GapMind for catabolism of small carbon sources

 

GapMind for catabolism of small carbon sources

Searching NCBI assemblies for 'Nitratidesulfovibrio'

Found 13 assemblies, please choose one:

Nitratidesulfovibrio vulgaris DP4 (GCF_000015485.1)
Nitratidesulfovibrio liaohensis XJ01 (GCF_011682075.1)
Nitratidesulfovibrio termitidis HI1 (GCF_000504305.1)
Nitratidesulfovibrio oxamicus NCIMB 9442 (GCF_015731765.1)
Nitratidesulfovibrio vulgaris str. Hildenborough (GCF_000195755.1)
Nitratidesulfovibrio vulgaris L2 (GCF_027947635.1)
Nitratidesulfovibrio vulgaris RCH1 (GCF_000166115.1)
Nitratidesulfovibrio liaohensis KPS (GCF_031326125.1)
Nitratidesulfovibrio vulgaris str. Hildenborough (GCF_902167245.1)
Nitratidesulfovibrio sp. HK-II (GCF_003402415.1)
Nitratidesulfovibrio sp. SRB-5 (GCF_019931275.1)
Nitratidesulfovibrio sp. 1201_IL3209 (GCF_036763125.1)
Nitratidesulfovibrio sp. SMAG_U10791 (GCA_035776595.1)

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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