GapMind for catabolism of small carbon sources

 

Protein GFF559 in Pseudomonas stutzeri RCH2

Annotation: Psest_0564 urea ABC transporter, ATP-binding protein UrtD

Length: 283 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 9 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 lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 36% 89% 144.1 UrtD, component of The high-affinity (<1 μM) urea porter 45% 201.1
L-glutamate catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 36% 89% 144.1 UrtD, component of The high-affinity (<1 μM) urea porter 45% 201.1
L-histidine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 36% 89% 144.1 UrtD, component of The high-affinity (<1 μM) urea porter 45% 201.1
L-isoleucine catabolism livG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 36% 89% 144.1 UrtD, component of The high-affinity (<1 μM) urea porter 45% 201.1
L-leucine catabolism livG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 36% 89% 144.1 UrtD, component of The high-affinity (<1 μM) urea porter 45% 201.1
L-valine catabolism livG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 36% 89% 144.1 UrtD, component of The high-affinity (<1 μM) urea porter 45% 201.1
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 98% 138.3 UrtD, component of The high-affinity (<1 μM) urea porter 45% 201.1
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 98% 138.3 UrtD, component of The high-affinity (<1 μM) urea porter 45% 201.1
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 98% 138.3 UrtD, component of The high-affinity (<1 μM) urea porter 45% 201.1

Sequence Analysis Tools

View GFF559 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

MKTVPCSAVIDGFDPTGGGLTRDAIGLGRVAEKGLDVRHGTILSLEDINVSFDGFKALTD
LSLYIGVGELRCIIGPNGAGKTTMMDVITGKTRPTSGSAWFGETLDLTRMSEVDIAQAGI
GRKFQKPTVFEALSVFENLELAQKTDKSVWASLRAKLSGEQKDRIDEVLETIRLGQSRHR
PAGLLSHGQKQFLEIGMLLMQSPQLLLLDEPVAGMTDAETEFTAELFKSLARKHSLMVVE
HDMGFVETIADHVTVLHQGQVLAEGSLQQVQADERVIEVYLGR

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