GapMind for catabolism of small carbon sources

 

Protein WP_011513215.1 in Psychrobacter cryohalolentis K5

Annotation: NCBI__GCF_000013905.1:WP_011513215.1

Length: 504 amino acids

Source: GCF_000013905.1 in NCBI

Candidate for 42 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 med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 496.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-arginine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 496.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-citrulline catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 496.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
2'-deoxyinosine catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 496.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
2-deoxy-D-ribose catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 496.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
ethanol catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 496.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
putrescine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 496.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-threonine catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 496.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
thymidine catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 496.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-tryptophan catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 496.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 44% 90% 372.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 371.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 371.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 97% 359 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 97% 359 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 97% 359 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-tryptophan catabolism nbaE med 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized) 40% 98% 344.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-lysine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 40% 95% 340.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 96% 342.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 96% 342.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 96% 342.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 96% 342.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-arginine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 95% 331.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-citrulline catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 95% 331.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
putrescine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 95% 331.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 37% 100% 325.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 37% 100% 325.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 37% 100% 325.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 37% 100% 325.9 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 95% 267.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 95% 267.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 95% 267.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 95% 267.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 95% 267.3 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 91% 240.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 91% 240.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 91% 240.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 91% 240.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 91% 240.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 33% 95% 218 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 33% 95% 218 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 31% 80% 191.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 73% 716.8

Sequence Analysis Tools

View WP_011513215.1 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

MTDSKTVLNNLTDIIDLEQIQTAYINGRYLAVDETLTTFEDINPATGEVLATIQQTTNEQ
IDEAVKAAQKGQKVWAALTAVERGRILSKAVEILRDRNDVLALLETKDTGKAYSETKYVD
IVTGADVVEYYAGLAPMIEGRQIPLRDTSFVYTRREPLGVVAGIGAWNYPIQIAMWKAAP
ALAAGNAMIFKPSEVTPLTALKLAEIFTEAGLPDGVFNVVQGNYKVGEALTQHPDIAKVS
FTGGVPTGKKVMSSAASSSLKDVTLELGGKSPLIIFDDADIDTAADIAMMANFYSSGQVC
TNGTRVFVPKAMQAKFEQAILTRVERIKLGDPMDENINMGPLVSFPHMERVLGYIEQGKA
SGARLLIGGDRVTTGELANGAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIR
RANDTEYGLAAGVVTAALTRAHRVIAQIEAGICWLNTWGESAAQMPVGGYKHSGVGRENG
IEALEHYTQTKSIQVELGKFESVF

This GapMind analysis is from Sep 24 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