GapMind for catabolism of small carbon sources


Protein Ac3H11_909 in Acidovorax sp. GW101-3H11

Annotation: FitnessBrowser__acidovorax_3H11:Ac3H11_909

Length: 374 amino acids

Source: acidovorax_3H11 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
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC (characterized) 46% 76% 257.3 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 352.8
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 43% 74% 224.6 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 352.8
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 48% 64% 244.2 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 352.8
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 39% 74% 178.3 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 352.8
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 35% 84% 155.6 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 352.8
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 77% 134.8 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 352.8

Sequence Analysis Tools

View Ac3H11_909 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