GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_05872 in Paraburkholderia bryophila 376MFSha3.1

Annotation: FitnessBrowser__Burk376:H281DRAFT_05872

Length: 214 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism peb1B med PEP1B, component of Uptake system for glutamate and aspartate (characterized) 34% 83% 151 L-cystine transport system permease protein YecS 37% 150.6
L-aspartate catabolism peb1B med PEP1B, component of Uptake system for glutamate and aspartate (characterized) 34% 83% 151 L-cystine transport system permease protein YecS 37% 150.6
L-glutamate catabolism peb1B med PEP1B, component of Uptake system for glutamate and aspartate (characterized) 34% 83% 151 L-cystine transport system permease protein YecS 37% 150.6
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-glucosamine, permease component 2 (characterized) 32% 90% 132.9 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0
L-asparagine catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 33% 95% 130.6 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0
L-aspartate catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 33% 95% 130.6 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 32% 71% 123.6 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0
L-asparagine catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 33% 51% 123.6 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 32% 71% 123.6 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0
L-aspartate catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 33% 51% 123.6 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 32% 55% 119.8 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0
L-asparagine catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 31% 94% 119 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0
L-aspartate catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 31% 94% 119 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0
L-glutamate catabolism gltK lo Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 31% 95% 114.8 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0
L-histidine catabolism aapQ lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized) 31% 53% 92 PEP1B, component of Uptake system for glutamate and aspartate 34% 151.0

Sequence Analysis Tools

View H281DRAFT_05872 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MSLELLKNSLSILLQGLVTTLLLSIAAIVGSTLIGLLAAVLRSFGPWGTDRIAKLYTELF
RGTPVLITLMFIYFGVSYFGYAIDVFAAGVIGLSVYQGAYIAEVFRAGIESVPKGQWEVS
QILGLSRIQTFASVVLPQTGRIVLPPLVGQYLSLIKDTSIVSMIGMSELMHGGQAIVDRV
GKPVEIYGLVALIYFVVCFPLSQWVRHHDRRRLT

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