GapMind for catabolism of small carbon sources

 

Protein PP_0213 in Pseudomonas putida KT2440

Annotation: FitnessBrowser__Putida:PP_0213

Length: 480 amino acids

Source: Putida in FitnessBrowser

Candidate for 31 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism davD hi glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 100% 100% 943.7
L-citrulline catabolism davD hi glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 100% 100% 943.7
L-lysine catabolism davD hi glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 100% 100% 943.7
L-proline catabolism davD hi glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 100% 100% 943.7
L-arginine catabolism gabD hi NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 91% 100% 876.3
L-citrulline catabolism gabD hi NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 91% 100% 876.3
putrescine catabolism gabD hi NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 91% 100% 876.3
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 91% 541.6 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 91% 541.6 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 91% 541.6 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 91% 541.6 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 91% 541.6 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 91% 541.6 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 91% 541.6 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-arabinose catabolism xacF med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 43% 98% 379 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
D-galacturonate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 43% 98% 379 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
D-glucuronate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 43% 98% 379 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
D-xylose catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 43% 98% 379 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 98% 341.3 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 98% 341.3 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 98% 341.3 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 98% 341.3 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 98% 341.3 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 90% 257.3 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 90% 257.3 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 90% 257.3 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 90% 257.3 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 90% 257.3 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 33% 91% 229.9 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 221.9 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 221.9 glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) 100% 943.7

Sequence Analysis Tools

View PP_0213 at FitnessBrowser

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

MQLKDAQLFRQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKA
LPAWRALTAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFA
EEAKRIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK
PASQTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQ
LMEECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDG
VYDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKL
IEGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARD
MSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCISV

This GapMind analysis is from Sep 17 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