GapMind for catabolism of small carbon sources

 

Protein WP_066048767.1 in Halioglobus japonicus S1-36

Annotation: NCBI__GCF_002869505.1:WP_066048767.1

Length: 497 amino acids

Source: GCF_002869505.1 in NCBI

Candidate for 47 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism kauB hi gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 58% 100% 611.7 aldehyde dehydrogenase 51% 504.2
L-arginine catabolism puuC hi gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 58% 100% 611.7 aldehyde dehydrogenase 51% 504.2
L-citrulline catabolism puuC hi gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 58% 100% 611.7 aldehyde dehydrogenase 51% 504.2
putrescine catabolism puuC hi gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 58% 100% 611.7 aldehyde dehydrogenase 51% 504.2
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 99% 494.2 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 99% 494.2 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 99% 494.2 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 99% 494.2 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 99% 494.2 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 99% 494.2 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
4-hydroxybenzoate catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 43% 96% 415.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 43% 96% 415.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 43% 96% 415.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
ethanol catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 43% 96% 415.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-threonine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 43% 96% 415.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
thymidine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 43% 96% 415.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 43% 96% 415.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 92% 391.3 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 345.9 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 345.9 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 96% 339.3 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 96% 339.3 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 96% 339.3 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 96% 339.3 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 94% 339 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 94% 339 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 94% 339 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 98% 318.2 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-tryptophan catabolism nbaE lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 34% 98% 317.4 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 37% 97% 308.5 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 37% 97% 308.5 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 37% 97% 308.5 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 37% 97% 308.5 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 34% 88% 266.9 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 34% 88% 266.9 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 34% 88% 266.9 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 34% 88% 266.9 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 34% 88% 266.9 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 34% 94% 242.3 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 94% 231.5 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 94% 231.5 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 94% 231.5 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 94% 231.5 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 94% 231.5 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-lysine catabolism amaB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 31% 89% 208.8 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 32% 95% 202.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 32% 95% 202.6 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) 58% 611.7

Sequence Analysis Tools

View WP_066048767.1 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

MTEKTLADWQQAAADIRIDGRAFINGRRVDAASGQTRTTYNPATGQALAEVANCAPADAD
EAVRIARETFEQGTWAGMPAAERKMVLVRWAELIEQHADELALLETLDVGKPIADTVNVD
VPSSVRTIRWTGEAIDKVYDQISPTRDNCMGLITRLPLGVVAAIVPWNFPLSTTAWKLAP
ALATGNSVILKPASNTPLTALRIADLATQAGLPDGVLHVLPGPGGSLGEHIATHMGIDGL
TFTGSTPVGKQLMVYSGQSNLKRVFLELGGKSPNIVFPDADIDKAASAAALAVYYNGGQT
CTAGTRLIVHESIHDTFIEKVIEAASGWAPGNPLDPATAMGPMVDKGQCDTVAEYVAIGR
DEGAKLVAGGGTVMEDTGGHYHEPTIFAGVNNQMRIAQEEIFGPVLAVIPFSTESEAVAI
ANDSIYGLAGAVWSQNINTAHRVAEQVRVGTMGINNYFGGDITVPFGGFKESGNGRDKSM
HAFDDYTELKTTWLEFD

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