GapMind for catabolism of small carbon sources

 

Protein AO353_16120 in Pseudomonas fluorescens FW300-N2E3

Annotation: FitnessBrowser__pseudo3_N2E3:AO353_16120

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

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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:

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