Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate SMa1410 SMa1410 oxidoreductase
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__Smeli:SMa1410 Length = 277 Score = 156 bits (394), Expect = 5e-43 Identities = 90/243 (37%), Positives = 134/243 (55%), Gaps = 2/243 (0%) Query: 21 GLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFITSKV 80 G G + ++ G +V+ AI GYR+ DTA +Y NE G + ESG+AR+EL IT+KV Sbjct: 16 GFGTYPLK-GEPLKAAVREAITVGYRAFDTAQMYGNEAETGEALAESGLARDELCITTKV 74 Query: 81 WNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPG-KDKYKDTWRALEKLYKDGKIRAIG 139 ++ E L + E SL+ L++D D+ ++HWP + + R L+K + G R IG Sbjct: 75 HPDNYSEEAFLPSVEASLKALRVDQADVLMLHWPEINGENARSLRLLQKAFDIGLARNIG 134 Query: 140 VSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQLLD 199 VSN+ + E E + NQVEFHP + Q L D + I L ++ + +G++ Sbjct: 135 VSNYTAPMMREAQSIVEAPLVTNQVEFHPLIDQSRLLDAAEETKIALSSYCSVARGEVFK 194 Query: 200 NEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKID 259 + V +I ++ K+ AQ +LRW LQ GV S K I N +I DF LS DM +ID Sbjct: 195 HPVFAEIGARYGKTAAQTVLRWILQKGVSMNTMSTKPENIRANFEILDFALSPHDMKRID 254 Query: 260 ALN 262 A+N Sbjct: 255 AMN 257 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: 171 Number of extensions: 6 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: 276 Length of database: 277 Length adjustment: 25 Effective length of query: 251 Effective length of database: 252 Effective search space: 63252 Effective search space used: 63252 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: 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