GapMind for catabolism of small carbon sources

 

Protein 8500826 in Desulfovibrio vulgaris Miyazaki F

Annotation: FitnessBrowser__Miya:8500826

Length: 474 amino acids

Source: Miya in FitnessBrowser

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-lactate catabolism lctD med lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized) 37% 93% 274.2 D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) 34% 268.1
L-threonine catabolism lctD med lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized) 37% 93% 274.2 D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) 34% 268.1
D-lactate catabolism glcD lo D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized) 34% 94% 266.9 lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) 37% 274.2
L-threonine catabolism glcD lo D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized) 34% 94% 266.9 lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) 37% 274.2
D-lactate catabolism D-LDH lo D-lactate dehydrogenase (EC 1.1.1.28); D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized) 36% 94% 260.8 lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) 37% 274.2
L-threonine catabolism D-LDH lo D-lactate dehydrogenase (EC 1.1.1.28); D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized) 36% 94% 260.8 lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) 37% 274.2
L-lysine catabolism ydiJ lo D-2-hydroxyglutarate--pyruvate transhydrogenase DLD2; D-2HG--pyruvate transhydrogenase DLD2; Actin-interacting protein 2; D-lactate dehydrogenase [cytochrome] 2, mitochondrial; D-lactate ferricytochrome C oxidoreductase; D-LCR; EC 1.1.99.40; EC 1.1.2.4 (characterized) 31% 90% 201.1 lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) 37% 274.2
D-lactate catabolism glcE lo D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized) 34% 57% 84 lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) 37% 274.2
L-threonine catabolism glcE lo D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized) 34% 57% 84 lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) 37% 274.2

Sequence Analysis Tools

View 8500826 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MPHTSDRSLPPTSDSAPRFVLTDAHRAAIVAAVGEAAVLHSPGEPYDRDASELRAPADLV
VLPETVEQVQALLRCASAHAIPVIPRGGGTGLAGGCLAVRGGVVLSLERMNRIRAIDTRN
LVAEVEAGVISQRVRDAAAEQGLYYPPDPAGMDRSTIGGNVATNAGGPACVKYGVTRDYV
LGVEAVLPDGELLRAGVRTRKGVVGYDMAHLLCGSEGTLGVITALTLKLVPLPPATVSMA
VAFPDMAAAMRGVAAVLGGGHLPSAIEFLDHRCIRLLGELLPIPVPGDKPSLLIIELDGA
REQIVPELDLVAAICRQQGATHVLPAADEETRVRVWGARRQVSLRIHDYAALYMSEDVAV
PLGAIAELVAALPEFEQRYGMEIFAFGHAGDGNIHLNVTAPTRDTRDVVEQGIVELVGKV
LELGGTISGEHGIGEAKKHLLPLELSPASIRLQRGIRQVFDPRGIMNPGKVFGQ

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