GapMind for catabolism of small carbon sources

 

Protein 3606889 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Length: 411 amino acids

Source: Dino in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism bztB hi glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 53% 99% 419.1 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 45% 312.0
L-aspartate catabolism bztB hi glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 53% 99% 419.1 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 45% 312.0
L-glutamate catabolism bztB hi glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 53% 99% 419.1 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 45% 312.0
L-histidine catabolism aapQ med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized) 45% 99% 312 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
D-alanine catabolism Pf6N2E2_5403 med ABC transporter for D-Alanine, permease component 2 (characterized) 44% 100% 293.9 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-asparagine catabolism aapQ med AapQ, 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) 43% 94% 292 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-aspartate catabolism aapQ med AapQ, 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) 43% 94% 292 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-glutamate catabolism aapQ med AapQ, 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) 43% 94% 292 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-leucine catabolism aapQ med AapQ, 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) 43% 94% 292 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-proline catabolism aapQ med AapQ, 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) 43% 94% 292 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-asparagine catabolism natG med NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 42% 78% 156.8 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-aspartate catabolism natG med NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 42% 78% 156.8 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-asparagine catabolism bgtB' lo ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 36% 97% 213.8 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-aspartate catabolism bgtB' lo ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 36% 97% 213.8 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 95% 95.5 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 95% 95.5 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-glutamate catabolism gltJ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 95% 95.5 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 36% 54% 76.6 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 36% 54% 76.6 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 36% 54% 76.6 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-lysine catabolism hisM lo ABC transporter for L-Lysine, permease component 2 (characterized) 31% 69% 68.6 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1
L-arginine catabolism artQ lo ABC transporter for L-Arginine, permease component 1 (characterized) 31% 51% 61.6 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB 53% 419.1

Sequence Analysis Tools

View 3606889 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

MTTFSDPPPASGPPNQPFNLGMLINDTRYRGYTFQFIALIALIFFFGWLVSNAIYNLAAL
GQDINFSFLGQPASYEIDQTLIPYTSTDTHMRAAFVGLLNTLLVAFLGCITATIFGVLAG
VLRLSKNWLVAKVMSVYVEIFRNIPVLIWIVIISAVMSQALPQPRAFRGEDATATMVLWD
SVAFTNRGVYIPAPVWNPGSGIVVAVFVLSIIGIFVFRRYAKNLLFNTGKLLPVGRISLA
IFFVPTLLAFFVMGRPIGLDYPELGGFNFRGGINIRGTLIALWFALALYTGAFIAENVRA
GILAVSKGQTEAAAALGMRPNRIMSLIILPQALRVIIPPVISQYLNLTKNSSLAAAIGYM
DLTGTLGGVTLNQTGRSFECVLLLMLFYLLISLSISALMNLYNNAVKLKER

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