GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_801 in Pseudomonas fluorescens FW300-N1B4

Annotation: D-serine/D-alanine/glycine transporter

Length: 473 amino acids

Source: pseudo1_N1B4 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
D-alanine catabolism cycA hi L-alanine and D-alanine permease (characterized) 96% 100% 912.5 Proline-specific permease (ProY) 57% 528.5
L-alanine catabolism cycA hi L-alanine and D-alanine permease (characterized) 96% 100% 912.5 Proline-specific permease (ProY) 57% 528.5
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 57% 96% 528.5 L-alanine and D-alanine permease 96% 912.5
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 56% 92% 512.7 L-alanine and D-alanine permease 96% 912.5
L-histidine catabolism permease med histidine permease (characterized) 54% 96% 507.7 L-alanine and D-alanine permease 96% 912.5
L-tyrosine catabolism aroP med L-tyrosine transporter (characterized) 44% 100% 412.1 L-alanine and D-alanine permease 96% 912.5
L-phenylalanine catabolism aroP med Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) 45% 98% 411 L-alanine and D-alanine permease 96% 912.5
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 45% 96% 405.6 L-alanine and D-alanine permease 96% 912.5
L-tryptophan catabolism aroP med Aromatic amino acid transport protein AroP (characterized, see rationale) 45% 100% 402.1 L-alanine and D-alanine permease 96% 912.5
D-serine catabolism cycA med D-serine/D-alanine/glycine transporter (characterized) 43% 93% 377.5 L-alanine and D-alanine permease 96% 912.5
L-asparagine catabolism ansP med Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 41% 92% 367.9 L-alanine and D-alanine permease 96% 912.5
L-lysine catabolism lysP med Lysine permease LysP (characterized) 40% 90% 314.7 L-alanine and D-alanine permease 96% 912.5
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 37% 98% 326.2 L-alanine and D-alanine permease 96% 912.5
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) 37% 98% 293.5 L-alanine and D-alanine permease 96% 912.5
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 87% 239.2 L-alanine and D-alanine permease 96% 912.5
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 87% 239.2 L-alanine and D-alanine permease 96% 912.5
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 87% 239.2 L-alanine and D-alanine permease 96% 912.5
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 34% 66% 206.1 L-alanine and D-alanine permease 96% 912.5

Sequence Analysis Tools

View Pf1N1B4_801 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

MPVGNHLPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI
IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA
VAVYMGVWFPDVPRWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVVGGIG
VIAFGFGNDGVALGISNLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQ
KTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFV
VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSNNGVPRRALLLSIGALLLGVLLN
YLVPEKVFVWVTAIATFGAIWTWVMILLAQLKFRQGLSASERAGLKYRMWLYPVSSYLAL
AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQPSNVSQGAVRSAS

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