GapMind for catabolism of small carbon sources

 

Protein BWI76_RS13425 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS13425

Length: 475 amino acids

Source: Koxy in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 81% 100% 793.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 372.1
L-arginine catabolism patD med ydcW: 1-pyrroline dehydrogenase (EC 1.2.1.19) (TIGR03374) 100% 957.7 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 372.1
L-citrulline catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 81% 100% 793.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 372.1
L-citrulline catabolism patD med ydcW: 1-pyrroline dehydrogenase (EC 1.2.1.19) (TIGR03374) 100% 957.7 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 372.1
putrescine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 81% 100% 793.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 372.1
putrescine catabolism patD med ydcW: 1-pyrroline dehydrogenase (EC 1.2.1.19) (TIGR03374) 100% 957.7 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 372.1
L-lysine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 81% 100% 793.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 372.1
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 351.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 81% 793.5
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 351.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 81% 793.5
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 351.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 81% 793.5
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 99% 300.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 81% 793.5
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 99% 300.4 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 81% 793.5
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 32% 88% 218.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 81% 793.5
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 33% 95% 191 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 81% 793.5
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 33% 95% 191 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 81% 793.5

Sequence Analysis Tools

View BWI76_RS13425 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

MQNNLLINGKLVAGEGEAVPVFNPATGEEIVSIAEATAAQVEAAVEAADQAFISWSQTTP
RSRAECLLALANVIDEHAQTLAKLESLNCGKPLHCVINDELPAVADVFRFFAGAARCLPG
MAAGEYLEGHTSMIRRDPVGVVASIAPWNYPLMMAAWKLAPALAAGNCVVIKPSEITPLT
ALKLGELAKEIFPAGVLNVLFGRGATVGDPLTAHAKVRMVSLTGSIATGAHIIGHTASSI
KRTHMELGGKAPVIVFDDADIDAVVEGVRTFGFYNAGQDCTAACRIYAQAGIYDQLVEKL
GAAVASLKMGPPEDETTELGPLSSQAHLDRVSAAVDAARALPHIQVIAGGSKAPGNGYYY
QPTLLAGARQEDAIVQREVFGPVVSITSFTDEEQALSWANDSQYGLASSVWTRDVGRAHR
LSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTTIRHVMIKHG

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