GapMind for catabolism of small carbon sources


Protein Pf1N1B4_3559 in Pseudomonas fluorescens FW300-N1B4

Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559

Length: 473 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 15 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) 96% 100% 903.3 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 58% 552.4
L-tryptophan catabolism aroP hi Aromatic amino acid transport protein AroP (characterized, see rationale) 73% 100% 698.7 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 58% 552.4
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% 100% 613.6 L-tyrosine transporter 96% 903.3
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 65% 96% 609 L-tyrosine transporter 96% 903.3
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 44% 98% 408.3 L-tyrosine transporter 96% 903.3
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 44% 98% 408.3 L-tyrosine transporter 96% 903.3
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 43% 94% 397.9 L-tyrosine transporter 96% 903.3
L-histidine catabolism permease med histidine permease (characterized) 42% 97% 382.9 L-tyrosine transporter 96% 903.3
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 42% 99% 368.2 L-tyrosine transporter 96% 903.3
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 39% 96% 349.7 L-tyrosine transporter 96% 903.3
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 38% 91% 330.1 L-tyrosine transporter 96% 903.3
L-serine catabolism serP lo Serine permease SerP1 (characterized) 37% 86% 282.7 L-tyrosine transporter 96% 903.3
L-arginine catabolism rocE lo Amino-acid permease GAP1 (characterized) 34% 75% 248.4 L-tyrosine transporter 96% 903.3
L-lysine catabolism lysP lo lysine-specific permease (characterized) 34% 71% 246.5 L-tyrosine transporter 96% 903.3
L-asparagine catabolism AGP1 lo general amino acid permease AGP1 (characterized) 31% 69% 208 L-tyrosine transporter 96% 903.3

Sequence Analysis Tools

View Pf1N1B4_3559 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 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