GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_2488 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase

Length: 463 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 33 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 45% 98% 398.3
L-citrulline catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 45% 98% 398.3
putrescine catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 45% 98% 398.3
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 41% 97% 334.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 41% 97% 334.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 41% 97% 334.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 41% 97% 334.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 41% 97% 334.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 41% 97% 334.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 41% 97% 334.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 34% 93% 278.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 34% 93% 278.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 34% 93% 278.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 34% 93% 278.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-arabinose catabolism xacF lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 33% 96% 242.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
D-galacturonate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 33% 96% 242.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
D-glucuronate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 33% 96% 242.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
D-xylose catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 33% 96% 242.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 33% 92% 240 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 33% 92% 240 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 33% 92% 240 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-fucose catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 32% 94% 226.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-rhamnose catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 32% 94% 226.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-threonine catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 32% 94% 226.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-phenylalanine catabolism pad-dh lo Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized) 31% 92% 224.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 30% 95% 216.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 30% 94% 214.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 30% 94% 214.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 92% 203.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 92% 203.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 92% 203.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 92% 203.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 92% 203.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 45% 398.3

Sequence Analysis Tools

View N515DRAFT_2488 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSYATINPYTGETVKTFPSATDAEVTQALDQAQAMFEAWKDVGVAARVKVLQKAADLLRE
SHTQYAKVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYTQSWVE
HVPQGILLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQ
GGFTNLYATRDQLKAIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAFVV
LADADLDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPMEP
STTLAPMSSRGAVDDLKKQLEQAVAHGAKVEVIGAEVPSRGAFFRPVLLSHVSDDNPARY
WEFFGPVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYINHPT
GVAADLPFGGVRRSGYGRELTGLGIKEFVNHKLIAVTDIDGAF

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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