GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_02565 in Paraburkholderia bryophila 376MFSha3.1

Annotation: FitnessBrowser__Burk376:H281DRAFT_02565

Length: 241 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aatP hi Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 69% 100% 339.3 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 59% 279.3
L-aspartate catabolism aatP hi Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 69% 100% 339.3 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 59% 279.3
L-glutamate catabolism gltL hi Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 69% 100% 339.3 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 59% 279.3
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 58% 93% 278.1 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-asparagine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 56% 93% 267.7 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-aspartate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 56% 93% 267.7 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-glutamate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 56% 93% 267.7 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-histidine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 56% 93% 267.7 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-leucine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 56% 93% 267.7 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-proline catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 56% 93% 267.7 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 57% 95% 266.9 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 57% 91% 265.8 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 57% 91% 265.8 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 55% 92% 249.2 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 55% 92% 249.2 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 53% 99% 235 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 53% 99% 235 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 69% 339.3

Sequence Analysis Tools

View H281DRAFT_02565 at FitnessBrowser

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MIDLNNVSKWYGGIRVLNHCTASIARGEVAVICGPSGSGKSTLIKSVNGLEAVQSGQIVV
DGIDVTAKRANLSRLRTRVGMVFQHFELFPHLSVQRNLMLAQMNVLGRARDEAGERARSL
LRRVGLSGHEDKYPAQLSGGQQQRVAIARALSMDPVAMLFDEPTSALDPEMVNEVLDVMT
TLAQDGMTMLCVTHEMGFAKRVADRVLFMDRGVIVEDETREAFFERPRSERARDFLSRIL
H

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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