GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_4195 in Pseudomonas fluorescens FW300-N2E2

Annotation: transport permease protein of gamma-aminobutyrate

Length: 464 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 12 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) 51% 98% 461.8 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5
L-histidine catabolism permease med Aromatic amino acid permease, AroP (characterized) 42% 97% 362.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5
L-phenylalanine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 42% 97% 362.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5
L-tryptophan catabolism aroP med Aromatic amino acid permease, AroP (characterized) 42% 97% 362.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5
L-tyrosine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 42% 97% 362.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 37% 96% 317.8 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5
L-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 37% 96% 317.8 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 37% 95% 313.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 37% 98% 304.7 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5
L-asparagine catabolism ansP lo L-asparagine permease; L-asparagine transport protein (characterized) 34% 90% 271.2 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 31% 96% 270 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 32% 71% 208 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 627.5

Sequence Analysis Tools

View Pf6N2E2_4195 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSGTQTSNHLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVL
VMRMLGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAW
FPNVAIWAFTLVITLLLTVTNLFSVKNYGEFEFWFALVKVVAIIGFIGLGVMAIFGVLPT
SQVSGVSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNS
VIWRIGLFYLVSIFIVVALVPWNDPLLASVGSYQTVLERMGIPNAKLIVDIVVLVAVTSC
LNSALYTASRMMFSLGKRGDAPAVSQRTNKSGTPYWAVMLSTGAAFLAVFANYVAPAAVF
DFLLASSGAIALLVYLVIAVSQLRMRKQRMARGEKVAFSMWLFPGLTYAVIVFIVGALTI
MLFQEAHRVEILATGLLSVLVVISGVLVQRRRIAKTGRLVPTLG

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, 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