Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate BPHYT_RS08410 BPHYT_RS08410 dehydrogenase
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__BFirm:BPHYT_RS08410 Length = 313 Score = 167 bits (422), Expect = 3e-46 Identities = 109/285 (38%), Positives = 153/285 (53%), Gaps = 35/285 (12%) Query: 12 HNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVG----IGIKES 67 H G +P G G + + T + + A++ GYR D A Y+NE VG G+ Sbjct: 16 HGGGRVPALGFGTL-IPDAATTTSATRDALEAGYRHFDCAERYRNEREVGDALRAGLAAG 74 Query: 68 GVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDK--------- 118 G+AREE+F+T+K+WN + E AF+ SLERL LDYLDLYLIH P K Sbjct: 75 GIAREEIFVTTKLWNSNHRPERVEPAFDASLERLGLDYLDLYLIHTPFAFKPGDEQDPRD 134 Query: 119 ------------YKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEF 166 DTW A+E+L G+ RAIG+S+ + L L + A IKP V QVE Sbjct: 135 ENGDVIYDKGVTLLDTWSAMEELVDRGRCRAIGLSDIGLDELRPLYESARIKPAVVQVEA 194 Query: 167 HPRLTQKELRDYCKGQGIQLEAWSPLMQG---QLLDNEVLTQIAEKHNKSVAQVILRWDL 223 HP L + EL ++CK +GI A++PL G L++ V+ QIAE+ K+ AQV+L W + Sbjct: 195 HPYLPETELLEFCKEKGIVFLAFAPLGHGIRPGPLEDPVILQIAERIGKTPAQVLLAWAI 254 Query: 224 QHG--VVTIPKSIKEHRIIENADIFDFELSQEDMDKIDALNKDER 266 Q G ++T P++ R EN DI L E D+I+ + +R Sbjct: 255 QRGGALLTTPRTAARAR--ENFDI--AALPAEAFDEINRIETRQR 295 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: 227 Number of extensions: 13 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: 313 Length adjustment: 26 Effective length of query: 250 Effective length of database: 287 Effective search space: 71750 Effective search space used: 71750 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