Align Hydroxyacylglutathione hydrolase GloC; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2; EC 3.1.2.6 (characterized)
to candidate 8502142 DvMF_2853 beta-lactamase domain protein (RefSeq)
Query= SwissProt::P75849 (215 letters) >FitnessBrowser__Miya:8502142 Length = 210 Score = 124 bits (311), Expect = 1e-33 Identities = 68/185 (36%), Positives = 100/185 (54%), Gaps = 3/185 (1%) Query: 26 AALVDPGGDAEKIKQEVDDSGLTLMQILLTHGHLDHVGAAAELAQHYGVPVFGPEKEDEF 85 A VDPGG + Q + +GL L IL+TH H DH+ AA L + G PV D F Sbjct: 26 AVAVDPGGTPRPMLQYAEKNGLALTHILITHLHFDHIYGAAALVEASGAPVLA-SAADAF 84 Query: 86 WLQGLPAQSRMFGLEECQPLTPDRWLNEGDTISIGNVTLQVLHCPGHTPGHVVFFDDRAK 145 ++ + FG P + + EGD + +G +T + L PGHTPG + F + Sbjct: 85 LMETELGRGGAFGFPRVTPFSYQP-VEEGD-LDLGAITCRALATPGHTPGSLSFHFPQVG 142 Query: 146 LLISGDVIFKGGVGRSDFPRGDHNQLISSIKDKLLPLGDDVIFIPGHGPLSTLGYERLHN 205 +I GD++F +GR+DFP GD + L S+ K+ L DD + PGHG +T+G E+L+N Sbjct: 143 AVIVGDLLFHRSIGRTDFPGGDLDALRRSVVQKIFTLPDDTVVYPGHGRETTVGSEKLNN 202 Query: 206 PFLQD 210 P+ + Sbjct: 203 PYFTE 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: 183 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: 210 Length adjustment: 21 Effective length of query: 194 Effective length of database: 189 Effective search space: 36666 Effective search space used: 36666 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