GapMind for catabolism of small carbon sources

 

Protein AO353_16120 in Pseudomonas fluorescens FW300-N2E3

Annotation: AO353_16120 D-alanine/D-serine/glycine permease

Length: 472 amino acids

Source: pseudo3_N2E3 in FitnessBrowser

Candidate for 16 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 D-alanine and L-alanine transporter (characterized) 100% 100% 939.9 Proline-specific permease (ProY) 57% 529.6
L-alanine catabolism cycA hi D-alanine and L-alanine transporter (characterized) 100% 100% 939.9 Proline-specific permease (ProY) 57% 529.6
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 57% 96% 529.6 D-alanine and L-alanine transporter 100% 939.9
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 56% 92% 508.8 D-alanine and L-alanine transporter 100% 939.9
L-histidine catabolism permease med histidine permease (characterized) 54% 97% 504.2 D-alanine and L-alanine transporter 100% 939.9
L-tyrosine catabolism aroP med L-tyrosine transporter (characterized) 43% 100% 406 D-alanine and L-alanine transporter 100% 939.9
L-phenylalanine catabolism aroP med Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) 44% 98% 405.6 D-alanine and L-alanine transporter 100% 939.9
L-tryptophan catabolism aroP med Aromatic amino acid transport protein AroP (characterized, see rationale) 45% 99% 402.9 D-alanine and L-alanine transporter 100% 939.9
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 44% 98% 402.5 D-alanine and L-alanine transporter 100% 939.9
D-serine catabolism cycA med D-serine/D-alanine/glycine transporter (characterized) 43% 93% 375.9 D-alanine and L-alanine transporter 100% 939.9
L-asparagine catabolism ansP med L-asparagine permease; L-asparagine transport protein (characterized) 42% 88% 364.4 D-alanine and L-alanine transporter 100% 939.9
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 37% 96% 322 D-alanine and L-alanine transporter 100% 939.9
L-lysine catabolism lysP lo The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) 38% 95% 308.1 D-alanine and L-alanine transporter 100% 939.9
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 80% 233.8 D-alanine and L-alanine transporter 100% 939.9
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 80% 233.8 D-alanine and L-alanine transporter 100% 939.9
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 80% 233.8 D-alanine and L-alanine transporter 100% 939.9

Sequence Analysis Tools

View AO353_16120 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

MTVGNHLPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI
IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA
VAVYMGIWFPEVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVVGGVG
VIAFGFGNDGVALGISNLWSHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQ
KTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFV
VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSNGVPRRALLLSIGALLLGVLLNY
LVPEKVFVWVTAIATFGAIWTWVMILLAQLKFRKGLSPAERAALKYRMWLYPVSSYLALA
FLVMVVGLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQPTGVPQAAVRTAS

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