAVRGMAFGGGCEIALACDMAIAGESAQ
FGVPEVKLGVLPGAGGTQRLVHALGKAKAMRMLLTGEPVTATWAESAGLVAEVVADVDVL
DTAVGIGETIAGNAPLAVRLTADAARHAEELGLSRGLDLERRNFLLLLGTEDAAEGISAF
AERRTADFKGA

This GapMind analysis is from Sep 24 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 (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