GapMind for catabolism of small carbon sources

 

Protein GFF1660 in Pseudomonas stutzeri RCH2

Annotation: Psest_1697 Gamma-aminobutyrate permease and related permeases

Length: 464 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-tryptophan catabolism aroP hi Aromatic amino acid transport protein AroP (characterized, see rationale) 79% 98% 738.4 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 61% 567.8
L-tyrosine catabolism aroP hi L-tyrosine transporter (characterized) 74% 98% 708.4 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 61% 567.8
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 69% 98% 633.6 L-tyrosine transporter 74% 708.4
L-phenylalanine catabolism aroP med Aromatic amino acid transport protein AroP (characterized, see rationale) 67% 95% 624.4 L-tyrosine transporter 74% 708.4
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 44% 97% 404.1 L-tyrosine transporter 74% 708.4
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 45% 94% 403.7 L-tyrosine transporter 74% 708.4
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 45% 94% 403.7 L-tyrosine transporter 74% 708.4
L-histidine catabolism permease med histidine permease (characterized) 43% 98% 381.7 L-tyrosine transporter 74% 708.4
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 44% 99% 381.7 L-tyrosine transporter 74% 708.4
D-serine catabolism cycA med D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized) 40% 80% 332 L-tyrosine transporter 74% 708.4
L-asparagine catabolism ansP lo L-asparagine permease; L-asparagine transport protein (characterized) 36% 90% 320.5 L-tyrosine transporter 74% 708.4
L-serine catabolism serP lo Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized) 38% 91% 303.5 L-tyrosine transporter 74% 708.4
L-threonine catabolism serP1 lo Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized) 38% 91% 303.5 L-tyrosine transporter 74% 708.4
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 37% 94% 303.1 L-tyrosine transporter 74% 708.4
L-lysine catabolism lysP lo Lysine permease LysP (characterized) 36% 92% 287.7 L-tyrosine transporter 74% 708.4
L-asparagine catabolism AGP1 lo general amino acid permease AGP1 (characterized) 32% 70% 228.8 L-tyrosine transporter 74% 708.4
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 79% 228.8 L-tyrosine transporter 74% 708.4
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 79% 228.8 L-tyrosine transporter 74% 708.4
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 79% 228.8 L-tyrosine transporter 74% 708.4
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 33% 66% 212.2 L-tyrosine transporter 74% 708.4

Sequence Analysis Tools

View GFF1660 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTAETLHTGSLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAF
LIMRQLGEMIVEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQF
WWPEVPTWATAAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVSGKG
GEQASISNLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQ
VVYRILIFYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFV
VLTAALSVYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVN
YLFPQGALELLMSLAVAALVINWAMISLAHLKFRRAMQQQGVEPSFKAFWFPLSNYLCLA
FVAGILIIMLWLPGIRMSVFAIPVWVGFLWLCYRLRARLLARAV

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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