GapMind for catabolism of small carbon sources

 

Protein WP_010178330.1 in Aquimarina agarilytica ZC1

Annotation: NCBI__GCF_000255455.1:WP_010178330.1

Length: 481 amino acids

Source: GCF_000255455.1 in NCBI

Candidate for 49 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 43% 99% 417.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-fucose catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 43% 99% 417.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-rhamnose catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 43% 99% 417.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-threonine catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 43% 99% 417.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
D-xylose catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 43% 99% 417.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-arginine catabolism gabD med succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 40% 97% 364.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-citrulline catabolism gabD med succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 40% 97% 364.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
putrescine catabolism gabD med succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 40% 97% 364.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 97% 354.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 97% 354.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 97% 354.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 97% 354.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
4-hydroxybenzoate catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) 39% 91% 325.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
2'-deoxyinosine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) 39% 91% 325.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
2-deoxy-D-ribose catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) 39% 91% 325.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
ethanol catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) 39% 91% 325.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-threonine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) 39% 91% 325.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
thymidine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) 39% 91% 325.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-tryptophan catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized) 39% 91% 325.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-arabinose catabolism xacF lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 39% 99% 322.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
D-galacturonate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 39% 99% 322.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
D-glucuronate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 39% 99% 322.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 92% 322.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
D-xylose catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 39% 99% 322.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 309.7 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 309.7 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 96% 307.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 96% 307.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 96% 307.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 36% 96% 285 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 36% 96% 285 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 36% 96% 285 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 36% 96% 285 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 35% 100% 278.9 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-tryptophan catabolism nbaE lo 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized) 35% 98% 271.9 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
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% 271.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
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% 271.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
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% 271.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
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% 271.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
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% 271.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 243 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 243 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 243 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 243 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 243 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 243 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 33% 92% 233 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 33% 84% 182.6 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 33% 84% 182.6 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 66% 663.3

Sequence Analysis Tools

View WP_010178330.1 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

MSAKKYQLFIGGEWVDSTTGKTAEITSPIDESVVGEVAMGVEEDANIALEAAEKAQKEWK
KVPARKRAELMRKFAAEIRANKAYLADLLTREQGKIISLAEIEVEVTATFIEYACDWARH
IEGDILPSDNENEHIYIHKIPRGVVVAITAWNFPLALAGRKLGPALVAGNAVVIKPTQET
PLATLELGFLAEKVGLPKGLLNVVTGSGRVLGNALVENPITKMVTMTGSTPAGQSIFKAA
AKNLTHVQLELGGKAPSIVFADADIDVAVDATFNSRFDNCGQVCTCNERMYVHEDIYDVF
MEKFMEKVKSFKVGNPLNRDTQMGPKVNANELKNMEHLVKVSLEEGATLAHGGKRPEGAE
FEKGHWFEPTVLTDVTQDMTIVHEESFGPILPVIKFTDFDQVIGYANDCEYGLAAMVFTK
DMATILRCNDELECGEIYVNRGHGEQHQGFHNGYKLSGSGGEDGKYGFEQYLEKKTFYVK
Y

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