GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_04267 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_04267 L-glutamate ABC transporter ATP-binding protein /L-aspartate ABC transporter ATP-binding protein

Length: 241 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 20 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) 82% 100% 393.7 GluA aka CGL1950, component of Glutamate porter 63% 300.1
L-aspartate catabolism aatP hi Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 82% 100% 393.7 GluA aka CGL1950, component of Glutamate porter 63% 300.1
L-glutamate catabolism gltL hi Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 82% 100% 393.7 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 59% 292.7
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 60% 95% 288.1 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 60% 91% 287.7 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 60% 91% 287.7 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
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) 59% 93% 285 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
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) 59% 93% 285 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
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) 59% 93% 285 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
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) 59% 93% 285 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
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) 59% 93% 285 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
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) 59% 93% 285 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 56% 98% 272.7 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 56% 93% 271.2 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 58% 92% 269.6 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 58% 92% 269.6 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 55% 100% 261.5 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 54% 99% 247.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 54% 99% 247.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7
L-tryptophan catabolism ecfA2 med Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 40% 77% 137.5 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 82% 393.7

Sequence Analysis Tools

View H281DRAFT_04267 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

MISIKNVSKWYGQFQVLTDCTTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPFQKGEIVI
NGQSLTDKKTNLSKLRSKVGMVFQHFELFPHLSIVQNLTLAQIKVLGRSKDEASAKGLKL
LDRVGLRAHADKFPGQLSGGQQQRVAIARALSMDPIAMLFDEPTSALDPEMINEVLDVMV
ELAQEGMTMMCVTHEMGFAKKVAHRVIFMDKGLIVEDDRKEDFFANPKSDRAKDFLAKIL
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 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