GapMind for catabolism of small carbon sources

 

Protein AO356_18530 in Pseudomonas fluorescens FW300-N2C3

Annotation: AO356_18530 aromatic amino acid transporter

Length: 471 amino acids

Source: pseudo5_N2C3_1 in FitnessBrowser

Candidate for 16 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) 100% 100% 937.6 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 59% 563.5
L-tryptophan catabolism aroP hi Aromatic amino acid transport protein AroP (characterized, see rationale) 73% 99% 697.6 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 59% 563.5
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% 98% 620.2 L-tyrosine transporter 100% 937.6
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 65% 97% 617.8 L-tyrosine transporter 100% 937.6
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 44% 98% 413.3 L-tyrosine transporter 100% 937.6
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 44% 98% 413.3 L-tyrosine transporter 100% 937.6
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 43% 94% 396.4 L-tyrosine transporter 100% 937.6
L-histidine catabolism permease med histidine permease (characterized) 42% 97% 387.1 L-tyrosine transporter 100% 937.6
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 42% 99% 372.9 L-tyrosine transporter 100% 937.6
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 38% 96% 352.1 L-tyrosine transporter 100% 937.6
L-asparagine catabolism ansP lo L-asparagine permease; L-asparagine transport protein (characterized) 37% 91% 327 L-tyrosine transporter 100% 937.6
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) 37% 86% 289.7 L-tyrosine transporter 100% 937.6
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) 37% 86% 289.7 L-tyrosine transporter 100% 937.6
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 34% 100% 284.6 L-tyrosine transporter 100% 937.6
L-lysine catabolism lysP lo Probable lysine/arginine permease CAN2; Basic amino acids permease CAN2 (characterized) 32% 82% 240.7 L-tyrosine transporter 100% 937.6
L-asparagine catabolism AGP1 lo general amino acid permease AGP1 (characterized) 31% 69% 208.8 L-tyrosine transporter 100% 937.6

Sequence Analysis Tools

View AO356_18530 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

MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF
MIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY
WAPDIPTWVSAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG
GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ
VIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV
VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLN
YLVPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALWYPYGNYICLA
FVVFILGVMLLIPGIQISVYAIPVWVVFMWVCYVIKNKRSARQELAVAAAK

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 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