Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate WP_017359243.1 BA79_RS05245 aldo/keto reductase
Query= SwissProt::O32210 (276 letters) >NCBI__GCF_000691145.1:WP_017359243.1 Length = 281 Score = 425 bits (1093), Expect = e-124 Identities = 210/276 (76%), Positives = 238/276 (86%), Gaps = 2/276 (0%) Query: 1 MPTSLKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGV 60 M SL DTV L+NGVEMPWFGLGVFKVE+GN+ ++VKAAI+NGYRSIDTAA+YKNE GV Sbjct: 1 MVKSLNDTVTLNNGVEMPWFGLGVFKVEDGNQVVDAVKAAIRNGYRSIDTAAVYKNETGV 60 Query: 61 GIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGK--DK 118 G IKESGV REELFITSKVWN DQGY+ LAAF+ SL RL LDYLDLYLIHWPG D Sbjct: 61 GKAIKESGVKREELFITSKVWNTDQGYDKALAAFDASLNRLGLDYLDLYLIHWPGPNADT 120 Query: 119 YKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDY 178 +K+TWRALEKLYKDGK+RAIGVSNF V HLEELLKDAE+ P VNQVEFHP+LT ELR Y Sbjct: 121 FKETWRALEKLYKDGKVRAIGVSNFYVQHLEELLKDAEVVPAVNQVEFHPKLTLVELRQY 180 Query: 179 CKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHR 238 K +GIQ+EAWSPLMQG+LLD++VL +IA ++NKSVAQVILRWDLQ GVVTIPKSI E R Sbjct: 181 AKEKGIQIEAWSPLMQGKLLDHDVLKEIAAQYNKSVAQVILRWDLQSGVVTIPKSINEER 240 Query: 239 IIENADIFDFELSQEDMDKIDALNKDERVGPNPDEL 274 I +NADIFDFELSQEDM+KI+ALN +ERVG NP+ + Sbjct: 241 IKQNADIFDFELSQEDMEKINALNNNERVGSNPETM 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: 368 Number of extensions: 21 Number of successful extensions: 2 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: 281 Length adjustment: 25 Effective length of query: 251 Effective length of database: 256 Effective search space: 64256 Effective search space used: 64256 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 24 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