GapMind for catabolism of small carbon sources

 

Protein GFF2162 in Pseudomonas simiae WCS417

Annotation: PS417_11030 L-arabinose transporter ATP-binding protein

Length: 500 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism BPHYT_RS16930 hi Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 86% 96% 825.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.8
L-arabinose catabolism araG hi L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 60% 97% 582.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 44% 411.0
D-ribose catabolism rbsA med ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 44% 98% 411 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.8
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 42% 95% 392.5 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.8
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 43% 97% 389.4 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.8
myo-inositol catabolism iatA med Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 45% 95% 387.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.8
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 43% 94% 365.9 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.8
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 43% 94% 365.9 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.8
L-rhamnose catabolism rhaT' med RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) 41% 96% 361.7 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.8
D-xylose catabolism xylG med Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized) 40% 97% 353.6 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.8
D-galactose catabolism ytfR lo galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 38% 97% 349.7 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.8

Sequence Analysis Tools

View GFF2162 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

MTAAALRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNSG
TLHIGEQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGHLPSRFGVVNRGLLRK
QALACLKGLADEIDPAEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRL
MAIIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALTHDQLVTCMVG
RDIQDIYDYRPREHGEVALKVDGLLGPGLREPVSFNVRKGEILGLFGLVGAGRTELFRLL
SGLERASAGQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGA
HSTFGWLLREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVLL
LDEPTRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQT
REHATESNLLQLALPRSVAN

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, the preprint 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