GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_5459 in Pseudomonas fluorescens FW300-N2E2

Annotation: D-serine/D-alanine/glycine transporter

Length: 473 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism cycA hi L-alanine and D-alanine permease (characterized) 98% 100% 916.8 Proline-specific permease (ProY) 57% 529.3
L-alanine catabolism cycA hi L-alanine and D-alanine permease (characterized) 98% 100% 916.8 Proline-specific permease (ProY) 57% 529.3
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 57% 96% 529.3 L-alanine and D-alanine permease 98% 916.8
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 56% 95% 520.8 L-alanine and D-alanine permease 98% 916.8
L-histidine catabolism permease med histidine permease (characterized) 55% 95% 513.8 L-alanine and D-alanine permease 98% 916.8
L-phenylalanine catabolism aroP med Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) 44% 98% 410.2 L-alanine and D-alanine permease 98% 916.8
L-tyrosine catabolism aroP med L-tyrosine transporter (characterized) 45% 96% 410.2 L-alanine and D-alanine permease 98% 916.8
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 44% 99% 405.2 L-alanine and D-alanine permease 98% 916.8
L-tryptophan catabolism aroP med Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) 44% 96% 400.2 L-alanine and D-alanine permease 98% 916.8
D-serine catabolism cycA med D-serine/D-alanine/glycine transporter (characterized) 43% 93% 379.8 L-alanine and D-alanine permease 98% 916.8
L-asparagine catabolism ansP med L-asparagine permease; L-asparagine transport protein (characterized) 40% 91% 367.1 L-alanine and D-alanine permease 98% 916.8
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 38% 96% 327 L-alanine and D-alanine permease 98% 916.8
L-lysine catabolism lysP lo The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) 39% 94% 316.6 L-alanine and D-alanine permease 98% 916.8
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) 37% 99% 298.9 L-alanine and D-alanine permease 98% 916.8
L-threonine catabolism serP1 lo Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized) 37% 93% 287 L-alanine and D-alanine permease 98% 916.8
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 87% 239.2 L-alanine and D-alanine permease 98% 916.8
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 87% 239.2 L-alanine and D-alanine permease 98% 916.8
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 87% 239.2 L-alanine and D-alanine permease 98% 916.8

Sequence Analysis Tools

View Pf6N2E2_5459 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

MAVGNHLPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI
IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA
VAVYMGIWFPDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVG
IIAFGFGNDGVALGISNLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQ
KTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFV
VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFATTSANGVPRRALLLSIAALLLGVLLN
YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLAL
AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQPTGETHGSVRSVS

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