GapMind for catabolism of small carbon sources

 

Protein WP_038806392.1 in Streptococcus oralis 7747

Annotation: NCBI__GCF_000382825.1:WP_038806392.1

Length: 243 amino acids

Source: GCF_000382825.1 in NCBI

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 36% 100% 157.9 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
4-hydroxybenzoate catabolism badH lo BadH (characterized) 36% 98% 147.9 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
phenylacetate catabolism badH lo BadH (characterized) 36% 98% 147.9 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
L-phenylalanine catabolism badH lo BadH (characterized) 36% 98% 147.9 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
L-rhamnose catabolism LRA1 lo NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 37% 98% 146.4 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized) 34% 96% 139 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
D-sorbitol (glucitol) catabolism srlD lo Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) 33% 97% 134 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 37% 92% 133.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 37% 92% 133.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 37% 92% 133.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
D-sorbitol (glucitol) catabolism sdh lo Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized) 35% 98% 133.3 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
ethanol catabolism etoh-dh-nad lo alcohol dehydrogenase (EC 1.1.1.1) (characterized) 33% 98% 131.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
4-hydroxybenzoate catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 33% 94% 125.2 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
4-hydroxybenzoate catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 33% 94% 125.2 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
L-arginine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 33% 94% 125.2 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
L-citrulline catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 33% 94% 125.2 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
L-lysine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 33% 94% 125.2 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
phenylacetate catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 33% 94% 125.2 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
phenylacetate catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 33% 94% 125.2 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
L-phenylalanine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 33% 94% 125.2 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
L-phenylalanine catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 33% 94% 125.2 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
L-proline catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 33% 94% 125.2 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
L-fucose catabolism fucDH lo SDR family oxidoreductase (characterized, see rationale) 31% 97% 122.1 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
D-xylose catabolism DKDP-dehydrog lo SDR family oxidoreductase (characterized, see rationale) 31% 97% 122.1 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
L-rhamnose catabolism LRA5 lo 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized) 34% 94% 121.3 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate 3-dehydrogenase (characterized) 34% 94% 119 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate 3-dehydrogenase (characterized) 34% 94% 119 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 30% 94% 95.1 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 236.9

Sequence Analysis Tools

View WP_038806392.1 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

MQLTNKNVFVTGSSRGIGLAIAHKFAQLGANVVLNSRGEISEELLAEFSNYGVKVVPISG
DVSDFADAKRMIDQAIAELGSVDVLVNNAGITQDTLMLKMTEQDFEKVIKINLTGAFNMT
QAVLKQMIKAREGAIINMSSVVGLMGNIGQANYAASKAGLIGFTKSVAREVANRNVRVNA
LAPGMIESDMTAVLSDKVKEATLAQIPMKHFGQAEHIADTTVFLAGQDYLTGQVLAVDGG
LSM

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