Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate Echvi_3562 Echvi_3562 Aldo/keto reductases, related to diketogulonate reductase
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__Cola:Echvi_3562 Length = 319 Score = 201 bits (512), Expect = 1e-56 Identities = 120/284 (42%), Positives = 167/284 (58%), Gaps = 36/284 (12%) Query: 13 NGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKES----G 68 NG MP GLG ++ + G E +V AI+ GYR D A IYKNE+ +G ++ Sbjct: 8 NGDTMPIIGLGTWQSKPG-EVYNAVLKAIEIGYRHFDCAYIYKNEKEIGDAFAKAFADGT 66 Query: 69 VAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWP-------------G 115 + RE++++TSK+WN+ E L A E +L+ LQLDYLDLYL+HWP G Sbjct: 67 IKREDIWVTSKLWNDSHKPEHVLPALESTLKDLQLDYLDLYLVHWPLALKHGVDFPEENG 126 Query: 116 KDKYKD------TWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPR 169 ++ D TW A+E L + GK++ IGVSNF++ L+E+L A+ KP VNQVE HP Sbjct: 127 DFEHLDNIPLSTTWAAMEGLLETGKVKHIGVSNFKIEKLKEILASAKSKPEVNQVEMHPF 186 Query: 170 LTQKELRDYCKGQGIQLEAWSPL-----MQGQ-------LLDNEVLTQIAEKHNKSVAQV 217 L Q+ L DYCK +GI L A++PL QGQ LL+N+ + IA K N + AQV Sbjct: 187 LPQQGLVDYCKKEGIHLTAYAPLGAAYRTQGQDGVDLPILLENDQVKNIANKLNATTAQV 246 Query: 218 ILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKIDAL 261 +L W++Q + IPKS+ RI EN LSQE+MD+++ L Sbjct: 247 VLAWNIQRDIAVIPKSVTPSRIEENFKSNLLTLSQEEMDQLNQL 290 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: 276 Number of extensions: 13 Number of successful extensions: 5 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: 319 Length adjustment: 26 Effective length of query: 250 Effective length of database: 293 Effective search space: 73250 Effective search space used: 73250 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