Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate Pf1N1B4_85 Oxidoreductase, aldo/keto reductase family
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_85 Length = 273 Score = 125 bits (313), Expect = 1e-33 Identities = 92/257 (35%), Positives = 137/257 (53%), Gaps = 17/257 (6%) Query: 14 GVEMPWFGLGVFKV-ENGNEATESVKA---AIKNGYRSIDTAAIYKN---EEGVGIGIKE 66 G ++P G G +++ E + T+ V A I+ G IDTA +Y EE VG I Sbjct: 8 GSQVPVIGQGTWRMGEERSRHTKEVAALRLGIELGMTLIDTAEMYAEGGAEEVVGEAIAG 67 Query: 67 SGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYKDTWRAL 126 R+++F+ SKV+ + + A E+SL RL DY+DLYL+HW G +T A Sbjct: 68 R---RDQVFLVSKVYPYNASRKGIPQACERSLRRLNTDYIDLYLLHWRGDYPLVETVEAF 124 Query: 127 EKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFH--PRLTQKELRDYCKGQGI 184 E+L +DGKI GVSNF + LEEL A NQV ++ R + +L + + Q + Sbjct: 125 ERLREDGKIGRWGVSNFDLDDLEELASPA---CATNQVLYNLEERGIEFDLLPWSQHQRM 181 Query: 185 QLEAWSPLMQ-GQLLDNEVLTQIAEKHNKSVAQVILRWDL-QHGVVTIPKSIKEHRIIEN 242 + A+ P+ Q G +L N L QIA +H + AQV L W L Q+GV+ IPK+++ + N Sbjct: 182 PVMAYCPIGQGGHMLANSTLKQIAARHEATPAQVALAWILRQNGVIAIPKAVRPEHVQLN 241 Query: 243 ADIFDFELSQEDMDKID 259 A L D++ +D Sbjct: 242 AQAAQLRLEVGDLEALD 258 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: 174 Number of extensions: 9 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: 276 Length of database: 273 Length adjustment: 25 Effective length of query: 251 Effective length of database: 248 Effective search space: 62248 Effective search space used: 62248 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