GapMind for catabolism of small carbon sources

 

Protein 7025957 in Shewanella sp. ANA-3

Annotation: FitnessBrowser__ANA3:7025957

Length: 498 amino acids

Source: ANA3 in FitnessBrowser

Candidate for 40 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism kauB hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 73% 100% 760.8 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 56% 564.3
L-arginine catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 73% 100% 760.8 aldehyde dehydrogenase 54% 543.9
L-citrulline catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 73% 100% 760.8 aldehyde dehydrogenase 54% 543.9
putrescine catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 73% 100% 760.8 aldehyde dehydrogenase 54% 543.9
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 56% 98% 564.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 56% 98% 564.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 56% 98% 564.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 56% 98% 564.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 56% 98% 564.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 56% 98% 564.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
4-hydroxybenzoate catabolism adh med Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 43% 95% 413.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
2'-deoxyinosine catabolism adh med Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 43% 95% 413.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
2-deoxy-D-ribose catabolism adh med Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 43% 95% 413.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
ethanol catabolism adh med Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 43% 95% 413.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-threonine catabolism adh med Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 43% 95% 413.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
thymidine catabolism adh med Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 43% 95% 413.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-tryptophan catabolism adh med Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized) 43% 95% 413.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 44% 92% 402.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 364 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 364 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 364 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 329.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 329.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-tryptophan catabolism nbaE lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 36% 97% 308.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-arabinose catabolism xacF lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 94% 293.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
D-galacturonate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 94% 293.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
D-glucuronate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 94% 293.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
D-xylose catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 94% 293.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 290.8 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 290.8 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 290.8 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 290.8 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 246.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 246.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 246.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 246.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 246.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 246.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 94% 204.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 94% 204.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 73% 760.8

Sequence Analysis Tools

View 7025957 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

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Sequence

MSTPKKRSDWESLAASLAINGKAYINGEYRDAAAGSTFDCVSPIDGRVLAKVASCDQMDA
NIAVANAREVFESGVWSKTAPVKRKQVMIRFAELLEENANELALLETLDMGKPIRFSKAV
DIAGAARAIRWSGEAVDKLYDELAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLG
PALATGNSVILKPSEKSPLTAIRIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDT
LVFTGSTKIAKQLMIYAGESNMKRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIAFNQG
EVCTAGSRLLVESGVKDQLIELIAEELASWQPGHPLDPATVSGAVVDKQQLDTILSYIKA
GQDEGASLVHGGQQVLAETGGVYVQPTIFSQVNNKMKIASEEIFGPVLSVIEFNGMEEAI
AIANDTIYGLAAGVWTADISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDK
SMHSFDKYTEIKATWIAL

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