GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_2488 in Dyella japonica UNC79MFTsu3.2

Annotation: FitnessBrowser__Dyella79:N515DRAFT_2488

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

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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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 (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