GapMind for catabolism of small carbon sources

 

Protein WP_104913346.1 in Pontimonas salivibrio CL-TW6

Annotation: NCBI__GCF_002950575.1:WP_104913346.1

Length: 486 amino acids

Source: GCF_002950575.1 in NCBI

Candidate for 36 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 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 408.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 43% 391.7
2'-deoxyinosine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 408.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 43% 391.7
2-deoxy-D-ribose catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 408.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 43% 391.7
ethanol catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 408.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 43% 391.7
L-threonine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 408.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 43% 391.7
thymidine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 408.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 43% 391.7
L-tryptophan catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 408.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 43% 391.7
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 96% 387.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 96% 387.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 96% 387.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 91% 368.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 94% 342.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 94% 342.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 94% 342.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 94% 342.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 94% 335.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 94% 335.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 94% 335.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 95% 343.6 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 95% 343.6 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 38% 94% 315.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 98% 285.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 34% 99% 281.6 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 34% 99% 281.6 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 35% 96% 281.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 35% 96% 281.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 35% 96% 281.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 35% 96% 281.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
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) 32% 92% 223.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
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) 32% 92% 223.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
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) 32% 92% 223.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
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) 32% 92% 223.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
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) 32% 92% 223.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 34% 90% 221.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 34% 90% 221.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 30% 86% 194.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 53% 501.9

Sequence Analysis Tools

View WP_104913346.1 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

MGFLDYSPAPESTGIVSLADEYGLFINGEFRPGRGGVFDSISPATEEVLTRFSEASEEDV
DYAIGQARAAYDKVWSKMPGRERSKYLFRIARIVQERSRELAIAETMDNGKPIKETRDVD
IPLVAAWFFYYAGWADKLEEATGSHQPHAWGVVGQVIPWNFPLMMLAWKVAPALAAGNTV
VLKPAETTSVTAMLFAEICQQAGVPAGVVNIVTGAGATGRALVSHAGIDKVAFTGSTPVG
REIAKTLAGRPTALTLELGGKGANIVFDDAAMDEAVEGIISGIFFNQGHVCCAGSRLLVQ
ENVHDELLARLTSRIQTLRLGDPLDKNTDIGAINSRAQLDTISTLTQSGVDEGASIWQSD
CALPERGFWFPPTVFTDVSTSHRIAQDEIFGPVLSVLTFRTPDEAVAKANNTPYGLSAGV
WTEKASRMLAVVDRLRAGVVWSNTFNKFDPTSPFGGYQESGYGREGGLPGLLSYLRPHSV
PAGGKQ

This GapMind analysis is from Sep 24 2021. 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