GapMind for catabolism of small carbon sources

 

Protein GFF196 in Phaeobacter inhibens BS107

Annotation: PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC

Length: 432 amino acids

Source: Phaeo 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 bztC hi BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 100% 417.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 51% 236.9
L-aspartate catabolism bztC hi BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 100% 417.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 51% 236.9
L-glutamate catabolism bztC hi BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 100% 417.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 51% 236.9
D-alanine catabolism Pf6N2E2_5404 med ABC transporter for D-Alanine, permease component 1 (characterized) 45% 76% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 51% 62% 236.9 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-asparagine catabolism aapM lo AapM, 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) 48% 64% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-aspartate catabolism aapM lo AapM, 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) 48% 64% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-glutamate catabolism aapM lo AapM, 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) 48% 64% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-leucine catabolism aapM lo AapM, 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) 48% 64% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-proline catabolism aapM lo AapM, 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) 48% 64% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-asparagine catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 35% 95% 223 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-aspartate catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 35% 95% 223 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
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) 32% 98% 116.7 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-glucosamine, permease component 2 (characterized) 32% 93% 107.1 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 32% 74% 106.3 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2

Sequence Analysis Tools

View GFF196 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

MSDTHAQTVAFVRETQIPPAPPPGRETGVYKWIRENLFSSVPNSILTLAALALIYALLSS
TLPWLLNGVWTTNSLAECREVLDGKLGACFSVLTERWNQLLYGFKYPGTEYWRPNLALVL
LLVALAPVLFFDLPRKLLAFTAIYPFLAFWLIWGGSILVPIVALLGFVAAGFVFQKFGKG
SFALGFFGAIVAAVVVWNIGGFLIPEGASDNAMLSAVPSRDLGGFMLNMMLGVTCVSLSV
PLGIALALGRQSNMPLIKWICVVFIEFVRGVPLITLLFVASVMLSYFFPPDATVDLFLRV
VIMITLFSAAYIAEVIRGGLAALPKGQYEAADSLGLDYPQAMRLIILPQALKISIPGIVN
VAVGLFKDTTLVSVISMFDLVGMIRGPILASTEWNGVYWELLGFAAFLFFIVCYGISQYS
QWLERRLATDHH

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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, 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