GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_1379 in Pseudomonas fluorescens FW300-N1B4

Annotation: Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Length: 290 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-isoleucine catabolism livG hi High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 53% 99% 290.8 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 42% 202.2
L-phenylalanine catabolism livG hi High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 53% 99% 290.8 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 42% 202.2
L-arginine catabolism braF hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 91% 268.9 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 50% 227.3
L-glutamate catabolism braF hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 91% 268.9 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 50% 227.3
L-histidine catabolism braF hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 91% 268.9 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 50% 227.3
L-leucine catabolism livG hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 91% 268.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 42% 202.2
L-valine catabolism livG hi ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 48% 91% 268.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 42% 202.2
L-proline catabolism HSERO_RS00895 med ABC transporter ATP-binding protein (characterized, see rationale) 42% 97% 217.6 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 50% 227.3
L-serine catabolism Ac3H11_1693 med ABC transporter ATP-binding protein (characterized, see rationale) 42% 97% 217.6 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 50% 227.3
L-tyrosine catabolism Ac3H11_1693 med ABC transporter ATP-binding protein (characterized, see rationale) 42% 97% 217.6 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 50% 227.3
D-alanine catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 56% 64% 206.5 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 50% 227.3
L-proline catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 56% 64% 206.5 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 50% 227.3

Sequence Analysis Tools

View Pf1N1B4_1379 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

MSEVVLSVDKLMMHFGGIKALSDVSLKVKRNSIFALIGPNGAGKTTVFNCLTGFYKASGG
HIELNTRGVKTDVIKMLGEPFKAVDFVSPKSFINRLRYKMFGGTHLINRAGLARTFQNIR
LFREMSVLENLLVAQHMWVNRGMLAGILNTKGYRKAESDALDHAFYWLEVVDLVDCANRL
AGELSYGQQRRLEIARAMCTRPQIICLDEPAAGLNPQETEALSAMIRLLRDEHDLTVVLI
EHDMGMVMSISDHIVVLDHGVVIAEGGPEAIRHDPKVIAAYLGAEEEEVV

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