Align Hydroxyacylglutathione hydrolase; EC 3.1.2.6; Glyoxalase II; Glx II (uncharacterized)
to candidate Dsui_0987 Dsui_0987 Zn-dependent hydrolase, glyoxylase
Query= curated2:Q60BX0 (256 letters) >FitnessBrowser__PS:Dsui_0987 Length = 311 Score = 67.4 bits (163), Expect = 3e-16 Identities = 52/149 (34%), Positives = 67/149 (44%), Gaps = 26/149 (17%) Query: 37 VLEALDARGWRLGHVLNTHHHGDHVGGNLELKAATGCTVVGAAGDRHRIP---------- 86 V +ALD R RL ++NTH H DH+GGN LK ATGC V+ AG I Sbjct: 56 VEKALDGR--RLTRLINTHSHSDHIGGNAALKHATGCRVLVPAGMAATIAEWDEEALLLS 113 Query: 87 ---------GIDVALKDGEEFRLGSASARMLDVPGHTSGHVAFWFEDDAALFCGDTLFAL 137 D L G+ LG + L VPGH +A++ D L GD L+ Sbjct: 114 PLGQQAARFQHDATLAAGDRLTLGGLEWQALAVPGHDMDALAYFNADQGILISGDALWQD 173 Query: 138 GCGRLFE----GSAEQMWR-SLERLRALP 161 G G +F G + R +L+ L ALP Sbjct: 174 GFGVIFAELLGGDGLRTTRQTLDMLAALP 202 Lambda K H 0.321 0.138 0.418 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: 161 Number of extensions: 8 Number of successful extensions: 2 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: 256 Length of database: 311 Length adjustment: 26 Effective length of query: 230 Effective length of database: 285 Effective search space: 65550 Effective search space used: 65550 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. 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