GapMind for catabolism of small carbon sources

 

Protein WP_106709045.1 in Phyllobacterium brassicacearum STM 196

Annotation: NCBI__GCF_003010955.1:WP_106709045.1

Length: 487 amino acids

Source: GCF_003010955.1 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 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 55% 93% 491.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-citrulline catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 55% 93% 491.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
putrescine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 55% 93% 491.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 95% 376.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 95% 376.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 95% 376.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 42% 92% 374.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 361.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 361.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-arginine catabolism kauB med gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 348.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-arginine catabolism puuC med gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 348.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-citrulline catabolism puuC med gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 348.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
putrescine catabolism puuC med gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 348.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-tryptophan catabolism nbaE lo 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized) 39% 99% 335.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 99% 334.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 40% 98% 320.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 40% 98% 320.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 40% 98% 320.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 40% 98% 320.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 261.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 261.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 261.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 261.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 261.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-lysine catabolism amaB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 31% 86% 228.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 32% 98% 204.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 32% 98% 204.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 77% 772.3

Sequence Analysis Tools

View WP_106709045.1 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

MRAQPKASHFINGRFVEDKAGKPLDVIYPATGEIIARLFGATPVLIEQAVQAAAAAQPAW
AALKPVERGRILRRAADILRERNAEIAELETLDTGKAIQETLVADPASAADALEFYGGII
AGFNGEMIELGGSYAYTRREPLGVCVGIGAWNYPIQGAGWKSAPALAAGNAMIFKPSENT
PLSALALAEIYKEAGLPDGLFNVVQGFGDVGSQLVDHPLVAKVSLTGSVPTGRRVLAQAG
SHMKHATMELGGKSPLIIFDDADVENAVGGALLGNFYSTGQVCSNGTRVFVQGGIKDKFL
DRLTARTKAIRLGDPLDPDIHLGPLVNAAQRNKVVSYIEKGKAEGATLHLGGGVPQMQGF
EGGCFVEPTIFTNVTDDMVIAREEIFGPVMAVLDFKDEDEVIARANDTEFGLSAGVFTKD
LSRAHRVISQLKAGTCWINTYNLAPVEMPFGGFKQSGVGRENGLAALYHYSQIKSVYVET
GKVESPY

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