Align Hydroxyacylglutathione hydrolase GloC; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2; EC 3.1.2.6 (characterized)
to candidate Ac3H11_3348 Hypothetical metal-binding enzyme, YcbL homolog
Query= SwissProt::P75849 (215 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3348 Length = 184 Score = 216 bits (551), Expect = 2e-61 Identities = 97/181 (53%), Positives = 120/181 (66%) Query: 28 LVDPGGDAEKIKQEVDDSGLTLMQILLTHGHLDHVGAAAELAQHYGVPVFGPEKEDEFWL 87 ++DPGGD + + E+ GLTL QI LTH H+DH G ELA G+P+ GP D+FW+ Sbjct: 1 VIDPGGDLDVLLAEIQRLGLTLSQIWLTHAHIDHAGGTGELATRLGLPIVGPHPGDQFWI 60 Query: 88 QGLPAQSRMFGLEECQPLTPDRWLNEGDTISIGNVTLQVLHCPGHTPGHVVFFDDRAKLL 147 GLP QS MFG Q TP RWL +GDT+ IG+ TL V HCPGHTPGHVVF + Sbjct: 61 DGLPQQSAMFGFPPAQHFTPTRWLADGDTVQIGDETLAVRHCPGHTPGHVVFHAPQIDRA 120 Query: 148 ISGDVIFKGGVGRSDFPRGDHNQLISSIKDKLLPLGDDVIFIPGHGPLSTLGYERLHNPF 207 GDV+F G +GR+DFP G+H LI SI +L P+GD +FIPGHGP ST G ER NP+ Sbjct: 121 FVGDVLFAGSIGRTDFPMGNHQDLIDSITQRLWPMGDQTVFIPGHGPESTFGRERKSNPY 180 Query: 208 L 208 + Sbjct: 181 V 181 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: 243 Number of extensions: 12 Number of successful extensions: 1 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: 184 Length adjustment: 21 Effective length of query: 194 Effective length of database: 163 Effective search space: 31622 Effective search space used: 31622 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 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