Align Hydroxyacylglutathione hydrolase GloC; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2; EC 3.1.2.6 (characterized)
to candidate SMc01587 SMc01587 hypothetical protein
Query= SwissProt::P75849 (215 letters) >FitnessBrowser__Smeli:SMc01587 Length = 213 Score = 219 bits (558), Expect = 3e-62 Identities = 104/206 (50%), Positives = 140/206 (67%), Gaps = 1/206 (0%) Query: 5 IIPVTAFSQNCSLIWCEQTRLAALVDPGGDAEKIKQEVDDSGLTLMQILLTHGHLDHVGA 64 IIPVT F QNC++++ +T+ +VDPGGD + I Q + ++G+ L I LTHGH+DH G Sbjct: 6 IIPVTHFEQNCTVLFDSETKEGVVVDPGGDVDIILQTIRENGIALKAIWLTHGHIDHAGG 65 Query: 65 AAELAQHYGVPVFGPEKEDEFWLQGLPAQSRMFGLE-ECQPLTPDRWLNEGDTISIGNVT 123 A EL + G+ + GP K+D L+ L Q+ FGL + Q + PDRWL EGDT+S G+ Sbjct: 66 AKELKEALGLDIVGPHKDDLPLLERLEDQAERFGLAMKVQNVVPDRWLEEGDTVSFGDHV 125 Query: 124 LQVLHCPGHTPGHVVFFDDRAKLLISGDVIFKGGVGRSDFPRGDHNQLISSIKDKLLPLG 183 +VLHCPGH PGHVV+F+ GDV+F G +GR+D P G+H QL+ SI+DK+LPLG Sbjct: 126 FEVLHCPGHAPGHVVYFNRAQNFAHVGDVLFHGSIGRTDLPGGNHQQLLDSIRDKILPLG 185 Query: 184 DDVIFIPGHGPLSTLGYERLHNPFLQ 209 D+V FI GHGP +G ER NPFL+ Sbjct: 186 DNVGFICGHGPGGQIGEERRTNPFLR 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: 257 Number of extensions: 14 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: 213 Length adjustment: 22 Effective length of query: 193 Effective length of database: 191 Effective search space: 36863 Effective search space used: 36863 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