GapMind for catabolism of small carbon sources

 

Protein WP_008507129.1 in Brucella inopinata BO1

Annotation: NCBI__GCF_000182725.1:WP_008507129.1

Length: 257 amino acids

Source: GCF_000182725.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
glycerol catabolism dhaD med NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 51% 98% 264.6 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
D-sorbitol (glucitol) catabolism sdh med Sorbitol dehydrogenase (EC 1.1.1.14) (characterized) 40% 97% 172.9 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
4-hydroxybenzoate catabolism badH lo BadH (characterized) 37% 98% 151.8 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
phenylacetate catabolism badH lo BadH (characterized) 37% 98% 151.8 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
L-phenylalanine catabolism badH lo BadH (characterized) 37% 98% 151.8 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 34% 94% 133.7 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 34% 94% 133.7 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
lactose catabolism galdh lo L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 34% 94% 133.7 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 36% 98% 133.7 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
L-rhamnose catabolism LRA1 lo L-rhamnose 1-dehydrogenase (NADP(+)); RHAD; EC 1.1.1.377 (characterized) 33% 96% 125.2 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
D-sorbitol (glucitol) catabolism srlD lo Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) 34% 97% 122.9 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Cla h 8; EC 1.1.1.138 (characterized) 34% 93% 120.2 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4
L-fucose catabolism fdh lo Short-chain dehydrogenase (characterized, see rationale) 33% 98% 111.3 D-threitol dehydrogenase; EC 1.1.1.403 61% 307.4

Sequence Analysis Tools

View WP_008507129.1 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

MSDQAPQIDLNFPLSEKVAIVTGGASGIGAAISKAFIAKGAKVAVLDISADIAKAKAEEL
GENAKPFVCDVSSQQSVNDAITAVITQFGKIDIAVNSAGVVYLAPAEDISLDYWDKTINI
NLKGSFLVTQAVGRAMIAAGNGGKIINLASQAGTVAIEEHVAYCASKFGVIGMSKTFAAE
WGKHGICVNTLSPTIVLTELGKKAWAGEKGEAAKKRIPAGRFAYPEEIAAAAVFLASAGA
DMITGADLLIDGGYTIL

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