Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate GFF2883 HP15_2827 oxidoreductase, aldo/keto reductase family
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__Marino:GFF2883 Length = 329 Score = 97.4 bits (241), Expect = 3e-25 Identities = 80/278 (28%), Positives = 129/278 (46%), Gaps = 50/278 (17%) Query: 32 EATESVKAAIKNGYRSIDTAAIY---KNEEGVGIGIKESGVAREELFITSKV---WNEDQ 85 ++ +++ AI G +DTA +Y ++EE VG + + R+++ + +KV WN+D Sbjct: 35 QSIDTIHRAIDKGIGLVDTAPVYGFGRSEEIVGKALSDG--RRDQVALATKVALNWNDDH 92 Query: 86 GYETTLAA-------FEKSLERLQLDYLDLYLIHWPG-KDKYKDTWRALEKLYKDGKIRA 137 A+ E SL+RLQ D +D+Y +HWP K ++T RALEKLY+ GKIRA Sbjct: 93 DKVWRDASASRIEREVEDSLKRLQTDRIDIYQVHWPDPKTPMEETARALEKLYQAGKIRA 152 Query: 138 IGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQL 197 IGVSNF ++EL K + + R ++++ YC+ GI + L +G L Sbjct: 153 IGVSNFTPSQMDELQKSVPLHSLQPPYNLFEREIEQDILPYCRENGIATITYGGLCRGFL 212 Query: 198 LD-------------------------NEVLTQIA-------EKHNKSVAQVILRWDL-Q 224 + L +A E++ KSV + LRW + Q Sbjct: 213 TGKMREDTQFTGDDLRKNDPKFQGDRYRQYLNAVAELDAFARERYQKSVLALALRWLVDQ 272 Query: 225 HGVVTIPKSIKEHRIIENADIFD-FELSQEDMDKIDAL 261 GV T + ++ D D + L + M +ID + Sbjct: 273 PGVTTALWGARRPEQLDPVDEIDGWSLDKNAMAEIDGI 310 Lambda K H 0.316 0.135 0.397 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: 230 Number of extensions: 12 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 276 Length of database: 329 Length adjustment: 27 Effective length of query: 249 Effective length of database: 302 Effective search space: 75198 Effective search space used: 75198 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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