GapMind for Amino acid biosynthesis

 

Finding step trpD_1 for L-tryptophan biosynthesis in Thioalkalivibrio paradoxus ARh 1

4 candidates for trpD_1: glutamine amidotransferase of anthranilate synthase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi THITH_RS15390 aminodeoxychorismate/anthranilate synthase component II anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized) 71% 98% 292.7
hi THITH_RS15390 aminodeoxychorismate/anthranilate synthase component II glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase (TIGR00566) 100% 280.9
lo THITH_RS12380 glutamine-hydrolyzing GMP synthase Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized) 31% 80% 71.6 GMP synthase (glutamine-hydrolysing) (EC 6.3.5.2) 71% 763.5
lo THITH_RS12630 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized) 31% 91% 70.9 Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 67% 524.6
lo THITH_RS04045 glutamine amidotransferase Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized, see rationale) 30% 72% 53.1 GMP synthase (glutamine-hydrolysing) (EC 6.3.5.2) 35% 66.2

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.

Definition of step trpD_1

Or cluster all characterized trpD_1 proteins

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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 (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