GapMind for catabolism of small carbon sources

 

Protein WP_012114716.1 in Xanthobacter autotrophicus Py2

Annotation: NCBI__GCF_000017645.1:WP_012114716.1

Length: 493 amino acids

Source: GCF_000017645.1 in NCBI

Candidate for 42 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 med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 55% 96% 535.4 aldehyde dehydrogenase 59% 563.1
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 55% 96% 535.4 aldehyde dehydrogenase 59% 563.1
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 55% 96% 535.4 aldehyde dehydrogenase 59% 563.1
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 55% 96% 535.4 aldehyde dehydrogenase 59% 563.1
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 96% 477.6 aldehyde dehydrogenase 59% 563.1
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 96% 477.6 aldehyde dehydrogenase 59% 563.1
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 96% 477.6 aldehyde dehydrogenase 59% 563.1
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 96% 477.6 aldehyde dehydrogenase 59% 563.1
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 96% 477.6 aldehyde dehydrogenase 59% 563.1
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 96% 477.6 aldehyde dehydrogenase 59% 563.1
4-hydroxybenzoate catabolism adh med Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) 44% 91% 414.8 aldehyde dehydrogenase 59% 563.1
2'-deoxyinosine catabolism adh med Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) 44% 91% 414.8 aldehyde dehydrogenase 59% 563.1
2-deoxy-D-ribose catabolism adh med Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) 44% 91% 414.8 aldehyde dehydrogenase 59% 563.1
ethanol catabolism adh med Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) 44% 91% 414.8 aldehyde dehydrogenase 59% 563.1
L-threonine catabolism adh med Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) 44% 91% 414.8 aldehyde dehydrogenase 59% 563.1
thymidine catabolism adh med Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) 44% 91% 414.8 aldehyde dehydrogenase 59% 563.1
L-tryptophan catabolism adh med Aldehyde dehydrogenase family 2 member B4, mitochondrial; ALDH2a; EC 1.2.1.3 (characterized) 44% 91% 414.8 aldehyde dehydrogenase 59% 563.1
L-phenylalanine catabolism pad-dh med phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 46% 94% 390.6 aldehyde dehydrogenase 59% 563.1
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 99% 358.2 aldehyde dehydrogenase 59% 563.1
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 99% 358.2 aldehyde dehydrogenase 59% 563.1
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 95% 324.3 aldehyde dehydrogenase 59% 563.1
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 95% 324.3 aldehyde dehydrogenase 59% 563.1
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 95% 324.3 aldehyde dehydrogenase 59% 563.1
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 36% 95% 310.5 aldehyde dehydrogenase 59% 563.1
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 99% 307.8 aldehyde dehydrogenase 59% 563.1
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 97% 292.7 aldehyde dehydrogenase 59% 563.1
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 97% 292.7 aldehyde dehydrogenase 59% 563.1
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 97% 292.7 aldehyde dehydrogenase 59% 563.1
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 97% 292.7 aldehyde dehydrogenase 59% 563.1
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 35% 95% 247.3 aldehyde dehydrogenase 59% 563.1
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 94% 243 aldehyde dehydrogenase 59% 563.1
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 94% 243 aldehyde dehydrogenase 59% 563.1
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 94% 243 aldehyde dehydrogenase 59% 563.1
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 94% 243 aldehyde dehydrogenase 59% 563.1
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 94% 243 aldehyde dehydrogenase 59% 563.1
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 36% 85% 226.1 aldehyde dehydrogenase 59% 563.1
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 36% 85% 226.1 aldehyde dehydrogenase 59% 563.1
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 36% 85% 226.1 aldehyde dehydrogenase 59% 563.1
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 36% 85% 226.1 aldehyde dehydrogenase 59% 563.1
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 36% 85% 226.1 aldehyde dehydrogenase 59% 563.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 225.3 aldehyde dehydrogenase 59% 563.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 225.3 aldehyde dehydrogenase 59% 563.1

Sequence Analysis Tools

View WP_012114716.1 at NCBI

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

Fitness BLAST: loading...

Sequence

MAAAERTADHYPSFRTQALIDGVFAPAASGRTFDAVNPATGKVLAQVAACDSADVDRAVK
AARAAFEDRRWAGLRPVERKRILQRFAELIRAHRDELALTETLNMGKPIADARSIDVRAA
ADCFAYYGECCDKVYGEVAPTTADNLALVLREPLGVVGCVTPWNFPMIMAAWKVAPALAM
GNSVVLKPAEESPLTALRLGELALEAGVPAGVFNVVPGLGVEAGKALGLHMDVDAIAFTG
STEVGRYFLRYSSDSNLKRVFLELGGKTAFVVAHDVPDLDEVAQAVASGIFFNQGEMCTA
ASRLLVDNRIREDLVARVAALAPRWMPGDPQDPAARAGAVVSFEHQGRILSAIEEGVASG
ALLVTGGTAVRQETGGAFVAPTVFDGVVPSSALAQKEIFGPVLSVIGFDGLEEAVAIANG
TVYGLGAAVWSGDLSAAHKVARRFKAGIVYVNCFDADDITTPFGGVKQSGFGRDKSLHAL
DKYCDLKTVWTRL

This GapMind analysis is from Apr 09 2024. 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