GapMind for catabolism of small carbon sources

 

Protein WP_012465362.1 in Chlorobium limicola DSM 245

Annotation: NCBI__GCF_000020465.1:WP_012465362.1

Length: 458 amino acids

Source: GCF_000020465.1 in NCBI

Candidate for 48 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabD hi aldehyde dehydrogenase-like protein yneI (characterized) 47% 98% 417.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 35% 285.4
L-citrulline catabolism gabD hi aldehyde dehydrogenase-like protein yneI (characterized) 47% 98% 417.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 35% 285.4
putrescine catabolism gabD hi aldehyde dehydrogenase-like protein yneI (characterized) 47% 98% 417.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 35% 285.4
4-hydroxybenzoate catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 45% 99% 393.7 aldehyde dehydrogenase-like protein yneI 47% 417.9
2'-deoxyinosine catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 45% 99% 393.7 aldehyde dehydrogenase-like protein yneI 47% 417.9
2-deoxy-D-ribose catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 45% 99% 393.7 aldehyde dehydrogenase-like protein yneI 47% 417.9
ethanol catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 45% 99% 393.7 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-threonine catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 45% 99% 393.7 aldehyde dehydrogenase-like protein yneI 47% 417.9
thymidine catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 45% 99% 393.7 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-tryptophan catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 45% 99% 393.7 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 34% 94% 263.1 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 34% 94% 263.1 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 34% 94% 263.1 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 34% 94% 263.1 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 34% 92% 260 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 34% 92% 260 aldehyde dehydrogenase-like protein yneI 47% 417.9
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 34% 92% 260 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 35% 95% 252.3 aldehyde dehydrogenase-like protein yneI 47% 417.9
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 33% 93% 248.4 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 33% 93% 248.4 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 33% 95% 246.9 aldehyde dehydrogenase-like protein yneI 47% 417.9
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 33% 95% 246.9 aldehyde dehydrogenase-like protein yneI 47% 417.9
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 33% 95% 246.9 aldehyde dehydrogenase-like protein yneI 47% 417.9
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 33% 95% 246.9 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 95% 246.5 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 95% 246.5 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 95% 246.5 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 95% 246.5 aldehyde dehydrogenase-like protein yneI 47% 417.9
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 95% 246.5 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 88% 243 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 92% 228 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 92% 228 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 92% 228 aldehyde dehydrogenase-like protein yneI 47% 417.9
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 92% 228 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 30% 95% 213.4 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 85% 198.4 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 85% 198.4 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 85% 198.4 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 85% 198.4 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 85% 198.4 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 92% 194.5 aldehyde dehydrogenase-like protein yneI 47% 417.9
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 92% 194.5 aldehyde dehydrogenase-like protein yneI 47% 417.9
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 92% 194.5 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 92% 194.5 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 92% 194.5 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 32% 77% 172.6 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 90% 152.1 aldehyde dehydrogenase-like protein yneI 47% 417.9
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 90% 152.1 aldehyde dehydrogenase-like protein yneI 47% 417.9

Sequence Analysis Tools

View WP_012465362.1 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

MIVTINPATEGVLAEYPAMSHGDINEAVNAAYLDFTRWRQVSIPERARLMLRVAELLRER
KAEYGTLATREMGKPFAQAAAEVEKSAWVCDFYAAHAEGYLEPETVDMDGGKGMVVFEPL
GLVLGVMPWNFPYWQVFRFAVPALMAGNGVIVKHAPNVTGCAAAIEQVFRDAGFPENLYR
TLHIELQDVDRLTGIVIEHPFVKAVSVTGSTAAGRAVAARAGRALKRSVMELGGNDPYIV
LDDADLEKAVTVCAASRLLNSGQSCIAAKRFIVHRSIRSRFEGMLLERMLGAKTGDPFDS
ATEVGPIARADLRLQVHRQVEESVAQGAVVLCGGVLPEGQGYFYPPTILTGVKKGMAAYG
EEIFGPVATIIEAADDDEAVAIANDSEYGLGSAVFSADTLRAAEIASRLETGNCFINAMV
KSDPRMPFGGVKQSGYGRELSSYGIKEFTNIRSLFLEA

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