Align Hydroxyacylglutathione hydrolase GloC; EC 3.1.2.6; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2 (uncharacterized)
to candidate Dsui_0929 Dsui_0929 Zn-dependent hydrolase, glyoxylase
Query= curated2:Q57544 (212 letters) >FitnessBrowser__PS:Dsui_0929 Length = 238 Score = 80.5 bits (197), Expect = 2e-20 Identities = 61/187 (32%), Positives = 87/187 (46%), Gaps = 28/187 (14%) Query: 25 AAIIDPGGEAERL-IQRIEELDLNLKVLLLTHGHLDHVGAAMQLKQHFGVEIWGSNEKDK 83 A ++DP E L + + EL+LNL ++ TH H DH+ AA L +H G Sbjct: 27 ALLVDPVAEQSPLYLGLLGELELNLACVVDTHLHSDHLSAAPTLIRHTGC---------- 76 Query: 84 FLFESLPEQAQRFGLPNIDAFLPDRWFNQEGEILKLDGFNFEILHLPGHTPGHIGFIEHE 143 L G+ D L D G+ L L + E+L PGHTPG I + + Sbjct: 77 -----LYAAGLCSGIGGTDRQLAD------GDSLDLADLHLEVLATPGHTPGCITLLWED 125 Query: 144 KKVAFTGDVLFQGGIGRTDFPRGDYETLISSIRTKLLPLNDDIIIIAGHG----SYTTIG 199 + + TGD L G G T P G+ T S+ KLLPL D++++ GH + IG Sbjct: 126 RLL--TGDALLIGSCGATGEPGGNAGTHYDSVTRKLLPLPDELLVFPGHDRDGRRVSCIG 183 Query: 200 QEKRSNP 206 E++ NP Sbjct: 184 DERQGNP 190 Lambda K H 0.321 0.142 0.430 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: 121 Number of extensions: 9 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: 212 Length of database: 238 Length adjustment: 22 Effective length of query: 190 Effective length of database: 216 Effective search space: 41040 Effective search space used: 41040 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: 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