GapMind for catabolism of small carbon sources

 

Protein CA265_RS24850 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: FitnessBrowser__Pedo557:CA265_RS24850

Length: 454 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 33 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
L-arginine catabolism gabD med Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 (characterized) 32% 93% 248.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 34% 245.0
L-citrulline catabolism gabD med Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 (characterized) 32% 93% 248.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 34% 245.0
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
ethanol catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
putrescine catabolism gabD med Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 (characterized) 32% 93% 248.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 34% 245.0
L-threonine catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
thymidine catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
L-tryptophan catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 93% 248.1 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 93% 248.1 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 93% 248.1 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 93% 248.1 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 241.5 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 241.5 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 241.5 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 241.5 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 241.5 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 32% 94% 240.4 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 91% 234.6 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 91% 234.6 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 91% 234.6 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 33% 91% 230.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 33% 91% 230.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 85% 225.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 85% 225.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 85% 225.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 85% 225.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 31% 93% 218.4 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 30% 94% 215.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 31% 90% 185.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 31% 90% 185.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8

Sequence Analysis Tools

View CA265_RS24850 at FitnessBrowser

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

MQIINPATAEIITSLEEDNLSTLQLKFDALQKAQPQWAGKTLQERIAVITHFSDLLEVEI
EKLASVLTSEVGKPLQQSRNEINGARARIKWMLANAEKYLADEVMTDEPGIKEIIKYEPL
GVVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDDVFH
IAIGAKETGSALLNMDFNGYFFTGSYKTGKLIYEKVAAKMVPCQLELGGKDPLYITDDVT
DVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAEGVYI
GALTRKEQISVLENQVKDALNKGAKLLTGGKAVEGKGYYFEPTVLTDVTNDMLVMQEESF
GPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCCDRVSA
ALPWSGRKYSGIGATLSHQGIRAFTKPKGYHLRR

This GapMind analysis is from Sep 17 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