Align Hydroxyacylglutathione hydrolase GloC; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2; EC 3.1.2.6 (characterized)
to candidate Echvi_2827 Echvi_2827 Zn-dependent hydrolases, including glyoxylases
Query= SwissProt::P75849 (215 letters) >FitnessBrowser__Cola:Echvi_2827 Length = 217 Score = 158 bits (400), Expect = 6e-44 Identities = 79/212 (37%), Positives = 126/212 (59%), Gaps = 6/212 (2%) Query: 1 MNYRIIPVTAFSQNCSLIWCEQTRLAALVDPG----GDAEKIKQEVDDSGLTLMQILLTH 56 +N + F +NC +++ + T+ A ++DPG + E +KQ + + L +++L TH Sbjct: 2 LNVQTFTFNPFQENCYVLY-DDTKEAVIIDPGCYAKEEQETLKQFLQSNDLRPVRLLNTH 60 Query: 57 GHLDHVGAAAELAQHYGVPVFGPEKEDEFWLQGLPAQSRMFGLEECQPLTPDRWLNEGDT 116 H+DHV + Q+YG+P+ K DE L + + + +G P +++L EGD Sbjct: 61 CHIDHVLGNFFINQNYGLPLEIHPK-DEPVLMAVGSYASNYGFPAYTPCKAEKYLEEGDK 119 Query: 117 ISIGNVTLQVLHCPGHTPGHVVFFDDRAKLLISGDVIFKGGVGRSDFPRGDHNQLISSIK 176 ++ G L+V+ PGH PGHVVF+ +K I GD +F+G +GR+D P GDH L+ +IK Sbjct: 120 VTFGETDLEVIWVPGHAPGHVVFYHPESKTCIGGDTLFQGSIGRTDLPGGDHQTLLDAIK 179 Query: 177 DKLLPLGDDVIFIPGHGPLSTLGYERLHNPFL 208 KL L DDV PGHGP + +G+E++HNPF+ Sbjct: 180 AKLFTLPDDVKVHPGHGPATLIGHEKIHNPFV 211 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: 211 Number of extensions: 10 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: 215 Length of database: 217 Length adjustment: 22 Effective length of query: 193 Effective length of database: 195 Effective search space: 37635 Effective search space used: 37635 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