Align Hydroxyacylglutathione hydrolase GloC; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2; EC 3.1.2.6 (characterized)
to candidate WP_017357989.1 BA79_RS10790 MBL fold metallo-hydrolase
Query= SwissProt::P75849 (215 letters) >NCBI__GCF_000691145.1:WP_017357989.1 Length = 212 Score = 144 bits (363), Expect = 1e-39 Identities = 80/214 (37%), Positives = 127/214 (59%), Gaps = 13/214 (6%) Query: 1 MNYRIIPVTAFSQNCSLIWCEQTRLAALVDPGGDAEKIKQEVDDSGLTLMQILLTHGHLD 60 MN+R +P+ + Q + IW + + DPGG+A+K+ V + L + +LLTH H D Sbjct: 1 MNWRRMPL-GYVQANAYIWKNEQGECLIFDPGGEAQKLISYVKEKQLKPLAVLLTHAHFD 59 Query: 61 HVGAAAELAQHYGVPVFGPEKEDEFWLQG--LPAQSRMFG----LEECQPLTPDRWLNEG 114 H+GAA E+ Q +G+P++ EKE E WL L +R+ G ++E + L +EG Sbjct: 60 HIGAADEVRQEWGIPLYVHEKEKE-WLTNAQLNGSARLIGNGITVKEAEQLIT----SEG 114 Query: 115 DTISIGNVTLQVLHCPGHTPGHVVFFDDRAKLLISGDVIFKGGVGRSDFPRGDHNQLISS 174 + IG+ TL++ H PGH+PG V ++ +ISGD +F+GG+GR+D G+ + L+ S Sbjct: 115 P-LQIGSFTLEMFHTPGHSPGSVSYYSAEEGFVISGDTLFQGGIGRTDLTGGNQDVLLQS 173 Query: 175 IKDKLLPLGDDVIFIPGHGPLSTLGYERLHNPFL 208 I DKLL L + + + GHG +T+ E+ NPF+ Sbjct: 174 IHDKLLSLPESTLVLSGHGEETTVLTEQEQNPFI 207 Lambda K H 0.321 0.142 0.453 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: 185 Number of extensions: 12 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: 215 Length of database: 212 Length adjustment: 22 Effective length of query: 193 Effective length of database: 190 Effective search space: 36670 Effective search space used: 36670 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: 45 (21.9 bits)
This GapMind analysis is from Sep 24 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