GapMind for catabolism of small carbon sources

 

Protein WP_078427595.1 in Alkalihalobacterium alkalinitrilicum DSM 22532

Annotation: NCBI__GCF_002019605.1:WP_078427595.1

Length: 494 amino acids

Source: GCF_002019605.1 in NCBI

Candidate for 37 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 hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 69% 99% 709.9 retinal dehydrogenase (EC 1.2.1.36) 55% 520.8
2'-deoxyinosine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 69% 99% 709.9 retinal dehydrogenase (EC 1.2.1.36) 55% 520.8
2-deoxy-D-ribose catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 69% 99% 709.9 retinal dehydrogenase (EC 1.2.1.36) 55% 520.8
ethanol catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 69% 99% 709.9 retinal dehydrogenase (EC 1.2.1.36) 55% 520.8
L-threonine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 69% 99% 709.9 retinal dehydrogenase (EC 1.2.1.36) 55% 520.8
thymidine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 69% 99% 709.9 retinal dehydrogenase (EC 1.2.1.36) 55% 520.8
L-tryptophan catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 69% 99% 709.9 retinal dehydrogenase (EC 1.2.1.36) 55% 520.8
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 92% 546.2 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 50% 96% 474.9 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 50% 96% 474.9 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 50% 96% 474.9 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 48% 96% 453.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 48% 96% 453.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 48% 96% 453.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 48% 96% 453.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 100% 414.5 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 100% 414.5 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 44% 96% 409.8 retinal dehydrogenase (EC 1.2.1.36) 55% 520.8
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 44% 96% 409.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 44% 96% 409.8 retinal dehydrogenase (EC 1.2.1.36) 55% 520.8
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 44% 96% 409.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 44% 96% 409.8 retinal dehydrogenase (EC 1.2.1.36) 55% 520.8
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 44% 96% 409.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-arabinose catabolism xacF med Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 41% 97% 356.3 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
D-galacturonate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 41% 97% 356.3 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
D-glucuronate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 41% 97% 356.3 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
D-xylose catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 41% 97% 356.3 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 39% 96% 363.6 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 40% 99% 351.7 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
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) 35% 91% 268.9 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
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) 35% 91% 268.9 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
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) 35% 91% 268.9 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
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) 35% 91% 268.9 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
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) 35% 91% 268.9 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 33% 94% 213 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 33% 94% 213 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 31% 91% 209.1 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 69% 709.9

Sequence Analysis Tools

View WP_078427595.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MEQTMNLKNKVVNFLQGNKKLFINGRWVESVSGKTFETKNPATGEVLSLVNEAQEEDVNR
AVDAAREAFDNGPWSRMDASERSRLIYKLADLMENNLEELAQLETLDNGKPINESMGFDV
PAAIEHFRYYAGWSTKIVGQTIPVNGNFFNYTRHEPVGVVGQIIPWNFPLLMAAWKMGAA
LATGCTIVLKPAEQTPLTALYLAKLIEEAGFPEGVVNVIPGFGQTAGEPLVRHEKVDKIA
FTGSTIVGKQIMRQGSDTIKRVTLELGGKSPNIVLPDADLTKAVPGAFMGIMFNQGQVCT
AGSRLFVQKKAYDNVVADLISHSKSIKQGPGIDTNTQMGPLVSNVQQNRVLNYIEKGQEE
GAELLTGGRKPFDRGYFVEPTIFSAVNDEMTIAREEIFGPVLVAMPYDDIDEVIQRANNT
PYGLAAAVWTENVRNAHYVASKLKAGTVWINSYNVVDAASPFGGFKQSGNGREMGSYALD
NYTEVKSVFVNMDN

This GapMind analysis is from Apr 09 2024. 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