GapMind for catabolism of small carbon sources

 

Protein 8502073 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Length: 596 amino acids

Source: Miya 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 natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 39% 67% 155.2
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 39% 67% 155.2
L-asparagine catabolism aatQ lo ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized) 36% 97% 152.1 Basic amino acid uptake transporter, BgtAB 40% 163.3
L-aspartate catabolism aatQ lo ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized) 36% 97% 152.1 Basic amino acid uptake transporter, BgtAB 40% 163.3
L-glutamate catabolism gltJ lo ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized) 36% 97% 152.1 Basic amino acid uptake transporter, BgtAB 40% 163.3
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 36% 67% 144.4 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-asparagine catabolism aapM lo 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) 35% 67% 142.5 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-aspartate catabolism aapM lo 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) 35% 67% 142.5 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-glutamate catabolism aapM lo 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) 35% 67% 142.5 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-leucine catabolism aapM lo 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) 35% 67% 142.5 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-proline catabolism aapM lo 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) 35% 67% 142.5 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-asparagine catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 69% 140.6 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-aspartate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 69% 140.6 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-glutamate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 69% 140.6 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 39% 56% 137.1 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 32% 91% 132.5 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 32% 91% 132.5 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 32% 91% 132.5 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
L-asparagine catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 39% 88% 126.3 Basic amino acid uptake transporter, BgtAB 40% 163.3
L-aspartate catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 39% 88% 126.3 Basic amino acid uptake transporter, BgtAB 40% 163.3
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 33% 81% 112.5 Basic amino acid uptake transporter, BgtAB 40% 163.3
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 33% 96% 109 Basic amino acid uptake transporter, BgtAB 40% 163.3

Sequence Analysis Tools

View 8502073 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

MIRYWLEKTWVQNAVLISLATFAIYYCGWVFDFGYEFKWSMLFTRNETYGVVMGAEILKG
LANTVRISLISSALALLLGTMLGLARLSLFRPLRVTATCVIEFFRNTPLLIQLFFWYFAF
PAILPDNAREALFSIQFEFWCATIGLSIYTASFMAEVIRAGLQSIPKGLLEAAYSSGLSY
FQVLRTIILPLAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELTWHAQQVESLTFKGFEAT
SAATVLYLSLSLIISFILNGVNGRMRLDTAPGRSIPVLVVGALLTPLGLIRRMFIRPVTR
ALRARRRAAAQTTYTPLAAMLHQWGGYAARAAVLAGKGLFVALLAGLLYSVGKGLLGFQW
HVVFENLRSLLIWHFPTGRPDEMFLGLGGLAYSLLMAVIAISVSFFIGLAVGVGRSSSNR
VFRIPCLLYIELIRGNPLIIVIFWVYFFIPVMFGTTLNVFWSATWALTAFTGAYIAEIVR
TGIQNIPAGQVEAAYSTGLTYLQAMRRIVLPQALKQMIPAIVGQFIAIFKDTSLAFVLGV
LELTFVAQGINNRLMIHPMEIYGTVAFLYFICCYSMSVFAARLERRLSPEKVSLRM

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