GapMind for catabolism of small carbon sources

 

Protein 206676 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU1237 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Length: 256 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-histidine catabolism Ac3H11_2554 lo ABC transporter for L-Histidine, permease component 1 (characterized) 39% 95% 156.8 Basic amino acid uptake transporter, BgtAB 45% 176.8
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 37% 91% 139.8 Basic amino acid uptake transporter, BgtAB 45% 176.8
L-asparagine catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 33% 60% 129.8 Basic amino acid uptake transporter, BgtAB 45% 176.8
L-aspartate catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 33% 60% 129.8 Basic amino acid uptake transporter, BgtAB 45% 176.8
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 34% 64% 126.3 Basic amino acid uptake transporter, BgtAB 45% 176.8
L-lysine catabolism hisM lo Amino acid ABC transporter, membrane protein (characterized, see rationale) 34% 89% 123.6 Basic amino acid uptake transporter, BgtAB 45% 176.8
L-arginine catabolism artQ lo Histidine transport system permease protein HisQ (characterized) 32% 94% 119.4 Basic amino acid uptake transporter, BgtAB 45% 176.8
L-histidine catabolism hisQ lo Histidine transport system permease protein HisQ (characterized) 32% 94% 119.4 Basic amino acid uptake transporter, BgtAB 45% 176.8
L-citrulline catabolism PS417_17595 lo ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale) 31% 91% 115.9 Basic amino acid uptake transporter, BgtAB 45% 176.8
L-asparagine catabolism aatM lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 95% 108.2 Basic amino acid uptake transporter, BgtAB 45% 176.8
L-aspartate catabolism aatM lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 95% 108.2 Basic amino acid uptake transporter, BgtAB 45% 176.8
L-glutamate catabolism gltK lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 95% 108.2 Basic amino acid uptake transporter, BgtAB 45% 176.8
L-histidine catabolism aapQ lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized) 30% 53% 89 Basic amino acid uptake transporter, BgtAB 45% 176.8

Sequence Analysis Tools

View 206676 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

MRIEITDGASIPDPKERRLITAWSLSFLAAIGTLIYLCASQPDPYWRLLQFLPDGILVTF
QVTVFSIICSIPIGLITGLGRLSRNRGINLVASTYVEVVRGIPLLVQLFYIYYALGRFLK
VPDMLAAIIALSVCYGAYMGEVFRAGIEAIPKGQTEAARSLGFNRVETMFLVVLPQAWRT
ILPPVGNEFIAMLKDTSLVSIIAVADILRRGREFASESFQYFETYTMIALVYLLITLLLS
KGVSIMEARLNYYDRR

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