GapMind for catabolism of small carbon sources

 

Protein WP_057507564.1 in Stenotrophomonas chelatiphaga DSM 21508

Annotation: NCBI__GCF_001431535.1:WP_057507564.1

Length: 501 amino acids

Source: GCF_001431535.1 in NCBI

Candidate for 43 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-valine catabolism mmsA hi Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 80% 100% 823.5
L-valine catabolism mmsA hi mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27) (TIGR01722) 100% 737.3
L-isoleucine catabolism iolA hi Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 59% 91% 600.5
myo-inositol catabolism mmsA hi Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 59% 91% 600.5
propionate catabolism iolA hi Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 59% 91% 600.5
L-threonine catabolism iolA hi Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 59% 91% 600.5
L-valine catabolism iolA hi Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 59% 91% 600.5
L-arabinose catabolism xacF lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 35% 98% 264.6 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
D-galacturonate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 35% 98% 264.6 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
D-glucuronate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 35% 98% 264.6 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
D-xylose catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 35% 98% 264.6 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 98% 253.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 98% 253.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 98% 253.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
4-hydroxybenzoate catabolism adh lo Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 33% 96% 248.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
2'-deoxyinosine catabolism adh lo Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 33% 96% 248.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
2-deoxy-D-ribose catabolism adh lo Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 33% 96% 248.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
ethanol catabolism adh lo Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 33% 96% 248.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-threonine catabolism adh lo Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 33% 96% 248.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
thymidine catabolism adh lo Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 33% 96% 248.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-tryptophan catabolism adh lo Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 33% 96% 248.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 32% 97% 234.6 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 32% 97% 234.6 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 32% 98% 233.8 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 32% 98% 233.8 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 32% 98% 233.8 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 32% 97% 229.6 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-arginine catabolism gabD lo Putative succinate-semialdehyde dehydrogenase C139.05 [NADP(+)]; SSDH; EC 1.2.1.16 (characterized) 32% 94% 216.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-citrulline catabolism gabD lo Putative succinate-semialdehyde dehydrogenase C139.05 [NADP(+)]; SSDH; EC 1.2.1.16 (characterized) 32% 94% 216.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
putrescine catabolism gabD lo Putative succinate-semialdehyde dehydrogenase C139.05 [NADP(+)]; SSDH; EC 1.2.1.16 (characterized) 32% 94% 216.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 33% 90% 213 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 33% 90% 213 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 33% 90% 213 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 33% 90% 213 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 33% 90% 213 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 30% 95% 204.5 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 96% 203.4 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 96% 203.4 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 96% 203.4 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 96% 203.4 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 97% 201.4 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 32% 78% 177.9 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 92% 171 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 92% 171 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 80% 823.5

Sequence Analysis Tools

View WP_057507564.1 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

MTVAAPRIRLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFKT
WRKTPIGTRARIFLKYQQLIRENMSELAHTLSAEQGKTVPDAEGDVFRGLEVVEHAAAIG
NLQLGELANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSE
QDPMVTMRLVELALEAGIPKGVLNVVHGGEEVVNAICDHPDIKAVSFVGSTRVGTHVYNR
ASLAGKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEARSW
VPDLVAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDG
FEKGNFVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQ
SGAAARKFQEDIDVGQVGINVPIPVPVPLFSFTGSRASKLGDLGPYGKQVVMFYTQTKTI
TARWFDDETLGHGVNTTISLK

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