Align Hydroxyacylglutathione hydrolase; EC 3.1.2.6; Glyoxalase II; Glx II (uncharacterized)
to candidate Synpcc7942_0937 Synpcc7942_0937 hypothetical protein
Query= curated2:Q1H188 (250 letters) >FitnessBrowser__SynE:Synpcc7942_0937 Length = 230 Score = 89.4 bits (220), Expect = 6e-23 Identities = 58/152 (38%), Positives = 77/152 (50%), Gaps = 7/152 (4%) Query: 22 GHALVVDP--GDAHPVLEILDARGLQLRAILVTHHHQDHTGGVEELIQATSAQVFAPAKE 79 G A +VDP L +L GL L+ L TH H DH L + T + PA Sbjct: 24 GEAALVDPVLEQCDRDLALLQDLGLTLKFCLETHLHADHITAAGRLRELTGCETVVPAGA 83 Query: 80 QFSFPHHPVTAGDRLDIPGIALSLSVLDVPGHTVGHVAYY-GDGMLFSGDTLFGAGCGR- 137 + V GDRL + IA++ V++ GHT H AY L +GD+L GCGR Sbjct: 84 NATCADRFVVEGDRLQVGSIAIT--VIETRGHTDSHAAYLIHQAELLTGDSLLIRGCGRT 141 Query: 138 -LFEGTPGQMYSSLQQLAQLPVNTRVYCGHEY 168 G GQ++ S+Q+L QLP NTRV+ GH+Y Sbjct: 142 DFQSGDAGQLFDSVQRLFQLPDNTRVWPGHDY 173 Lambda K H 0.322 0.137 0.417 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: 188 Number of extensions: 8 Number of successful extensions: 4 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: 250 Length of database: 230 Length adjustment: 23 Effective length of query: 227 Effective length of database: 207 Effective search space: 46989 Effective search space used: 46989 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 (21.9 bits) S2: 46 (22.3 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