GapMind for catabolism of small carbon sources

 

Protein WP_104913707.1 in Pontimonas salivibrio CL-TW6

Annotation: NCBI__GCF_002950575.1:WP_104913707.1

Length: 478 amino acids

Source: GCF_002950575.1 in NCBI

Candidate for 41 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 49% 99% 446.4 cumic aldehyde dehydrogenase (EC 1.2.1.29) 40% 347.4
L-citrulline catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 49% 99% 446.4 cumic aldehyde dehydrogenase (EC 1.2.1.29) 40% 347.4
L-lysine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 49% 99% 446.4 cumic aldehyde dehydrogenase (EC 1.2.1.29) 40% 347.4
putrescine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 49% 99% 446.4 cumic aldehyde dehydrogenase (EC 1.2.1.29) 40% 347.4
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 40% 95% 342 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 40% 95% 342 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 40% 95% 342 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
ethanol catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 40% 95% 342 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-threonine catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 40% 95% 342 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
thymidine catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 40% 95% 342 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-tryptophan catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 40% 95% 342 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 40% 96% 329.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 94% 320.9 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 94% 320.9 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 94% 320.9 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 99% 300.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 99% 300.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 96% 298.5 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 96% 298.5 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 96% 298.5 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 95% 292.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 283.5 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 283.5 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 283.5 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 96% 283.5 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 34% 97% 266.2 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-arabinose catabolism xacF lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 34% 99% 265.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
D-galacturonate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 34% 99% 265.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
D-glucuronate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 34% 99% 265.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
D-xylose catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 34% 99% 265.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 98% 264.2 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 98% 264.2 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase; MSA dehydrogenase; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase; MMSA dehydrogenase; MSDH; EC 1.2.1.27 (uncharacterized) 33% 97% 239.6 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 97% 238.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 97% 238.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 97% 238.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 97% 238.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 97% 238.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-lysine catabolism amaB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 32% 88% 220.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 31% 93% 192.2 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 31% 93% 192.2 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 49% 446.4

Sequence Analysis Tools

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

MMTTTLKNFINGQYVDSKGSETIPLVDPATEEVYAHSPISSAADVDDAYQAASKAFEGWS
ETTPAERQLALFRIADELEKRGEEFADLESQDAGKPRASLVEDEISLSVDQIRFFAGAAR
NLEGKSAGEYMKDHTSFIRREPIGVVGQVAPWNYPLNMAVWKFAPAVAAGNTTVLKPSDT
TPQSTLLLAEICAMHLPEGVVNVITGDRTTGGAMIDHKIPEMVSITGSVRAGLEVAKAAA
TDLKRVHLELGGKAPVIVFDDADIPSAIEGIGIAGYFNAGQDCTAATRVVVHESIHDEFI
AELKKWVAANVTTGLPSDPNTFYGPVNNANQMDRVMGILGELPSHSTVEAGGVRQGERGY
FIEPTIVSGLKQNDAAIQTEIFGPVITVQPFRTEEEAMTMANGVPYGLSSSVWTKDHARA
MRFAKGLDFGAVWINCHIPLVAEMPHGGFKHSGHGKDLSQYGFEEYTRVKHVMSFIGK

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