GapMind for catabolism of small carbon sources

 

Protein 5210745 in Shewanella loihica PV-4

Annotation: FitnessBrowser__PV4:5210745

Length: 485 amino acids

Source: PV4 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
L-arginine catabolism davD med Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 100% 597.8 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.5
L-citrulline catabolism davD med Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 100% 597.8 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.5
L-lysine catabolism davD med Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 100% 597.8 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.5
L-proline catabolism davD med Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 61% 100% 597.8 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.5
L-arginine catabolism gabD med succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 59% 99% 586.3 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.5
L-citrulline catabolism gabD med succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 59% 99% 586.3 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.5
putrescine catabolism gabD med succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 59% 99% 586.3 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.5
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 92% 517.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 92% 517.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 92% 517.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 92% 517.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 92% 517.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 92% 517.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 92% 517.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-arabinose catabolism xacF med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 40% 97% 342.8 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
D-galacturonate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 40% 97% 342.8 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
D-glucuronate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 40% 97% 342.8 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
D-xylose catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 40% 97% 342.8 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 39% 95% 330.1 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 39% 95% 330.1 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 39% 95% 330.1 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 98% 317.4 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 98% 317.4 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 98% 317.4 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 98% 317.4 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 98% 317.4 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 38% 95% 309.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 302 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 302 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 302 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 302 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 98% 301.6 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
4-hydroxybenzoate catabolism praB lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 35% 96% 297.7 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 35% 96% 297.7 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-tryptophan catabolism praB lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 35% 96% 297.7 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 269.2 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 269.2 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 269.2 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 269.2 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 269.2 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 98% 269.2 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 33% 95% 223.8 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 33% 95% 223.8 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8
L-lysine catabolism amaB lo L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 31% 93% 201.4 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 61% 597.8

Sequence Analysis Tools

View 5210745 at FitnessBrowser

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MQGIKDTQLIKLSSYIDGRWTVGEQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRAL
PEWSKRSANERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAE
EGKRVYGDTIPAPANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARP
SPLTPLSALAMAELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKI
LLAQCATSVKKVSMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKG
VAAAFTEKFTAAVANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQP
SELGESFLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYA
RDIGRIFRVAEGLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIKYLCL
GGLDK

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