Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate GFF854 HP15_833 2,5-diketo-D-gluconic acid reductase B
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__Marino:GFF854 Length = 269 Score = 171 bits (434), Expect = 1e-47 Identities = 97/262 (37%), Positives = 154/262 (58%), Gaps = 10/262 (3%) Query: 17 MPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFI 76 +P G+G F+++ GN+A ++VK+A+ GYR IDTA +Y NE VG GI SG+ R E+F+ Sbjct: 6 LPKIGMGTFRLK-GNDARDAVKSALSLGYRHIDTAQMYGNEAEVGDGITSSGIPRREIFL 64 Query: 77 TSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPG---KDKYKDTWRALEKLYKDG 133 T+K+W++ + + SL RL+ D++DL LIHWP + K+ AL ++G Sbjct: 65 TTKIWHDQLHASDLINSLHDSLARLKTDHVDLALIHWPSPGDEVPMKEYLGALRDSQREG 124 Query: 134 KIRAIGVSNFQVHHLEE---LLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWS 190 IG+SNF ++E +L D I NQVE HP L +++ + + GI + + Sbjct: 125 LAEHIGISNFTCAQMDEAKAILGDTPI--FTNQVEVHPFLANRKVVAHAQKLGITVTGYM 182 Query: 191 PLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFEL 250 PL G+++++E L +IA + N + AQV + W GVV IP S + N + + EL Sbjct: 183 PLAVGKVMEDETLQRIAAERNLTPAQVAIAWVASRGVVPIPSSTRPGHQKANLEALEVEL 242 Query: 251 SQEDMDKIDALNKDERVGPNPD 272 S+E++ ID L+++ER+ NPD Sbjct: 243 SEEEIRAIDELDRNERIA-NPD 263 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: 173 Number of extensions: 11 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: 269 Length adjustment: 25 Effective length of query: 251 Effective length of database: 244 Effective search space: 61244 Effective search space used: 61244 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