GapMind for catabolism of small carbon sources

 

Protein WP_062053068.1 in Aquimarina longa SW024

Annotation: NCBI__GCF_001401755.1:WP_062053068.1

Length: 480 amino acids

Source: GCF_001401755.1 in NCBI

Candidate for 48 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism praB hi 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 50% 99% 505.8 retinal dehydrogenase (EC 1.2.1.36) 50% 483.8
L-tryptophan catabolism praB hi 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 50% 99% 505.8 retinal dehydrogenase (EC 1.2.1.36) 50% 483.8
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 49% 98% 484.6 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 49% 98% 484.6 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 49% 98% 484.6 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 49% 98% 484.6 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 49% 98% 484.6 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 49% 98% 484.6 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 49% 98% 484.6 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-tryptophan catabolism nbaE med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 49% 98% 484.6 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 95% 351.7 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 95% 351.7 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 95% 351.7 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 40% 94% 350.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 40% 94% 350.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 40% 94% 350.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 340.5 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 340.5 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 340.5 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 340.5 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-arginine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 96% 335.9 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-citrulline catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 96% 335.9 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
putrescine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 96% 335.9 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 36% 91% 329.7 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 317 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 317 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 317 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 317 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 99% 310.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 97% 288.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 97% 288.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 97% 288.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 97% 288.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 34% 98% 276.9 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 34% 98% 276.9 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized) 33% 98% 255.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 255.4 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 255.4 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 255.4 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 255.4 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 255.4 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 89% 240 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 89% 240 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 89% 240 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 89% 240 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 89% 240 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 32% 93% 199.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 32% 93% 199.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 50% 505.8

Sequence Analysis Tools

View WP_062053068.1 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

MKKIENYINGEYSTPIENRWIDNYNPSTGEIYSLLPNSSVTDVQMAYEAAKTAFPSWSTT
SLQHRSDILAKIASLIIENLELLANAEAIDNGKPLSLATSVDIPRASSNFDFFAHAITQF
ASEAHESMGQNAINFTLRNPIGVVGCISPWNLPLYLFTWKIAPALAAGNTVVAKPSEITP
MTAYLLGDICTKAGLPKGVLNIVHGLGNTTGQAIIEHPDIKAISFTGGTATGAHIAKTAA
PMFKKLSLELGGKNPNLIFADCDYEKMLTTTLRSSFANQGQICLCGSRIFIERTIYDQFK
KDFIKKTKALKIGEPLNKETNIGALVSKSHLEKVKSYIDIAEQEGGTILYGGDYITVKGY
ENGYYLQPTIIEVTDSNCRLTQEEIFGPVVTIMPFDTDDQALSLANNVRYGLSATIWTNN
LNRSMYLAKHIQAGIIWINTWMMRDLRTPFGGVKDSGIGREGGFEALRFFTEPKNVCIHY

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