GapMind for catabolism of small carbon sources

 

Protein WP_048507183.1 in Chryseobacterium angstadtii KM

Annotation: NCBI__GCF_001045465.1:WP_048507183.1

Length: 482 amino acids

Source: GCF_001045465.1 in NCBI

Candidate for 23 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 lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 36% 97% 281.2 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 36% 97% 281.2 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-arginine catabolism gabD lo Putative succinate-semialdehyde dehydrogenase C139.05 [NADP(+)]; SSDH; EC 1.2.1.16 (characterized) 36% 96% 272.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-citrulline catabolism gabD lo Putative succinate-semialdehyde dehydrogenase C139.05 [NADP(+)]; SSDH; EC 1.2.1.16 (characterized) 36% 96% 272.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
putrescine catabolism gabD lo Putative succinate-semialdehyde dehydrogenase C139.05 [NADP(+)]; SSDH; EC 1.2.1.16 (characterized) 36% 96% 272.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 34% 100% 261.2 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 97% 256.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 97% 256.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 97% 256.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 97% 256.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 97% 256.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 34% 91% 255.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 34% 99% 250 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 34% 99% 250 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 34% 99% 250 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 34% 99% 250 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 94% 224.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 94% 224.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 94% 224.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 94% 224.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 87% 170.2 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 87% 170.2 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 30% 74% 157.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 36% 309.3

Sequence Analysis Tools

View WP_048507183.1 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

MNTTALNWIGGEWIDNGNYRESSNPANGEKIGFFADGGKEEAAQGIAAAKKAFKETSWKT
DRQLRYKVLNELADQFEIHHEELVDMLTLENGKIRGEAEFEFGLVVPKLRYFAAHVLTQH
GRALETSPGSFSVVLTEAIGVAGVIAPWNSPIILMIRSLAPALAAGCTAIIKMPAQTAQV
NALINKVFASVKSLPKGVINQFTESGSEGAALIVESPDVPAVSYTGSTHTGKILMHNGAP
QLKRFGFELGGKTPMLIFDDANLDVAVPTLEKAITVFAGQFCMTGSRILVQKGIADELIK
KLSERLENVKVGPAADSRSDMGPMIDKANVERVDKIVEKAISEGAEVRVRGGKITEGPLA
SGAFYRPTLLQVSDNKLEIIQDETFGPVATVQVFETAQEAVELANDNVYGLAASVWSQDV
DLPLKIVRELEAGTVWINAWAEVRDEFEEGGYKLSGLGRLNGLASLNDFLEHKHIVHQHG
TI

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