Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate Echvi_0089 Echvi_0089 methylmalonyl-CoA epimerase
Query= BRENDA::Q97H22 (128 letters) >FitnessBrowser__Cola:Echvi_0089 Length = 134 Score = 55.1 bits (131), Expect = 4e-13 Identities = 39/129 (30%), Positives = 65/129 (50%), Gaps = 4/129 (3%) Query: 2 KVHHIGYAVKNIDSALKKFKRLGYVEESEVVRDEVRKVYIQFVINGGYRVELVAPDGEDS 61 K+ H+G AVK++ + + F RL E + R E V F G ++EL+ DS Sbjct: 3 KIEHLGIAVKDLKKSNELFSRLFGKEAYKEERVEDEGVLTSFFQVGDVKIELLEATAPDS 62 Query: 62 PINKTI-KKGSTPYHICYEVEDIQKSIEEMSQIGYTLFKKAEIAPAIDNRKVAFLF--ST 118 PI K I K+ +H+ + V+DI ++ + + G+ + A D++ V FL ST Sbjct: 63 PIAKFIDKRAEGVHHVAFAVDDIYAEMDRLKKAGFEILNDVPKKGA-DHKLVVFLHPRST 121 Query: 119 DIGLIELLE 127 + L+EL + Sbjct: 122 NGVLVELCQ 130 Lambda K H 0.318 0.138 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 53 Number of extensions: 4 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 128 Length of database: 134 Length adjustment: 14 Effective length of query: 114 Effective length of database: 120 Effective search space: 13680 Effective search space used: 13680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 41 (20.4 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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:
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