GapMind for catabolism of small carbon sources


Protein GFF344 in Pseudomonas simiae WCS417

Annotation: FitnessBrowser__WCS417:GFF344

Length: 469 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism permease hi histidine permease (characterized) 86% 100% 808.9 ProY of 457 aas and 12 TMSs 61% 582.4
L-proline catabolism proY med ProY of 457 aas and 12 TMSs (characterized) 61% 97% 582.4 histidine permease 86% 808.9
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 54% 96% 520 histidine permease 86% 808.9
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 54% 96% 520 histidine permease 86% 808.9
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 45% 94% 419.9 histidine permease 86% 808.9
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 44% 98% 396.7 histidine permease 86% 808.9
L-phenylalanine catabolism aroP med Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) 45% 96% 396 histidine permease 86% 808.9
L-tyrosine catabolism aroP med L-tyrosine transporter (characterized) 44% 99% 391.7 histidine permease 86% 808.9
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) 45% 99% 391.3 histidine permease 86% 808.9
D-serine catabolism cycA med D-serine/D-alanine/glycine transporter (characterized) 40% 97% 369 histidine permease 86% 808.9
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 36% 93% 330.9 histidine permease 86% 808.9

Sequence Analysis Tools

View GFF344 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.



Related tools

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