GapMind for catabolism of small carbon sources

 

Protein WP_027180003.1 in Maridesulfovibrio bastinii DSM 16055

Annotation: NCBI__GCF_000429985.1:WP_027180003.1

Length: 478 amino acids

Source: GCF_000429985.1 in NCBI

Candidate for 39 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism aldA hi lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 56% 99% 541.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 45% 434.9
L-rhamnose catabolism aldA hi lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 56% 99% 541.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 45% 434.9
L-threonine catabolism aldA hi lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 56% 99% 541.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 45% 434.9
L-arabinose catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 56% 99% 541.2 NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) 56% 541.2
D-xylose catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 56% 99% 541.2 NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) 56% 541.2
L-arginine catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 35% 88% 310.8 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-citrulline catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 35% 88% 310.8 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
putrescine catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 35% 88% 310.8 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 310.5 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 310.5 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 310.5 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 310.5 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
4-hydroxybenzoate catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 33% 96% 286.6 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
2'-deoxyinosine catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 33% 96% 286.6 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
2-deoxy-D-ribose catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 33% 96% 286.6 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
ethanol catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 33% 96% 286.6 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-threonine catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 33% 96% 286.6 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
thymidine catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 33% 96% 286.6 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-tryptophan catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 33% 96% 286.6 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 36% 94% 283.9 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 36% 94% 283.9 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 36% 94% 283.9 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 34% 92% 273.1 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 34% 95% 266.2 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 31% 96% 262.3 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 31% 96% 262.3 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
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) 34% 92% 257.7 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
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) 34% 92% 257.7 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
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) 34% 92% 257.7 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
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) 34% 92% 257.7 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
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) 34% 92% 257.7 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 96% 245.4 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 96% 245.4 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 96% 245.4 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 96% 245.4 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 31% 98% 235 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-lysine catabolism amaB lo L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 30% 96% 205.7 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 31% 94% 179.5 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 31% 94% 179.5 lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) 56% 541.2

Sequence Analysis Tools

View WP_027180003.1 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

MKTYQQYIDGKFCESHSKDIIEVENPYTGEIIAHAPNGDVEDAEKALEAAEKAQPSWAAL
PVAERAGYLKKMAQAIRDNRKMLADTLTEEQAKVSGLAQVEIDVTAEYFDYYAGWARKYE
GEVIQSDRPKENILLYRQPIGVIVGICPWNFPFFVMARKVAPSLLTGSSIVLKPSSDTPN
TTFEFAKLVDQLGLPGGVANFVSGRGSTLGSALVKSPKTGMVTLTGSVEAGQRIIADSAP
NITKTSLELGGKAPCIVCKDADLDLAVKAIVASRVIFSGQVCNCAERVYVESAVADEFMA
KLTKAMSEVTYGDPFKDPNPDMSTQVNKGQLEKIEAMVAKAKTEGAEVLVGGERPAEMKT
GYFYKPTLLGNCSQDMEIIRKEIFGPVLPVVTVSDFDEALALSNDCEYGLTSSVFTTSIE
KMMRAINELKFGETYVNREHFEAMQGFHAGWRKSGIGGADGKHGLYEYLQTHVAYIQY

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