GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_05299 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_05299 amino acid ABC transporter membrane protein 1, PAAT family

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

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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