GapMind for catabolism of small carbon sources

 

Protein 3609634 in Dinoroseobacter shibae DFL-12

Annotation: FitnessBrowser__Dino:3609634

Length: 780 amino acids

Source: Dino in FitnessBrowser

Candidate for 32 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 hi acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized) 62% 100% 971.8 Aldehyde dehydrogenase family 16 member A1 39% 498.8
2'-deoxyinosine catabolism adh hi acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized) 62% 100% 971.8 Aldehyde dehydrogenase family 16 member A1 39% 498.8
2-deoxy-D-ribose catabolism adh hi acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized) 62% 100% 971.8 Aldehyde dehydrogenase family 16 member A1 39% 498.8
ethanol catabolism adh hi acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized) 62% 100% 971.8 Aldehyde dehydrogenase family 16 member A1 39% 498.8
L-threonine catabolism adh hi acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized) 62% 100% 971.8 Aldehyde dehydrogenase family 16 member A1 39% 498.8
thymidine catabolism adh hi acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized) 62% 100% 971.8 Aldehyde dehydrogenase family 16 member A1 39% 498.8
L-tryptophan catabolism adh hi acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized) 62% 100% 971.8 Aldehyde dehydrogenase family 16 member A1 39% 498.8
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 44% 88% 346.3 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 96% 341.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 96% 341.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 94% 336.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 94% 336.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 94% 336.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 40% 94% 319.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 40% 94% 319.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 40% 94% 319.7 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 312.8 Aldehyde dehydrogenase family 16 member A1 39% 498.8
L-arginine catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 312.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 312.8 Aldehyde dehydrogenase family 16 member A1 39% 498.8
L-citrulline catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 312.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 312.8 Aldehyde dehydrogenase family 16 member A1 39% 498.8
putrescine catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 312.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-arginine catabolism kauB med gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 94% 312.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 39% 96% 313.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 32% 94% 222.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 31% 96% 210.3 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 31% 96% 210.3 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 51% 98.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 51% 98.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 51% 98.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 51% 98.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 51% 98.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 63% 971.8

Sequence Analysis Tools

View 3609634 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

MTVKEIFETMEYGPAPEDDGPAQAWLDRHGRRFGVFIGGTFQAPGKTFATRNPARGTELA
QVTQGTEADIEAAVTAARRAQPAWARLGGQGWARVLYAIARLLQKHSRLFAVLETLDNGK
PIRESRDIDIPLAQRHFYYHAGMAALMEDELPDRVPVGVCGQIVPWNFPLLMLAWKIAPA
LAMGNTVVLKPAEWTPLTALLFAEICGEAGVPPGVVNIVTGDGATGAALVSHPGVDKIAF
TGSTDVGREIRRATAGTGKALTLELGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVCCA
GSRLLVQEGIAEAFYAKLRARMATLRIGDPLDKCIDVGAMVDPAHCAKVAEMVAGSNGEV
HQPGTVPAEGAFYPPTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLA
ATLWSENINRALDIAPKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEGLRAYTKQ
AAPPKALVPVAAIPAPAAPKPGGLDRTAKMYIGGKQARPDSGYSRPVWSPKGVLLGHAPE
GSRKDIRNAVEAATGAASWGRTTGHLRAQILYYVAENLSARTEEFATRIAEMTGSRVPRA
EAEVSAAIDRLFTYAAWADKYDGAVKPVPIRGVALAMPEPVGVIGAFAPDDAPLLGAVSI
LGAALAMGNRLVLVPSEPFPLAATDLYQVLDTSDVPAGVVNIVTGAHEALAKPLASHLGV
DAVWSFSGADISTTIEAEAAGNLKRTWVNHGRARDWMQVDARSFLAQATETKTIWVPYGA

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