Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate AO356_01320 AO356_01320 oxidoreductase
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_01320 Length = 273 Score = 126 bits (317), Expect = 4e-34 Identities = 86/257 (33%), Positives = 139/257 (54%), Gaps = 13/257 (5%) Query: 14 GVEMPWFGLGVFKV----ENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGV 69 GV +P G G +++ + + +++ I+ G IDTA +Y E G + E+ Sbjct: 8 GVSVPVIGQGTWRMGEEPSHHKKEVAALRLGIELGMTLIDTAEMYA-EGGAETVVGEAIT 66 Query: 70 A-REELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYKDTWRALEK 128 R+++F+ SKV+ + + A E+SL RL DY+DLYL+HW G+ +T A E+ Sbjct: 67 GLRDQVFLVSKVYPHNASRKGIPLACERSLRRLDTDYIDLYLLHWRGQYPLAETVEAFER 126 Query: 129 LYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFH--PRLTQKELRDYCKGQGIQL 186 L ++GKI GVSN V LEEL A NQV ++ R + +L +C+ + + + Sbjct: 127 LREEGKIGRWGVSNLDVDDLEELASPA---CATNQVLYNLQERGIEFDLLPWCQQRRMPI 183 Query: 187 EAWSPLMQ-GQLLDNEVLTQIAEKHNKSVAQVILRWDL-QHGVVTIPKSIKEHRIIENAD 244 A+ P+ Q G LL + L QIAE+H + AQ+ L W L Q V+ IPK++K + NA+ Sbjct: 184 MAYCPVGQGGHLLKDHTLAQIAERHRATPAQIALAWLLRQDNVIAIPKAVKPEHVRLNAE 243 Query: 245 IFDFELSQEDMDKIDAL 261 + L +D+ +D + Sbjct: 244 AANLRLEPQDLAALDLI 260 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: 176 Number of extensions: 8 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