GapMind for catabolism of small carbon sources

 

Protein WP_038806127.1 in Streptococcus oralis 7747

Annotation: NCBI__GCF_000382825.1:WP_038806127.1

Length: 474 amino acids

Source: GCF_000382825.1 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-fucose catabolism aldA lo Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 38% 100% 319.3 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-rhamnose catabolism aldA lo Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 38% 100% 319.3 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-threonine catabolism aldA lo Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 38% 100% 319.3 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 94% 293.5 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 94% 293.5 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 94% 293.5 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 94% 293.5 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized) 37% 99% 292 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized) 37% 99% 292 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized) 37% 99% 292 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 98% 285.8 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 98% 285.8 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 98% 285.8 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 98% 285.8 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
4-hydroxybenzoate catabolism adh lo Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 33% 97% 259.6 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
2'-deoxyinosine catabolism adh lo Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 33% 97% 259.6 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
2-deoxy-D-ribose catabolism adh lo Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 33% 97% 259.6 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
ethanol catabolism adh lo Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 33% 97% 259.6 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-threonine catabolism adh lo Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 33% 97% 259.6 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
thymidine catabolism adh lo Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 33% 97% 259.6 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-tryptophan catabolism adh lo Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized) 33% 97% 259.6 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-arginine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 257.7 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 257.7 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-citrulline catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 257.7 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 257.7 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
putrescine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 257.7 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 94% 257.7 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-phenylalanine catabolism pad-dh lo Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized) 34% 96% 246.1 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
4-hydroxybenzoate catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 31% 98% 238 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-tryptophan catabolism nbaE lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 31% 98% 238 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-tryptophan catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 31% 98% 238 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 95% 236.5 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
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) 32% 89% 235.3 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
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) 32% 89% 235.3 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
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) 32% 89% 235.3 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
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) 32% 89% 235.3 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
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) 32% 89% 235.3 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized) 31% 98% 231.9 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 96% 231.1 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 96% 231.1 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 96% 231.1 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 96% 231.1 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 96% 231.1 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 94% 224.9 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 94% 224.9 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 32% 99% 220.3 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-lysine catabolism amaB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 30% 84% 213.4 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 91% 207.2 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 91% 207.2 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 73% 695.7

Sequence Analysis Tools

View WP_038806127.1 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

MTNYQNLVNGNWKSSEKEITIYSPINQEKLGTVPAMSQAEVDEAMKAARAALPAWRDLAP
VERAAYLHKTADILERDKEKIGTILAKEVAKGIKAAIGEVVRTADLIRFAAEEGLRITGQ
AMEGGGFEAASKNKLAVVRREPVGVVLAIAPFNYPVNLSGSKIAPALIAGNVVMFKPPTQ
GSISGLLLAKAFDEAGIPAGVFNTITGRGSEIGDYIIEHKEVNFINFTGSTPIGERIGRL
AGMRPIMLELGGKDAAIVLEDADLEHAAKQIVGGAFSYSGQRCTAIKRVLVVESVADRLA
ELLQAEVAKLTVGDPFDNADITPVVDNASADFIWGLIQDAQEKGAKALSPIKREGNLIWP
GLFDYVTRDMKLAWEELFGPVLPIIRVADANEAVAIANESEFGLQSSVFTNDFKKAFEIA
EKLEVGTVHINNKTQRGPDNFPFLGVKGSGAGVQGIKYSIEAMTNVKSIVFDVK

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