GapMind for catabolism of small carbon sources


Protein PP_4495 in Pseudomonas putida KT2440

Annotation: FitnessBrowser__Putida:PP_4495

Length: 472 amino acids

Source: Putida in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-tyrosine catabolism aroP hi L-tyrosine transporter (characterized) 84% 99% 806.6 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 57% 549.3
L-tryptophan catabolism aroP hi Aromatic amino acid transport protein AroP (characterized, see rationale) 71% 98% 686.4 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 57% 549.3
L-phenylalanine 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) 66% 98% 612.1 L-tyrosine transporter 84% 806.6
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 65% 95% 597.8 L-tyrosine transporter 84% 806.6
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 46% 94% 412.9 L-tyrosine transporter 84% 806.6
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 46% 94% 412.9 L-tyrosine transporter 84% 806.6
L-histidine catabolism permease med histidine permease (characterized) 42% 97% 377.5 L-tyrosine transporter 84% 806.6
D-serine catabolism cycA lo D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized) 38% 80% 330.9 L-tyrosine transporter 84% 806.6
L-lysine catabolism lysP lo Lysine/arginine permease CAN1; Basic amino acids permease CAN1 (characterized) 33% 77% 239.6 L-tyrosine transporter 84% 806.6
L-asparagine catabolism AGP1 lo general amino acid permease AGP1 (characterized) 30% 68% 201.1 L-tyrosine transporter 84% 806.6

Sequence Analysis Tools

View PP_4495 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

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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