GapMind for catabolism of small carbon sources

 

Protein 8502446 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_3152 extracellular solute-binding protein family 3 (RefSeq)

Length: 271 amino acids

Source: Miya 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
L-asparagine catabolism aatJ lo glutamate-aspartate periplasmic-binding protein (characterized) 36% 87% 152.1 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-aspartate catabolism aatJ lo glutamate-aspartate periplasmic-binding protein (characterized) 36% 87% 152.1 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-glutamate catabolism gltI lo glutamate-aspartate periplasmic-binding protein (characterized) 36% 87% 152.1 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-asparagine catabolism peb1A lo major cell-binding factor (characterized) 34% 97% 135.6 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-aspartate catabolism peb1A lo major cell-binding factor (characterized) 34% 97% 135.6 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-glutamate catabolism peb1A lo major cell-binding factor (characterized) 34% 97% 135.6 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-asparagine catabolism natF lo Extracellular solute-binding protein, family 3 (characterized, see rationale) 32% 67% 124.4 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-aspartate catabolism natF lo Extracellular solute-binding protein, family 3 (characterized, see rationale) 32% 67% 124.4 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-asparagine catabolism aapJ lo AapJ, 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) 33% 74% 122.1 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-aspartate catabolism aapJ lo AapJ, 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) 33% 74% 122.1 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-glutamate catabolism aapJ lo AapJ, 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) 33% 74% 122.1 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-histidine catabolism aapJ lo AapJ, 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) 33% 74% 122.1 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-leucine catabolism aapJ lo AapJ, 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) 33% 74% 122.1 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-proline catabolism aapJ lo AapJ, 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) 33% 74% 122.1 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-asparagine catabolism bztA lo BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 75% 111.3 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-aspartate catabolism bztA lo BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 75% 111.3 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-glutamate catabolism bztA lo BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 75% 111.3 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-glutamate catabolism gtrC lo GtrC aka GLNH aka SLL1104, component of Tripartite glutamate:Na+ symporter (characterized) 31% 85% 106.7 ABC transporter glutamine-binding protein GlnH 41% 181.0
L-arginine catabolism artJ lo arginine ABC transporter, periplasmic arginine-binding protein ArtJ (characterized) 31% 99% 100.9 ABC transporter glutamine-binding protein GlnH 41% 181.0

Sequence Analysis Tools

View 8502446 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

MKRLVLLAVALCVVLTGTMAHAGKIEDIKARGALVCGVKDSTVPFGYIDEQSKQIVGFDI
DICKAVADKLGVKLELKTVTSATRIPMLTQGSVDMVAATMTHKFERDDVIDFSITYFMDG
QKLLVKKGGGVKSAADLKGKKVATAKGSTSEKNIKAAQPEATVVSFDEYPQAFLALKQGK
AEAVTTDSTILLGLRNSDPEPDKWEIVGDYISPEPYGLGLAENDSKFRDLVNRTLVDLWN
SGEYVKLYDKWFGKDTKYYLPLTWKMETWPY

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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