GapMind for catabolism of small carbon sources

 

Protein SMc02120 in Sinorhizobium meliloti 1021

Annotation: FitnessBrowser__Smeli:SMc02120

Length: 384 amino acids

Source: Smeli in FitnessBrowser

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism aapM hi ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 100% 100% 762.7 ABC transporter for D-Alanine, permease component 1 56% 401.7
L-asparagine catabolism aapM hi AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 74% 100% 583.6 ABC transporter for D-Alanine, permease component 1 56% 401.7
L-aspartate catabolism aapM hi AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 74% 100% 583.6 ABC transporter for D-Alanine, permease component 1 56% 401.7
L-glutamate catabolism aapM hi AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 74% 100% 583.6 ABC transporter for D-Alanine, permease component 1 56% 401.7
L-leucine catabolism aapM hi AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 74% 100% 583.6 ABC transporter for D-Alanine, permease component 1 56% 401.7
L-proline catabolism aapM hi AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 74% 100% 583.6 ABC transporter for D-Alanine, permease component 1 56% 401.7
D-alanine catabolism Pf6N2E2_5404 med ABC transporter for D-Alanine, permease component 1 (characterized) 56% 97% 401.7 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 100% 762.7
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 40% 99% 249.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 100% 762.7
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 40% 99% 249.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 100% 762.7
L-asparagine catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 47% 65% 239.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 100% 762.7
L-aspartate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 47% 65% 239.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 100% 762.7
L-glutamate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 47% 65% 239.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 100% 762.7
L-asparagine catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 33% 92% 118.6 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 100% 762.7
L-aspartate catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 33% 92% 118.6 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 100% 762.7
L-glutamate catabolism gltK lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 32% 96% 117.9 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 100% 762.7
L-asparagine catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 30% 90% 106.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 100% 762.7
L-aspartate catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 30% 90% 106.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 100% 762.7

Sequence Analysis Tools

View SMc02120 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MSTNQASFVRASMIEASPAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQ
WLFIDAAWSGGGRGVCATLSQGGSQPEGWSGACWAFVNAKFAQFLFGRYPLDERWRPALV
GILFVLLLVPMLIPRIPYKGLNALLLLVALPILSAILLPGGWFGLTYVETPLWGGLMVTL
VLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLP
QGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQ
ALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGLIFAGFV
FWLFCFGMSRYSGFMERLLDRSQR

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:

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