GapMind for catabolism of small carbon sources

 

Protein WP_011830162.1 in Methylibium petroleiphilum PM1

Annotation: NCBI__GCF_000015725.1:WP_011830162.1

Length: 477 amino acids

Source: GCF_000015725.1 in NCBI

Candidate for 27 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 95% 320.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 95% 320.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 95% 320.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 92% 298.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 95% 296.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 95% 296.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 95% 296.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 95% 296.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 36% 97% 286.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 36% 97% 286.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
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) 34% 97% 251.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
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) 34% 97% 251.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
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) 34% 97% 251.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
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) 34% 97% 251.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 35% 90% 236.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 88% 234.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 88% 234.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 88% 234.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 88% 234.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 88% 234.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 91% 211.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 91% 211.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 91% 211.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 91% 211.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 91% 211.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 93% 189.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 93% 189.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 546.2

Sequence Analysis Tools

View WP_011830162.1 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

MRDYLKFYIDGHWVDPVKAKSLDVVNPATEASAGRISMGTAADVDRAVKAARKAFASYSQ
TSVAERASLLERIIVEYKKRYADMAAAITEEMGAPVALSKDAQAAMGIAHLQIALDVLKN
YKFQELRDTTLMVKEPIGVCGFITPWNWPVNQIACKVAPALAVGCTMVLKPSEIAPFSAY
LWTEILHAAGVPAGVFNLVNGDGPTVGAALSSHPDVDMVSFTGSTRAGVEVARNAAPTVK
RVHQELGGKSPNIILPDADFKHAITAGVQGVMLNSGQSCNAPTRMLVPNARLDEALAIAK
EAAEATTVGDPASGAALGPVISATQWDKIQTLIHKGIEEGATVVAGGPGKPKGLETGYYV
KPTVLGHVNNQMTVAREEIFGPVLTILGYDTVDQAVEIGNDTPYGLAAYVSGTDPEATRK
VASRLRAGQVNINSVPLDFKAPFGGFKQSGNGREWGDHAFGEFLEVKAVLGYAPKAA

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