GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS21680 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS21680 amino acid permease-associated protein

Length: 476 amino acids

Source: BFirm 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-proline catabolism proY hi GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 51% 94% 468.8 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 46% 412.5
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 37% 94% 332.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 37% 94% 332.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-histidine catabolism permease lo Aromatic amino acid permease, AroP (characterized) 39% 98% 328.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-phenylalanine catabolism aroP lo Aromatic amino acid permease, AroP (characterized) 39% 98% 328.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-tryptophan catabolism aroP lo Aromatic amino acid permease, AroP (characterized) 39% 98% 328.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-tyrosine catabolism aroP lo Aromatic amino acid permease, AroP (characterized) 39% 98% 328.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 36% 94% 313.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 38% 98% 306.2 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 34% 98% 295.8 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-lysine catabolism lysP lo The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) 36% 94% 290 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 35% 94% 285 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 36% 89% 279.6 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
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) 31% 94% 218.8 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
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) 31% 94% 218.8 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 31% 78% 201.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 31% 78% 201.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 31% 78% 201.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 51% 468.8

Sequence Analysis Tools

View BPHYT_RS21680 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MQRSTDTTELKAGLKQRHMTMIALGGVIGAGLFVGSGVVVQQAGPAAVLSFLITGALVVL
VMRMLGEMACAMPAVGSFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGA
KLVQFWLPDVPAWAISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYV
LGLWPAAKHVTAVLPTLLSHGGLMPKGIGPVLSGAVAATGFYFGAEIVTIAAAEAQEPAK
AVAKATNSVITRVLVFYVGSILLVVALVPWNSPKMATPYVSALDAMGIPAAASVMNAIVL
TAVLSALNSGLYAASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFGYASVVMSYV
SPDTVFAFLVNSYGTVAIFVYVLIAISQLKLRARIERDAPEKLRVRMWCYPYLTWVAIIG
MVGILVAMAFIPEQRQPLWFGVASLGVLLLAYLLRVRKPDAGFGEPDTLEYRHHHH

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, 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