GapMind for catabolism of small carbon sources

 

Protein SMa2197 in Sinorhizobium meliloti 1021

Annotation: SMa2197 ABC transporter permease

Length: 304 amino acids

Source: Smeli 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-asparagine catabolism aatM lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 33% 93% 114.4 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 34% 136.7
L-aspartate catabolism aatM lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 33% 93% 114.4 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 34% 136.7
L-glutamate catabolism gltK lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 33% 93% 114.4 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 34% 136.7
L-asparagine catabolism aatQ lo ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized) 31% 96% 113.6 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 34% 136.7
L-aspartate catabolism aatQ lo ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized) 31% 96% 113.6 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 34% 136.7
L-glutamate catabolism gltJ lo ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized) 31% 96% 113.6 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 34% 136.7
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 30% 77% 100.9 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 34% 136.7
L-asparagine catabolism bgtB' lo ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 32% 53% 100.1 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 34% 136.7
L-aspartate catabolism bgtB' lo ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 32% 53% 100.1 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 34% 136.7

Sequence Analysis Tools

View SMa2197 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

MSNDLTLAPTASPDRPMLTYVPASTWKTRFAATLLILLVLYCATMIASNPNFGWDVVADY
LFDSRILWGLSLTVWLTVVTMVIGVVLGTIFAIMAMADNVVISTVANAYIWFFRGTPVLV
QLIFWYNLGALFPQLSVGVPFTSLWVSVPTNTLISPVTAAVLGLGLNEGAYMSEIIRSGL
MSVDPGQRQAAKSLGMTNGKTLWRILLPQAMPVIIPPTGNQTIGMLKTSSLVSVISLADL
LYSAQTIYSRNFQTIPLLIVACIWYLAATTILSAVQVRIERHFARSSQRANITQPRRLFR
QKAR

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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