GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_801 in Pseudomonas fluorescens FW300-N1B4

Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_801

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

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

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 (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