GapMind for catabolism of small carbon sources

 

Protein WP_089229754.1 in Tistlia consotensis USBA 355

Annotation: NCBI__GCF_900177295.1:WP_089229754.1

Length: 477 amino acids

Source: GCF_900177295.1 in NCBI

Candidate for 43 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 med 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 58% 91% 545 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
2'-deoxyinosine catabolism adh med 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 58% 91% 545 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
2-deoxy-D-ribose catabolism adh med 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 58% 91% 545 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
ethanol catabolism adh med 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 58% 91% 545 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-threonine catabolism adh med 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 58% 91% 545 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
thymidine catabolism adh med 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 58% 91% 545 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-tryptophan catabolism adh med 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 58% 91% 545 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-arginine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 56% 95% 532.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-citrulline catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 56% 95% 532.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
putrescine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 56% 95% 532.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 44% 96% 394 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 44% 96% 394 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 44% 91% 392.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 355.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 355.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 355.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-tryptophan catabolism nbaE med aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 41% 96% 354.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 346.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-arginine catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 346.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 346.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-citrulline catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 346.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 346.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
putrescine catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 94% 346.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 98% 349.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 95% 349 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 312.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 312.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 312.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 312.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 34% 95% 257.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
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) 34% 93% 256.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
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) 34% 93% 256.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
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) 34% 93% 256.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
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) 34% 93% 256.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
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) 34% 93% 256.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 93% 253.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 93% 253.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 93% 253.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 93% 253.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 93% 253.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
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% 219.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
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% 219.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7
L-lysine catabolism amaB lo L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 31% 94% 211.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 60% 584.7

Sequence Analysis Tools

View WP_089229754.1 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

MGSGFAEAGSGQSFETRDPATGEVLAEVQVAGEAAVEAAVAAAEAGFRVWSRMTGTERGR
VLRRAAEIVRARNDELSEIETRDTGKPIQETLVADAASGADCLEYYGGLAGSLAGEHIDL
GHAFAYTRREPLGICAGIGAWNYPIQIACWKSAPALACGNAMIFKPAELTPLTAVKLAEI
YREAGLPDGVFNVVQGFAETGRLLTRHPKIAKVSLTGEVGTGRKVMADAAGGLKHVTLEL
GGKSPILVFEDADLDRAVSGALLGNFFSAGEVCSNGTRVFVQESVRAAFLEKLVARTEAM
TVGDPLDPATQVGALISEGHMAKVLGYIETGKAEGATALTGGGRITEGACAKGWFVAPTV
FDGCRDDMTVVREEIFGPVMAVLSFEDEEEAIRRANATDFGLSAGVFTRDLARAHRTIAR
LQAGTCWINTYNVTPVEMPFGGVKQSGLGRENGKAAIEHYSQLKSVYVELDEIEAPY

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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