GapMind for catabolism of small carbon sources

 

Protein WP_044621957.1 in Photobacterium gaetbulicola Gung47

Annotation: NCBI__GCF_000940995.1:WP_044621957.1

Length: 488 amino acids

Source: GCF_000940995.1 in NCBI

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 91% 235.3 aldehyde dehydrogenase 37% 287.3
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 91% 235.3 aldehyde dehydrogenase 37% 287.3
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 91% 235.3 aldehyde dehydrogenase 37% 287.3
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 91% 235.3 aldehyde dehydrogenase 37% 287.3
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 91% 235.3 aldehyde dehydrogenase 37% 287.3
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 91% 227.3 aldehyde dehydrogenase 37% 287.3
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 91% 227.3 aldehyde dehydrogenase 37% 287.3
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 91% 227.3 aldehyde dehydrogenase 37% 287.3
4-hydroxybenzoate catabolism praB lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 32% 93% 224.2 aldehyde dehydrogenase 37% 287.3
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 32% 93% 224.2 aldehyde dehydrogenase 37% 287.3
L-tryptophan catabolism praB lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 32% 93% 224.2 aldehyde dehydrogenase 37% 287.3
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 31% 94% 223.4 aldehyde dehydrogenase 37% 287.3
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 31% 94% 223.4 aldehyde dehydrogenase 37% 287.3
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 31% 94% 223.4 aldehyde dehydrogenase 37% 287.3
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 32% 97% 223 aldehyde dehydrogenase 37% 287.3
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 96% 213.8 aldehyde dehydrogenase 37% 287.3
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 31% 95% 213.4 aldehyde dehydrogenase 37% 287.3
L-lysine catabolism amaB lo L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 30% 81% 174.5 aldehyde dehydrogenase 37% 287.3

Sequence Analysis Tools

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Fitness BLAST: loading...

Sequence

MRGKALKHSAQTDNRQGVTQDTISPADGSVVATVVMATHEDIQHSLDKSSNAQQRWKQTP
LAQRQEYCRRAIDALLSHRDMIASELSWMMGRPIRHSSSELKGVEERARYMIKHCEQALA
TIELPEKTGYTRYMVREPLGTVMVISPWNYPYLTAVNAIIPALLAGNSVILKPSSHTPLS
AQRFQQAFDEAQLPAGVFQHLFLSHEATEFIVSSDQVQHVVFTGSVAGGASIEKAAAGHF
HGLGLELGGNDPAYVCNDADINQAVETIVDGALYNAGQSCCAIERVYVDYRIHDEFVEKV
VQLVNQYQLGFPLDKNTTLGPLISTSAADHVRKQIVEAKQKGAQAHISEACFPNSKPGSP
YLAPQVLTDVNHQMQVMTEETFGPVLPIQKVFSDQEAIDLMNDSEYGLTASIFTPDMARA
IKIGEQVETGTFFANRCDYLDPALAWTGIKQSGKGYTLSSLGFETLTRPKSFHLKHISNT
TIAPKAAD

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