GapMind for catabolism of small carbon sources

 

Protein RR42_RS28305 in Cupriavidus basilensis 4G11

Annotation: RR42_RS28305 proline-specific permease

Length: 472 amino acids

Source: Cup4G11 in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-threonine catabolism RR42_RS28305 hi D-serine/D-alanine/glycine transporter (characterized, see rationale) 100% 100% 937.9 L-alanine and D-alanine permease 55% 519.2
D-alanine catabolism cycA hi L-alanine and D-alanine permease (characterized) 55% 96% 519.2 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 45% 427.6
L-alanine catabolism cycA hi L-alanine and D-alanine permease (characterized) 55% 96% 519.2 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 45% 427.6
D-serine catabolism cycA med D-serine/D-alanine/glycine transporter (characterized) 46% 99% 439.5 L-alanine and D-alanine permease 55% 519.2
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) 45% 99% 427.6 L-alanine and D-alanine permease 55% 519.2
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% 427.6 L-alanine and D-alanine permease 55% 519.2
L-tyrosine 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% 427.6 L-alanine and D-alanine permease 55% 519.2
L-histidine catabolism permease med histidine permease (characterized) 46% 94% 423.7 L-alanine and D-alanine permease 55% 519.2
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 45% 97% 422.2 L-alanine and D-alanine permease 55% 519.2
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 43% 98% 421.8 L-alanine and D-alanine permease 55% 519.2
L-asparagine catabolism ansP med Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 45% 93% 413.7 L-alanine and D-alanine permease 55% 519.2
L-lysine catabolism lysP lo The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) 38% 97% 328.9 L-alanine and D-alanine permease 55% 519.2
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 37% 95% 311.2 L-alanine and D-alanine permease 55% 519.2
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% 100% 291.6 L-alanine and D-alanine permease 55% 519.2
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% 100% 291.6 L-alanine and D-alanine permease 55% 519.2
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 30% 87% 217.2 L-alanine and D-alanine permease 55% 519.2
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 30% 87% 217.2 L-alanine and D-alanine permease 55% 519.2
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 30% 87% 217.2 L-alanine and D-alanine permease 55% 519.2

Sequence Analysis Tools

View RR42_RS28305 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

MTDVRKLLNEERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSY
AIGGVAIFFIMRALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEIT
AVAVYVHYWFPDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGL
AIIFFGVTPLGPTASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNP
EKVLPHATNGVVWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNL
VVITAAASSCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLL
NYIVPEQVFVWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLV
VAFMIAVAVLLSLDPGTRVALYVAPVWFALLGIGYRFTKSRALLEGHVQKSA

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