GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_05299 in Paraburkholderia bryophila 376MFSha3.1

Annotation: FitnessBrowser__Burk376:H281DRAFT_05299

Length: 216 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 39% 86% 142.9 Basic amino acid uptake transporter, BgtAB 40% 151.8
L-histidine catabolism BPHYT_RS24005 lo Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale) 36% 88% 124 Basic amino acid uptake transporter, BgtAB 40% 151.8
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 35% 93% 122.1 Basic amino acid uptake transporter, BgtAB 40% 151.8
L-histidine catabolism hisQ lo Histidine transport system permease protein HisQ (characterized) 31% 96% 117.9 Basic amino acid uptake transporter, BgtAB 40% 151.8
L-asparagine catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 34% 90% 102.8 Basic amino acid uptake transporter, BgtAB 40% 151.8
L-aspartate catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 34% 90% 102.8 Basic amino acid uptake transporter, BgtAB 40% 151.8
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 31% 76% 94.7 Basic amino acid uptake transporter, BgtAB 40% 151.8

Sequence Analysis Tools

View H281DRAFT_05299 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

MFSTTVFVQGMPLLLHAALATIGVSLTGLFIGFFVAVGVCAARLSPNRAARRFGGAYVFF
FRGVPMLVQLLLVYYLLPFAGINVSPLVAAISAVSLCSASYIAEILRGGFLSIPPGHIEA
ARMLGLSPFDTLRRILVPQAFRLTLPSLVNEMVLLIKASSLISVVGVAELTRTAQNIAAS
TYRPLEAYLAAGLIYFVICGALALIAHAAEFRLKHA

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