GapMind for catabolism of small carbon sources

 

Protein WP_085219599.1 in Sphingomonas indica Dd16

Annotation: NCBI__GCF_900177405.1:WP_085219599.1

Length: 685 amino acids

Source: GCF_900177405.1 in NCBI

Candidate for 36 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) 56% 95% 721.8 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 48% 590.5
phenylacetate catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 56% 95% 721.8 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 48% 590.5
L-phenylalanine catabolism pimF hi 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 56% 95% 721.8 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) 48% 590.5
4-hydroxybenzoate catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 48% 97% 590.5 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
4-hydroxybenzoate catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 48% 97% 590.5 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-arginine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 48% 97% 590.5 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-citrulline catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 48% 97% 590.5 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-lysine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 48% 97% 590.5 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
phenylacetate catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 48% 97% 590.5 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
phenylacetate catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 48% 97% 590.5 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-phenylalanine catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 48% 97% 590.5 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-phenylalanine catabolism paaH med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 48% 97% 590.5 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-proline catabolism fadB med 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized) 48% 97% 590.5 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-isoleucine catabolism ech med Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized) 42% 97% 506.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-isoleucine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 78% 154.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
propionate catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 78% 154.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-threonine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 78% 154.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-valine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 78% 154.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
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) 31% 58% 159.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
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) 31% 58% 159.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
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) 31% 58% 159.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
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) 31% 58% 159.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
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) 31% 58% 159.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
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) 31% 58% 159.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
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) 31% 58% 159.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
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) 31% 58% 159.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
4-hydroxybenzoate catabolism badK lo BadK (characterized) 37% 96% 135.2 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
phenylacetate catabolism badK lo BadK (characterized) 37% 96% 135.2 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-phenylalanine catabolism badK lo BadK (characterized) 37% 96% 135.2 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
4-hydroxybenzoate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 39% 78% 125.2 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
phenylacetate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 39% 78% 125.2 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-phenylalanine catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 39% 78% 125.2 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 38% 68% 112.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 36% 59% 112.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 38% 68% 112.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 38% 68% 112.1 6-carboxyhex-2-enoyl-CoA hydratase 56% 721.8

Sequence Analysis Tools

View WP_085219599.1 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

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Sequence

MSPITTRRHGDVLIVTSNNPPVNALGIAVREGLVKAIEEADGDDAVKAVVIRCDGNTFFA
GADITEFGKPMQMPMLPQVVDRIEACTKPVVAAIHGTALGGGLEVALSCHYRVAVPDAKL
GVPEVKLGLLPGAGGTQRLPRVAGVETALEMAATGNPIGAKRAAEIGLVDRIVEGDLEQH
AVAFAEEVREIRPLPKASERDDKLAAARANPGLFDDFRKANARKMKGFDAPEANIKAIEA
ALSKPYAEGVQDERRLFMELMSGTQARAQQYFFFAERKASKIEGVGEDVRPRDIRKVGVI
GAGTMGGGISMNFLSAGIPVTIVETAQDALDRGTALIRKNYEATAAKGRMTADQVEKAMG
LLTPSLSLDDLADCDLVIEAVFENMEVKKEVFGKLDGIVKQGAILASNTSYLNVDEIAAS
TGRPQDVVGLHFFSPANVMKLLEVVRGAKTADDVLVTAMALAKRIRKVAVVAGVCYGFIG
NRMLIPRQTQAMNLLLEGATPEQIDRVHVEFGMPMGPFQMADLAGVDIGWHRDPNRIENI
RDKLCAMDRWGQKKGAGFYDYDDKRRPSPSPVVADVIEEFRAKAGVEKRDISDQEIIERT
LYTMVNEGALILEGGFAQRASDIDVVWVYGYGWPVYRGGPMFWADTEGLPKIVEGLKRQQ
DRLGADFKLSDLLVKKAEAGEKLSR

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