GapMind for catabolism of small carbon sources

 

Protein WP_009762382.1 in Microvirga lotononidis WSM3557

Annotation: NCBI__GCF_000262405.1:WP_009762382.1

Length: 476 amino acids

Source: GCF_000262405.1 in NCBI

Candidate for 26 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% 342.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 95% 342.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 95% 342.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 97% 334 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 97% 334 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-arginine catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 38% 88% 332 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-citrulline catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 38% 88% 332 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
putrescine catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 38% 88% 332 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 91% 328.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 95% 313.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 95% 313.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 95% 313.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 95% 313.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 297.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 297.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 297.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 297.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 38% 94% 297 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 98% 272.3 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 98% 272.3 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 93% 243.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 93% 243.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 93% 243.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 93% 243.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 93% 243.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 34% 90% 226.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 58% 559.7

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Predict transmenbrane helices: Phobius

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Sequence

MQHHHHFYIDGRWANPVGQDLIDVVNPATEEVVATIAAGRRADVDKAVAAARSAFESYAS
TTRTERIDLLNSIVEIYRQRAQDLAEAVSTEMGAPFTFALERHVSAGLGHLTRAIEVLKD
YRFDERINSTLVVREPVGVVGLITPWNWPLNQIACKVGPALAAGCTMVLKPSEMAPLSAL
IIAEILHEAGVPAGAFNLVNGDGPHVGQAIASHPDVDMVSFTGSTRAGILVAKAAADTVK
RVHQELGGKSPNILLDDADFNGAVTHGVRGCFANSGQSCNAPTRLLVPADWQEKVMEIAG
RVAEETVAGDPRAAETTIGPVVSRTQFERIQDLIETGIKEGATLVTGGPGRPLGLRKGYY
VRPTIFADVRNDMTIAREEIFGPVLSIMPYRDEEEAIRIANDTVYGLSSYVTSRDIERSR
RVARRIRAGMVHVNGSRGDTAAAFGGYKQSGNGREWGRFGFEEFLEIKSIFGHYTA

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