GapMind for catabolism of small carbon sources

 

Protein GFF3978 in Marinobacter adhaerens HP15

Annotation: FitnessBrowser__Marino:GFF3978

Length: 436 amino acids

Source: Marino in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
pyruvate catabolism dctM med Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized) 37% 99% 336.3 GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter 39% 334.0
L-glutamate catabolism gtrB lo GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized) 39% 97% 334 Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids 37% 336.3
4-hydroxybenzoate catabolism fcbT3 lo FcbT3, component of Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (characterized) 36% 99% 276.9 Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids 37% 336.3
succinate catabolism dctM lo C4-dicarboxylate TRAP transporter large permease protein DctM (characterized, see rationale) 36% 98% 261.5 Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids 37% 336.3
L-malate catabolism dctM lo C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 35% 99% 257.7 Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids 37% 336.3
fumarate catabolism dctM lo C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 35% 99% 257.7 Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids 37% 336.3
D-gluconate catabolism gntB lo D-gluconate TRAP transporter, large permease component (characterized) 31% 99% 222.6 Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids 37% 336.3
2-oxoglutarate (alpha-ketoglutarate) catabolism dctM lo dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized) 32% 95% 166.4 Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids 37% 336.3

Sequence Analysis Tools

View GFF3978 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

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Sequence

MSIEALTLLFFGSLLFFLLLGLPLAFVLGGVSVVFLYFTWGFDSFYMVASQIWGTMGSFT
LVAIPLFVFMAMILERTGVARDLYRMMHLWCGGLRGGLALGTLGICAVFAAMVGISGAAV
VAMGTIALPSMLERGYDKSMALGVINTGGGWGILIPPSILMILYALITGVSVGKMFAAGI
MPGVLLMVLTAIYIIVRCHLQPELAPALPKEDRGTWPEKFRALRAVLLPIGVVVMVLGSI
IGGITTPTEAAAMGVLGALISAAVYRQFKWSILKEAAIRTFKLTGMIMWILFAAHAFSAA
YQSMGAQELIEGLMNMVPGGPWGIIIAMMVIVFLLAMVLDPVGIMLITLPVFMPIVESLG
FDPIWFGILFVINMEIGYMTPPFGFNLFYLKGIVPPSITMKDIYKSIIPFVIVEIVGIIL
IMVFPEIATWLPDLLF

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