GapMind for catabolism of small carbon sources

 

Protein Ga0059261_3374 in Sphingomonas koreensis DSMZ 15582

Annotation: FitnessBrowser__Korea:Ga0059261_3374

Length: 474 amino acids

Source: Korea in FitnessBrowser

Candidate for 44 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 50% 99% 451.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 50% 99% 451.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 50% 99% 451.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
ethanol catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 50% 99% 451.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-threonine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 50% 99% 451.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
thymidine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 50% 99% 451.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 50% 99% 451.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 40% 94% 320.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 40% 94% 320.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 40% 94% 320.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 38% 96% 305.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 38% 96% 305.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 38% 96% 296.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
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) 37% 88% 288.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
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) 37% 88% 288.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
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) 37% 88% 288.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 95% 287.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 95% 287.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 95% 287.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 95% 287.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-arabinose catabolism xacF lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 98% 279.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
D-galacturonate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 98% 279.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
D-glucuronate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 98% 279.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
D-xylose catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 98% 279.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 36% 95% 277.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 36% 97% 273.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 36% 97% 273.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 36% 97% 273.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 36% 97% 273.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 36% 97% 273.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 34% 99% 243.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase; MSA dehydrogenase; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase; MMSA dehydrogenase; MSDH; EC 1.2.1.27 (uncharacterized) 34% 97% 239.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 239.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 239.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 239.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 239.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 239.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
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) 33% 94% 229.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
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) 33% 94% 229.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
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) 33% 94% 229.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
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) 33% 94% 229.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
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) 33% 94% 229.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 34% 92% 198 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 34% 92% 198 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 55% 504.2

Sequence Analysis Tools

View Ga0059261_3374 at FitnessBrowser

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

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Sequence

MRSYLKHYIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDSFSR
TSVDERIALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHLMSTINALKA
FEFSEQIGQSLVVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSAA
IFAEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQVAKNAAETVK
RVHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAAQIAS
GLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDGIETGYF
VKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLSAVLFGSPEEVKR
VAPRLRAGMVYINGGQPDPSLPFGGYKQSGNGREHGKFGLAEFMEVKAMVGALA

This GapMind analysis is from Sep 17 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