Align Hydroxyacylglutathione hydrolase; EC 3.1.2.6; Glyoxalase II; Glx II (uncharacterized)
to candidate CCNA_02959 CCNA_02959 Zn-dependent hydrolase, glyoxalase II family
Query= curated2:Q4FP49 (239 letters) >FitnessBrowser__Caulo:CCNA_02959 Length = 286 Score = 83.2 bits (204), Expect = 5e-21 Identities = 58/190 (30%), Positives = 86/190 (45%), Gaps = 34/190 (17%) Query: 14 SYLIVDKAKNIACVIDP-------------SEAKPVIKYLEDKNIHLKYILNTHHHYDHV 60 SYL+VD A A +IDP + A ++ + D+ +HL Y+L TH H DH+ Sbjct: 17 SYLVVDPATKTAAIIDPVLDFEPKAGKLSTTSADALLAAVRDQGLHLAYVLETHAHADHL 76 Query: 61 GGNKELKEKYGAS-VIGYK-----------GDKDRIPE---IDILVGDQDIWHEENFQAK 105 ++ K GA VIG K + D P+ D+L+ + D Sbjct: 77 SAADLIRRKTGAKIVIGAKITEVQKTFIPVFESDARPDGAVFDVLMEEGDALPLGELSIA 136 Query: 106 IFHIPGHTLGHICFYFYNEESVFTGDTLFSLGCGKIFE----GTYSQMYNSLMKIKALPE 161 H PGHT C + ++ F GDTLF G G +Y S+ K+ ALP+ Sbjct: 137 ALHTPGHT--PACMTYRIGDAAFVGDTLFMPDYGTARADFPGGDARTLYRSIQKVLALPD 194 Query: 162 KTKIYCGHEY 171 +T+I+ GH+Y Sbjct: 195 ETRIFVGHDY 204 Lambda K H 0.319 0.139 0.419 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: 150 Number of extensions: 6 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: 239 Length of database: 286 Length adjustment: 25 Effective length of query: 214 Effective length of database: 261 Effective search space: 55854 Effective search space used: 55854 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 (21.7 bits) S2: 47 (22.7 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