GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_1423 in Pseudomonas fluorescens FW300-N2E2

Annotation: Gamma-aminobutyrate permease

Length: 466 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism proY med GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 47% 97% 424.9 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
L-histidine catabolism permease med Aromatic amino acid permease, AroP (characterized) 41% 96% 361.3 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
L-phenylalanine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 41% 96% 361.3 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
L-tryptophan catabolism aroP med Aromatic amino acid permease, AroP (characterized) 41% 96% 361.3 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
L-tyrosine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 41% 96% 361.3 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
D-alanine catabolism cycA lo D-alanine and L-alanine transporter (characterized) 37% 93% 305.8 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
L-alanine catabolism cycA lo D-alanine and L-alanine transporter (characterized) 37% 93% 305.8 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 37% 89% 298.1 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 37% 95% 282 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
L-lysine catabolism lysP lo lysine-specific permease (characterized) 35% 94% 278.9 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 36% 75% 230.3 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 36% 75% 230.3 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 36% 75% 230.3 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6
L-arginine catabolism rocE lo Probable lysine/arginine permease CAN3; Basic amino acids permease CAN3 (characterized) 31% 81% 225.3 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 68% 635.6

Sequence Analysis Tools

View Pf6N2E2_1423 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTSPSFKDSNGHLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVMLAYLFSGLL
VVLVMRMLGEMAVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVL
NQWFPAIDAWLFASVSIVLLAVTNLFSVSKYGEFEFWFAMAKVVAIIGFISLGFAVLMGW
IPEREASGLSRLMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPAQNIAK
ATRSVIWRIGVFYLLSIFVVISVVPWNDPLLASVGSYQRALELMNIPHAKFLVDMVVLIA
VASCMNSSIYIASRMLYSLGRRGDAPKALKVTSSAGVPRSAVIASTVLGAGVTLFSYFMP
AGLFQFLLASSGAIALLVYLVIAISQLRMRRMLQRQNIELPFRMWLFPWLTWLVIVFISA
ALAVMMVTPEHRSEVSTTLGLALVISFIGLVTSRHSPQPERVVSLG

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