GapMind for catabolism of small carbon sources

 

Protein 206400 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU0968 amino acid ABC transporter, ATP-binding protein

Length: 246 amino acids

Source: 882 in MicrobesOnline

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aatP med PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 57% 95% 271.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
L-aspartate catabolism aatP med PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 57% 95% 271.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
L-glutamate catabolism gltL med PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 57% 95% 271.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 55% 100% 256.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 53% 94% 250.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
L-lysine catabolism hisP med ABC transporter for L-Lysine, ATPase component (characterized) 51% 96% 235.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 47% 97% 221.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
L-histidine catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 40% 82% 157.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 40% 82% 157.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 94% 119 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 94% 119 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 94% 119 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 94% 119 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 281.2

Sequence Analysis Tools

View 206400 at MicrobesOnline

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

MTIISARNVNKYFYVPEELHALRDVSLDVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADS
GEILIEGRDILDPKCEINEVRAEVGMVFQSFNLFPHLSVLENVALAQMTVRKRSRAESEK
KGMELLTKVGIADKHAVYPDQLSGGQQQRVAIARSLAMDPKIMLFDEPTSALDPEMVGEV
LDVMRNLAREGMTMVVVTHEMGFAREVADRVVFMDHGAILEIATPKDLFTTGATHDRTKL
FLSQIL

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