GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_4790 in Pseudomonas fluorescens GW456-L13

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

Length: 473 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 17 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) 96% 100% 906 Proline-specific permease (ProY) 57% 528.9
L-alanine catabolism cycA hi L-alanine and D-alanine permease (characterized) 96% 100% 906 Proline-specific permease (ProY) 57% 528.9
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 57% 96% 528.9 L-alanine and D-alanine permease 96% 906.0
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 56% 92% 516.5 L-alanine and D-alanine permease 96% 906.0
L-histidine catabolism permease med histidine permease (characterized) 55% 95% 512.7 L-alanine and D-alanine permease 96% 906.0
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 96% 906.0
L-tyrosine catabolism aroP med L-tyrosine transporter (characterized) 44% 97% 407.9 L-alanine and D-alanine permease 96% 906.0
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 45% 99% 407.1 L-alanine and D-alanine permease 96% 906.0
L-tryptophan catabolism aroP med Aromatic amino acid transport protein AroP (characterized, see rationale) 45% 100% 402.5 L-alanine and D-alanine permease 96% 906.0
D-serine catabolism cycA med D-serine/D-alanine/glycine transporter (characterized) 43% 93% 378.6 L-alanine and D-alanine permease 96% 906.0
L-asparagine catabolism ansP med L-asparagine permease; L-asparagine transport protein (characterized) 42% 88% 367.9 L-alanine and D-alanine permease 96% 906.0
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 38% 98% 327.8 L-alanine and D-alanine permease 96% 906.0
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 96% 906.0
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) 38% 98% 297 L-alanine and D-alanine permease 96% 906.0
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 81% 240 L-alanine and D-alanine permease 96% 906.0
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 81% 240 L-alanine and D-alanine permease 96% 906.0
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 81% 240 L-alanine and D-alanine permease 96% 906.0

Sequence Analysis Tools

View PfGW456L13_4790 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

MPVGNHLPQGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI
IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA
VAVYMGIWFPDVPRWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVLGGIG
IIAFGFGNDGVALGISNLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQ
KTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFV
VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSNNGVPRRALLLSIGALLLGVLLN
YLVPEKVFVWVTAIATFGAIWTWVMILLAQLKFRKGLSASEAAGLKYRMWLYPVSSYLAL
AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQPTNVSQGAARSVS

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 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