GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS15500 in Burkholderia phytofirmans PsJN

Annotation: FitnessBrowser__BFirm:BPHYT_RS15500

Length: 461 amino acids

Source: BFirm 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
phenylacetate catabolism H281DRAFT_04042 hi Aromatic amino acid transporter AroP (characterized, see rationale) 96% 100% 883.6 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-phenylalanine catabolism aroP hi Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) 70% 98% 654.4 L-tyrosine transporter 66% 629.0
L-tryptophan catabolism aroP hi Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) 70% 98% 654.4 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 61% 572.8
L-tyrosine catabolism aroP hi Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) 70% 98% 654.4 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 61% 572.8
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 44% 96% 428.7 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 45% 97% 413.7 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 45% 97% 413.7 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 44% 98% 399.1 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-histidine catabolism permease med histidine permease (characterized) 43% 97% 392.9 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 39% 98% 362.1 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 38% 91% 336.3 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-lysine catabolism lysP lo The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) 36% 97% 306.6 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
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) 37% 100% 302.4 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 35% 99% 301.2 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
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% 98% 300.1 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 81% 231.5 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 81% 231.5 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 81% 231.5 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-asparagine catabolism AGP1 lo general amino acid permease AGP1 (characterized) 32% 69% 224.6 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 33% 74% 224.2 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 70% 654.4

Sequence Analysis Tools

View BPHYT_RS15500 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MNSAQQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIAFM
IMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYW
WPGVPTWVSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHGG
PQASITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQV
IYRILIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYN
SGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGL
LMALVVAALVLNWALISLTHLKSRKAMVAAGETLVFKSFWFPVSNWICLAFMALILVILA
MTPGLSVSVWLVPAWLVVMWAGYVFKRRRAAVQGGARVVGR

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:

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