GapMind for catabolism of small carbon sources

 

Protein 6938534 in Shewanella amazonensis SB2B

Annotation: FitnessBrowser__SB2B:6938534

Length: 480 amino acids

Source: SB2B in FitnessBrowser

Candidate for 47 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized) 83% 100% 808.1
L-citrulline catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized) 83% 100% 808.1
putrescine catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized) 83% 100% 808.1
L-arginine catabolism davD hi Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 73% 100% 719.5
L-citrulline catabolism davD hi Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 73% 100% 719.5
L-lysine catabolism davD hi Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 73% 100% 719.5
L-proline catabolism davD hi Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 73% 100% 719.5
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 91% 520.4 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 91% 520.4 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 91% 520.4 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 91% 520.4 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 91% 520.4 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 91% 520.4 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 54% 91% 520.4 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
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) 41% 98% 360.1 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
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) 41% 98% 360.1 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
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) 41% 98% 360.1 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
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) 41% 98% 360.1 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 98% 336.7 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 98% 336.7 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 98% 336.7 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 98% 336.7 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 98% 336.7 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 37% 97% 315.1 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 310.8 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 310.8 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 36% 96% 304.7 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 36% 96% 304.7 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 36% 96% 304.7 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 303.9 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 303.9 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 303.9 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 96% 303.9 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 34% 97% 284.6 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 244.6 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 244.6 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 244.6 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 244.6 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 244.6 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 90% 226.1 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 90% 226.1 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 90% 226.1 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 90% 226.1 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 90% 226.1 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-lysine catabolism amaB lo Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized) 31% 86% 221.9 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 214.5 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 214.5 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] 83% 808.1

Sequence Analysis Tools

View 6938534 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MQLKRPSLLKTKCYINGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAA
LPAWRALTAKERGAKLRRWYELMLENADDLALMMTTEQGKPLAEAKGEVVYAASFIEWFA
EEAKRLYGDTIPGHQGDKRIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVK
PAPQTPFTALALAELAAEAGIPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIK
LMQQCAPTLKKVSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDG
VYDAFAQKLAAAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGKP
LGGNFMEPAIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGRD
ISLIWKVAEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEIKYICLSV

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