GapMind for catabolism of small carbon sources

 

Protein 8502447 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_3153 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Length: 233 amino acids

Source: Miya in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltJ hi Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 41% 90% 176.4 Probable glutamine ABC transporter permease protein GlnM 39% 152.5
L-asparagine catabolism aatQ hi PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 41% 90% 171.4 Probable glutamine ABC transporter permease protein GlnM 39% 152.5
L-aspartate catabolism aatQ hi PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 41% 90% 171.4 Probable glutamine ABC transporter permease protein GlnM 39% 152.5
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 33% 97% 136.7 Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida 41% 176.4
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 33% 97% 136.7 Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida 41% 176.4
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 33% 97% 136.7 Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida 41% 176.4
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 37% 72% 136 Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida 41% 176.4
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 37% 72% 136 Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida 41% 176.4
L-asparagine catabolism bztB lo glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 35% 51% 106.7 Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida 41% 176.4
L-aspartate catabolism bztB lo glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 35% 51% 106.7 Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida 41% 176.4
L-glutamate catabolism bztB lo glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 35% 51% 106.7 Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida 41% 176.4
D-alanine catabolism Pf6N2E2_5403 lo ABC transporter for D-Alanine, permease component 2 (characterized) 35% 53% 102.4 Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida 41% 176.4

Sequence Analysis Tools

View 8502447 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

MQYNFDWKLVLSGEYLQWIIDGVVVTCQISALSLVLAMALGTLIAVMRLSAVRPLVWFSA
GFTEFFRNTPLLVQIFFWYFGSDAVLPTAVNQWLYKQNFEFAAGVISLAVYTAAFIAEEI
RSGIFSIPRTQLEASRACGLTFLQAMRYVVLPQAFRIIVPPLISQALNLFKNSSLCMTIG
VMELTYMARQIESYTFHGFEAFTVSTLIYLTISLLVSFSITQYNKYFLRTIKY

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