GapMind for catabolism of small carbon sources

 

Protein WP_009778885.1 in Leeuwenhoekiella blandensis MED217

Annotation: NCBI__GCF_000152985.1:WP_009778885.1

Length: 257 amino acids

Source: GCF_000152985.1 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
L-rhamnose catabolism LRA1 lo L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized) 35% 96% 151 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 32% 92% 142.1 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 32% 92% 142.1 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 32% 92% 142.1 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 36% 96% 141.7 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
4-hydroxybenzoate catabolism badH lo BadH (characterized) 32% 99% 138.3 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
phenylacetate catabolism badH lo BadH (characterized) 32% 99% 138.3 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
L-phenylalanine catabolism badH lo BadH (characterized) 32% 99% 138.3 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
D-sorbitol (glucitol) catabolism sdh lo Sorbitol dehydrogenase (EC 1.1.1.14) (characterized) 32% 98% 132.9 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 32% 99% 130.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 32% 99% 130.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
L-fucose catabolism fucDH lo Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 32% 99% 124.4 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
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) 31% 98% 118.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
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) 31% 98% 118.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
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) 31% 98% 118.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
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) 31% 98% 118.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
L-isoleucine catabolism ivdG 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) 31% 98% 118.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
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) 31% 98% 118.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
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) 31% 98% 118.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
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) 31% 98% 118.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
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) 31% 98% 118.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
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) 31% 98% 118.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
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) 31% 98% 118.2 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
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) 33% 97% 117.5 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized) 31% 94% 105.5 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 42% 213.0

Sequence Analysis Tools

View WP_009778885.1 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

MKRVKNKVAIVTGGASGLGKSSAKLLAREGAKIVVSDIDEEGGKKVVQQIKEDGGEAIFI
KQDVAKEDEWKNVIETTLETYGKLHILANSAGIGLGGTVEDVTLEDWKNLIDINLNGTFL
GTKYGIKGMRKTDEGGSIINFSSIEGLIGDPNLPAYNASKGGVTIFTKSAALHCAKQGYG
IRINSIHPAYIWTPMVENFLKAQGDVEEGKKQLESLHPIGHLGEPDDIGYGVVYLASDES
KFMTGSELVIDGGYTAQ

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