GapMind for catabolism of small carbon sources

 

Protein 3610346 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_3727 ABC transporter related (RefSeq)

Length: 246 amino acids

Source: Dino in FitnessBrowser

Candidate for 13 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 transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 41% 99% 186.8 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 39% 175.3
L-leucine catabolism livG hi High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 41% 99% 186.8 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 39% 175.3
L-valine catabolism livG hi High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 41% 99% 186.8 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 39% 175.3
L-phenylalanine catabolism livG hi High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 41% 98% 186.4 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 39% 175.3
L-alanine catabolism braF med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 41% 99% 186.8 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 40% 182.2
L-serine catabolism braF med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 41% 99% 186.8 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 40% 182.2
L-threonine catabolism braF med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 41% 99% 186.8 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 40% 182.2
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 35% 99% 174.5 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 41% 186.8
L-arginine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 39% 88% 170.2 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 41% 186.8
L-glutamate catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 39% 88% 170.2 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 41% 186.8
L-histidine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 39% 88% 170.2 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 41% 186.8
D-alanine catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 40% 89% 166.4 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 41% 186.8
L-proline catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 40% 89% 166.4 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 41% 186.8

Sequence Analysis Tools

View 3610346 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTPILQTDRLGISFGGLRAVDAISFDALPNQITTVIGPNGAGKTTLFNLISGALKPGSGS
VNLDGRDVTRAGPAELQRAGLARSFQITNLFFDMTVRENLRLATQVLEPASHLMRPLRRT
GRAANKVDELIARFELHDKVHEQVGYLSHGEQRRLEIAMCLACEPKVLMLDEPTQGMSHA
DTEETEALIRGLTDHVSILLIEHDIGIVMAVSDHVIVMHQGQKIADGTPTEVRANPAVQA
AYFGHG

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