Align Hydroxyacylglutathione hydrolase; EC 3.1.2.6; Glyoxalase II; Glx II (uncharacterized)
to candidate H281DRAFT_02289 H281DRAFT_02289 Glyoxylase, beta-lactamase superfamily II
Query= curated2:A6WXE0 (260 letters) >FitnessBrowser__Burk376:H281DRAFT_02289 Length = 357 Score = 74.7 bits (182), Expect = 2e-18 Identities = 50/137 (36%), Positives = 67/137 (48%), Gaps = 5/137 (3%) Query: 45 AALKRRGWTLDFIFTTHHHLDHVEGNEALKAKYGVSIIGPKAEETKIPGIDRTVKDGDEF 104 A ++ G L + TH H DHV G LK G I A + G DR + G++ Sbjct: 42 ALIEELGLHLLYTIDTHVHADHVTGAWLLKRHTGSQIAISAASGAQ--GADRYLNHGEQC 99 Query: 105 TFGLFRVKVIATPGHTAGEVSYYLPDAKAVFTGDTLFALGCGR--LFEGTPLTMFQSLQK 162 FG ++V ATPGHT G +S L D +FTGD L G GR G MF+S+Q Sbjct: 100 VFGSRHLEVRATPGHTNGCISLALDDGSMMFTGDCLLIRGTGRTDFQHGDAHAMFRSVQN 159 Query: 163 LVALPGDTA-VYCGHEY 178 + + DT +Y H+Y Sbjct: 160 QIFIQPDTCLLYPAHDY 176 Lambda K H 0.321 0.136 0.403 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: 174 Number of extensions: 6 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: 260 Length of database: 357 Length adjustment: 27 Effective length of query: 233 Effective length of database: 330 Effective search space: 76890 Effective search space used: 76890 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: 48 (23.1 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