GapMind for catabolism of small carbon sources

 

Protein WP_034525919.1 in Lactobacillus oryzae SG293

Annotation: NCBI__GCF_000740055.1:WP_034525919.1

Length: 260 amino acids

Source: GCF_000740055.1 in NCBI

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-sorbitol (glucitol) catabolism sdh lo Sorbitol dehydrogenase (EC 1.1.1.14) (characterized) 38% 98% 170.6 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 32% 99% 136.7 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 32% 99% 136.7 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 35% 95% 134 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 35% 95% 134 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase (characterized) 34% 98% 133.3 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 32% 94% 124.8 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
4-hydroxybenzoate catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 34% 99% 124.4 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
4-hydroxybenzoate catabolism paaH lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 34% 99% 124.4 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
L-arginine catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 34% 99% 124.4 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
L-citrulline catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 34% 99% 124.4 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 34% 99% 124.4 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
L-lysine catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 34% 99% 124.4 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
phenylacetate catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 34% 99% 124.4 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
phenylacetate catabolism paaH lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 34% 99% 124.4 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
L-phenylalanine catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 34% 99% 124.4 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
L-phenylalanine catabolism paaH lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 34% 99% 124.4 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
L-proline catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 34% 99% 124.4 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
L-rhamnose catabolism LRA1 lo NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 34% 98% 124 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 33% 95% 116.7 diacetyl reductase ((S)-acetoin forming); EC 1.1.1.304 68% 337.0

Sequence Analysis Tools

View WP_034525919.1 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

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Sequence

MAELTGKVAFVTGAAQGIGEAIAKRLADDGFAVAVADLNETSANAVAKEINDAGGKAVGL
KVDVSNRDDVFAAVKEAAKVLGGFDVIVNNAGLGPTTPIDTITPEQFDTVYHVNVAGTLW
GIQAAHEQFKKFGHGGKIINATSQAGVVGNPNLALYSGTKFAVRGITQVAARDLAEEGIT
VNAFAPGIVKTPMMFDIAHQVGQNAGKDDEWGMQTFAKDIALKRLSEPEDVAAGVSFLAG
PDSNYVTGQTLEVDGGMQFH

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