GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS07280 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS07280 amino acid permease

Length: 466 amino acids

Source: BFirm 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-tryptophan catabolism aroP hi Amino acid permease (characterized, see rationale) 68% 97% 615.1 L-alanine and D-alanine permease 39% 337.0
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 39% 93% 337 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 38% 329.3
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 39% 93% 337 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 38% 329.3
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 39% 97% 334.3 L-alanine and D-alanine permease 39% 337.0
L-proline catabolism proY lo GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 38% 97% 329.3 L-alanine and D-alanine permease 39% 337.0
L-histidine catabolism permease lo histidine permease (characterized) 38% 97% 323.6 L-alanine and D-alanine permease 39% 337.0
L-phenylalanine catabolism aroP lo Aromatic amino acid transport protein AroP (characterized, see rationale) 36% 97% 313.9 L-alanine and D-alanine permease 39% 337.0
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 35% 98% 302.4 L-alanine and D-alanine permease 39% 337.0
L-tyrosine catabolism aroP lo Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) 34% 96% 287.3 L-alanine and D-alanine permease 39% 337.0
D-serine catabolism cycA lo DL-alanine permease SerP2 (characterized) 30% 98% 220.3 L-alanine and D-alanine permease 39% 337.0
L-arginine catabolism rocE lo S-adenosylmethionine permease GAP4; SAM permease; Amino-acid permease GAP4 (characterized) 33% 73% 218.8 L-alanine and D-alanine permease 39% 337.0
L-serine catabolism serP lo Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized) 30% 98% 218.8 L-alanine and D-alanine permease 39% 337.0
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 30% 71% 199.5 L-alanine and D-alanine permease 39% 337.0
L-lysine catabolism lysP lo uncharacterized amino-acid permease C869.11 (characterized) 30% 69% 187.6 L-alanine and D-alanine permease 39% 337.0

Sequence Analysis Tools

View BPHYT_RS07280 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

MTQEQRGFDTIVEREKGLQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGPSVLVSYA
IGALIALLLMGCLAEMTVAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTA
IAVYMKYWFPAVPGWYWIVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAY
VVFGAPADSTIGFANYTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKA
ITRAFRATMFRLVFFYLLTLALMLAIVPWNAAGTDESPFVRVMAATHVPGAAGVINFVIL
VAALSAMNSQLYITTRMMFSLSRAGYAPRKLGALNGKGVPVAALWLSTIGIALATVLNVV
YPDASFVLMMSVSMFGAMFTWLMIFVTHFFFRHRHQGAPLAFRMWGYPGTSALGAGLMVS
ALVTTWFTREFRMTLVIGVPFIVSLLVVYFVWYRKRAVEGAAAELA

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