GapMind for catabolism of small carbon sources

 

Protein PP_4864 in Pseudomonas putida KT2440

Annotation: FitnessBrowser__Putida:PP_4864

Length: 291 amino acids

Source: Putida in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism braF hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 92% 270 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 49% 253.1
L-glutamate catabolism braF hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 92% 270 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 49% 253.1
L-histidine catabolism braF hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 92% 270 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 49% 253.1
L-isoleucine catabolism livG hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 92% 270 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 46% 146.0
L-leucine catabolism livG hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 92% 270 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 46% 146.0
L-valine catabolism livG hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 92% 270 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 46% 146.0
D-alanine catabolism AZOBR_RS08245 hi Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 48% 91% 263.5 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 49% 253.1
L-proline catabolism AZOBR_RS08245 hi Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 48% 91% 263.5 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 49% 253.1
L-alanine catabolism braF hi High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 48% 98% 250.4 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 53% 209.1
L-serine catabolism braF hi High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 48% 98% 250.4 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 53% 209.1
L-threonine catabolism braF hi High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 48% 98% 250.4 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 53% 209.1
L-proline catabolism HSERO_RS00895 med ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 40% 98% 191.4 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 49% 253.1
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 46% 70% 156.4 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 48% 172.9
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 46% 70% 156.4 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 49% 253.1
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 46% 70% 156.4 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 49% 253.1

Sequence Analysis Tools

View PP_4864 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

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Sequence

MSDDIILSVDNLMMQFGGIKALSDVSLKVRRNQIFALIGPNGAGKTTVFNCLTGFYKASG
GRIELNVRGSHTNVIQLLGERFQAADFVSPARFANRMYYKMFGGTHLVNRAGLARTFQNI
RLFKEMSVVENLLVAQHMWVNRNLLAGVLNTKAYRKAESDALDHAFYWLEVVDLVDCANR
LAGELSYGQQRRLEIARAMCTRPKIICLDEPAAGLNPQETEALSRMIRVLRDEHDITVVL
IEHDMGMVMSISDHIVVLDHGNVIAEGAPQDIRHNPTVIAAYLGADEEELV

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