GapMind for catabolism of small carbon sources

 

Protein PP_4495 in Pseudomonas putida KT2440

Annotation: FitnessBrowser__Putida:PP_4495

Length: 472 amino acids

Source: Putida in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-tyrosine catabolism aroP hi L-tyrosine transporter (characterized) 84% 99% 806.6 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 57% 549.3
L-tryptophan catabolism aroP hi Aromatic amino acid transport protein AroP (characterized, see rationale) 71% 98% 686.4 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 57% 549.3
L-phenylalanine 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) 66% 98% 612.1 L-tyrosine transporter 84% 806.6
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 65% 95% 597.8 L-tyrosine transporter 84% 806.6
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 46% 94% 412.9 L-tyrosine transporter 84% 806.6
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 46% 94% 412.9 L-tyrosine transporter 84% 806.6
L-histidine catabolism permease med histidine permease (characterized) 42% 97% 377.5 L-tyrosine transporter 84% 806.6
D-serine catabolism cycA lo D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized) 38% 80% 330.9 L-tyrosine transporter 84% 806.6
L-lysine catabolism lysP lo Lysine/arginine permease CAN1; Basic amino acids permease CAN1 (characterized) 33% 77% 239.6 L-tyrosine transporter 84% 806.6
L-asparagine catabolism AGP1 lo general amino acid permease AGP1 (characterized) 30% 68% 201.1 L-tyrosine transporter 84% 806.6

Sequence Analysis Tools

View PP_4495 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

MSGQNMHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVMKSAGPSMILGYAICGFIAF
MIMRQLGEMIVEEPVAGSFSHFAHTYWGGFAGFLSGWNCWVLYILVGMSELSAVGKYVHY
WWPEIPTWVTAAAFFVLINAINLMNVKFFGEAEFWFAIIKVVAIVSMIGLGAYLLTSGSG
GPEATVANLWTHGGFFPNGVSGLVMALAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ
VIYRILIFYVGALVVLLSLTPWDNLVASIDASGGSYGSSPFVQVFSLLGSDVAANLLNFV
VLTAALSVYNSGTYCNARMLLGMAEQGDAPASLAKVDKRGVPVRSILVSAAVTFVAVLLN
YLMPQNALELLMSLVVATLVINWAMISYSHLKFRQHLDRTGQKPLFKALWYPYGNYVVLA
FVVLILGIMLMIPGIQVSVYAIPVWLLAMLVVYMVKSRRQVNAGGAVETVAK

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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