GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_1639 in Pseudomonas fluorescens FW300-N1B4

Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1639

Length: 464 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 12 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 med GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 52% 97% 464.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
L-histidine catabolism permease med Aromatic amino acid permease, AroP (characterized) 42% 95% 362.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
L-phenylalanine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 42% 95% 362.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
L-tryptophan catabolism aroP med Aromatic amino acid permease, AroP (characterized) 42% 95% 362.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
L-tyrosine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 42% 95% 362.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
L-lysine catabolism lysP lo The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) 37% 90% 300.4 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
L-alanine catabolism cycA lo General amino-acid permease GAP2 (characterized) 35% 68% 243.8 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 82% 233.4 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 82% 233.4 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 82% 233.4 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
L-arginine catabolism rocE lo uncharacterized amino-acid permease C869.11 (characterized) 31% 76% 212.6 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 31% 77% 207.2 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3

Sequence Analysis Tools

View Pf1N1B4_1639 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

MSSSQSSSNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVV
LVMRMLGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHA
WFPNVAIWAFTLVITLLLTATNLFSVKNYGEFEFWFALVKVIAIIGFIGLGILAIFGFLP
TSQVSGVSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATN
SVIWRIGLFYLVSIFIVVALVPWNDPILASVGSYQTVLERMGIPNAKLIVDIVVLVAVTS
CLNSALYTASRMMFSLGKRGDAPAVSQRTNSSGTPYWAVMLSTAAAFLAVFANYVAPAAV
FEFLLASSGAIALLVYLVIAISQLRMRKQRMARGEKIAFSMWLFPGLTYAVIVFIVAALT
IMLFQEAHRVEILATGLLSALVVAAGLLVARRRRNEKLTAAIAR

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