GapMind for catabolism of small carbon sources

 

Protein GFF4632 in Pseudomonas simiae WCS417

Annotation: PS417_23700 aromatic amino acid transporter

Length: 467 amino acids

Source: WCS417 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) 85% 98% 785.8 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 58% 560.1
L-tyrosine catabolism aroP hi L-tyrosine transporter (characterized) 75% 96% 703.7 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 58% 560.1
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 67% 99% 636.7 L-tyrosine transporter 75% 703.7
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) 67% 97% 619.4 L-tyrosine transporter 75% 703.7
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 44% 94% 409.1 L-tyrosine transporter 75% 703.7
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 44% 92% 404.8 L-tyrosine transporter 75% 703.7
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 44% 92% 404.8 L-tyrosine transporter 75% 703.7
L-histidine catabolism permease med histidine permease (characterized) 43% 96% 384 L-tyrosine transporter 75% 703.7
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 42% 99% 370.5 L-tyrosine transporter 75% 703.7
D-serine catabolism cycA med D-serine/D-alanine/glycine transporter (characterized) 41% 94% 355.5 L-tyrosine transporter 75% 703.7
L-asparagine catabolism ansP lo L-asparagine permease; L-asparagine transport protein (characterized) 37% 91% 325.5 L-tyrosine transporter 75% 703.7
L-serine catabolism serP lo Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized) 39% 94% 313.2 L-tyrosine transporter 75% 703.7
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) 39% 91% 307.4 L-tyrosine transporter 75% 703.7
L-lysine catabolism lysP lo Lysine permease LysP (characterized) 38% 90% 297.4 L-tyrosine transporter 75% 703.7
L-arginine catabolism rocE lo arginine permease (characterized) 36% 74% 265.8 L-tyrosine transporter 75% 703.7
L-asparagine catabolism AGP1 lo general amino acid permease AGP1 (characterized) 31% 74% 228.8 L-tyrosine transporter 75% 703.7
L-isoleucine catabolism Bap2 lo Leu/Val/Ile amino-acid permease; Branched-chain amino-acid permease 2 (characterized) 32% 78% 225.3 L-tyrosine transporter 75% 703.7
L-valine catabolism Bap2 lo Leu/Val/Ile amino-acid permease; Branched-chain amino-acid permease 2 (characterized) 32% 78% 225.3 L-tyrosine transporter 75% 703.7
L-leucine catabolism Bap2 lo Leu/Val/Ile amino-acid permease (characterized) 31% 78% 218 L-tyrosine transporter 75% 703.7
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 33% 67% 208 L-tyrosine transporter 75% 703.7

Sequence Analysis Tools

View GFF4632 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MADDMVNPVGLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAF
LIMRQLGEMIVEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQF
WWPDIPTWVSALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTG
GPQASVSNLWSHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQ
VVYRILIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFV
VLTAALSVYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVN
YVAPQSALELLFALVVASLMINWALISITHIKFRKAMGEQGVTPSFKTFWFPFSNYLCLA
FMVMIISVMLAIPGISESVYAMPVWVGIIYVAYRLRVRRSHAVVNAQ

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 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