GapMind for catabolism of small carbon sources


Protein AO353_16950 in Pseudomonas fluorescens FW300-N2E3

Annotation: FitnessBrowser__pseudo3_N2E3:AO353_16950

Length: 254 amino acids

Source: pseudo3_N2E3 in FitnessBrowser

Candidate for 6 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism hisP hi ABC transporter for L-Lysine, ATPase component (characterized) 94% 100% 470.7 ABC transporter for L-Arginine, putative ATPase component 72% 361.3
L-arginine catabolism artP hi ABC transporter for L-Arginine, putative ATPase component (characterized) 72% 96% 361.3
L-citrulline catabolism PS417_17605 med ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 77% 91% 372.5 ABC transporter for L-Lysine, ATPase component 94% 470.7
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 68% 100% 350.1 ABC transporter for L-Lysine, ATPase component 94% 470.7
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 56% 95% 269.2 ABC transporter for L-Lysine, ATPase component 94% 470.7
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 37% 77% 144.1 ABC transporter for L-Lysine, ATPase component 94% 470.7

Sequence Analysis Tools

View AO353_16950 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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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