GapMind for catabolism of small carbon sources

 

Protein BWI76_RS07360 in Klebsiella michiganensis M5al

Annotation: BWI76_RS07360 phenylalanine transporter

Length: 458 amino acids

Source: Koxy 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-phenylalanine catabolism aroP hi Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) 89% 100% 818.5 L-tyrosine transporter 60% 567.8
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) 63% 98% 604 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
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) 63% 98% 604 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 62% 97% 577 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 46% 94% 415.6 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 46% 94% 415.6 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 45% 98% 397.5 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
L-histidine catabolism permease med histidine permease (characterized) 44% 94% 380.6 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 40% 88% 335.9 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
D-serine catabolism cycA 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) 36% 98% 305.4 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
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) 36% 98% 305.4 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
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% 305.1 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
L-arginine catabolism rocE lo arginine permease (characterized) 35% 81% 271.6 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 35% 80% 245.7 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 35% 80% 245.7 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 35% 80% 245.7 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
L-tryptophan catabolism TAT lo valine/tyrosine/tryptophan amino-acid permease (characterized) 32% 70% 213.4 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5
L-tyrosine catabolism TAT1 lo valine/tyrosine/tryptophan amino-acid permease (characterized) 32% 70% 213.4 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5

Sequence Analysis Tools

View BWI76_RS07360 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

MKDASTSSETIEESGPTLHRGLQNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYA
VAGIVAFLIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTA
AGIYMQYWLPDVPTWIWAAAFFLIINAVNLVNVRLYGEAEFWFALIKVLAIIGMIGFGLW
MLFGGHGGSKAGIDNLWKHGGFFATGWHGLIMSLAVIMFSFGGLELIGITAAEAQNPEKS
IPKAVNQVVYRILLFYIGSLVVLLALYPWVEIQSDSSPFVMIFHNLDSNVVASALNFVIL
VASLSVYNSGVYSNSRMLFGLSVQGNAPKFLARVSKRGVPVNSLLLSGIITSLVVVLNYL
LPQKALGLLMALVVATLLLNWIMICLAHLKFRAAQRRKGREPKFKALLSPASNYICIAFL
ALILVLMCTIDGMRLSAILLPVWILFLFAAFKTLRRTA

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