GapMind for catabolism of small carbon sources

 

Protein CCNA_03243 in Caulobacter crescentus NA1000

Annotation: FitnessBrowser__Caulo:CCNA_03243

Length: 499 amino acids

Source: Caulo in FitnessBrowser

Candidate for 40 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism kauB hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 56% 99% 555.8 aldehyde dehydrogenase 55% 495.4
L-arginine catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 56% 99% 555.8 aldehyde dehydrogenase 55% 495.4
L-citrulline catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 56% 99% 555.8 aldehyde dehydrogenase 55% 495.4
putrescine catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 56% 99% 555.8 aldehyde dehydrogenase 55% 495.4
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 98% 472.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 98% 472.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 98% 472.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 98% 472.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 98% 472.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 50% 98% 472.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 44% 92% 393.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 96% 363.6 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 96% 363.6 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 96% 363.6 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 360.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 360.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-tryptophan catabolism nbaE med aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 41% 95% 334.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 97% 303.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 97% 303.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 97% 303.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 97% 303.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 99% 301.6 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 97% 298.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 97% 298.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 97% 298.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 97% 298.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 88% 251.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 88% 251.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 88% 251.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 88% 251.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 88% 251.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 31% 94% 223 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 35% 93% 220.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 35% 93% 220.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 92% 216.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 92% 216.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 92% 216.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 92% 216.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 92% 216.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 31% 93% 179.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8

Sequence Analysis Tools

View CCNA_03243 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MPRVTLPADMTERLAKLAPPSQAVIDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDV
ERAVAGARAAFEDGRWRDQGPRQKKAVLFRLAELMERDADELALLESLDVGKPISDARNV
DIPLAINTCRWYAEALDKVYGEVGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVA
PALAMGNSVVLKPAEQSPLTALKLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDM
IAFTGSGPVGRRLMEYSARSNLKRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQG
EVCTAASRLLVEAPIKDAFLARVIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIAT
ADSQGARRVLGGQRVRQEAGGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAM
RLANDTVYGLAAGLWTADVSKALRGARRLKAGLVWVNGWDACDITMPFGGFKQSGFGRDR
SLHALHKYADLKSVSVTLR

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