GapMind for catabolism of small carbon sources

 

Protein SMc03135 in Sinorhizobium meliloti 1021

Annotation: SMc03135 amino-acid transport system ATP-binding ABC transporter protein

Length: 251 amino acids

Source: Smeli in FitnessBrowser

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism Pf6N2E2_5405 hi ABC transporter for D-Alanine, ATPase component (characterized) 74% 97% 382.9 AapP, 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) 69% 370.9
L-asparagine catabolism aapP med AapP, 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) 69% 97% 370.9 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-aspartate catabolism aapP med AapP, 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) 69% 97% 370.9 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-glutamate catabolism aapP med AapP, 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) 69% 97% 370.9 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-histidine catabolism aapP med AapP, 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) 69% 97% 370.9 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-leucine catabolism aapP med AapP, 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) 69% 97% 370.9 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-proline catabolism aapP med AapP, 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) 69% 97% 370.9 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 65% 94% 344.4 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 65% 94% 344.4 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-glutamate catabolism gltL med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 65% 94% 344.4 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 58% 99% 310.5 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 60% 97% 299.3 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 60% 97% 299.3 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 60% 100% 286.6 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 60% 100% 286.6 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 54% 99% 258.5 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 54% 99% 258.5 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 55% 100% 256.5 ABC transporter for D-Alanine, ATPase component 74% 382.9
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 52% 97% 251.1 ABC transporter for D-Alanine, ATPase component 74% 382.9

Sequence Analysis Tools

View SMc03135 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MPTSIDIASPEITLSGVHKWYGQYHALDDINLSIASREKVVICGPSGSGKSTLIRCVNRL
EAHQQGRIVVGGVEVGEDERKVDAIRREVGMVFQQFNLFPHLTILENCILAPMWVKRMPR
AQATEIAMDYLNRVRIPEQANKYPGQLSGGQQQRVAIARALCMNPKVMLFDEPTSALDPE
MVKEVLDTMVALANDGMTMVCVTHEMGFARQVADRVIFMDQGRIVEEGEPDEFFAHPKTD
RASLFLSQLLH

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