Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate AO353_28090 AO353_28090 dehydrogenase
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28090 Length = 316 Score = 165 bits (417), Expect = 1e-45 Identities = 99/260 (38%), Positives = 148/260 (56%), Gaps = 29/260 (11%) Query: 11 LHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKE---- 66 +H MP G G + + T+++K A++ G+R D A Y+NE+ VG+ IKE Sbjct: 18 VHGSGAMPAVGFGTL-FRDLSVTTQAIKHALETGFRHFDCAERYRNEDKVGVAIKEFLET 76 Query: 67 SGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWP-----GKDKYK- 120 V RE+LFIT+K+WN + E L AFE S RLQ+DY+D YLIH P G+D+ Sbjct: 77 GKVRREDLFITTKLWNTNHRPERVLPAFEASCRRLQVDYIDCYLIHTPFAFQPGEDQEPR 136 Query: 121 ---------------DTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVE 165 +TWRALE+L +G+ ++IG+S+ + L+E++ A IKP V QVE Sbjct: 137 DEQGRIIYDSGVTLIETWRALERLVDEGRCKSIGLSDITLQALQEIVAVARIKPAVVQVE 196 Query: 166 FHPRLTQKELRDYCKGQGIQLEAWSPL---MQGQLLDNEVLTQIAEKHNKSVAQVILRWD 222 HP L + EL ++C+ GI + A++PL MQ +L++ V+T +A + ++ AQV L W Sbjct: 197 SHPYLPEWELLEFCRQHGIIVLAFAPLGHGMQPNVLEDAVITGVARRLQQTPAQVALAWS 256 Query: 223 LQHGVVTIPKSIKEHRIIEN 242 +Q GV + S I EN Sbjct: 257 VQRGVAFLTTSATLSHIQEN 276 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: 238 Number of extensions: 15 Number of successful extensions: 4 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: 316 Length adjustment: 26 Effective length of query: 250 Effective length of database: 290 Effective search space: 72500 Effective search space used: 72500 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