Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate H281DRAFT_00358 H281DRAFT_00358 Aldo/keto reductase
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__Burk376:H281DRAFT_00358 Length = 312 Score = 164 bits (415), Expect = 2e-45 Identities = 111/291 (38%), Positives = 154/291 (52%), Gaps = 38/291 (13%) Query: 5 LKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVG--- 61 LK H G MP G G + + + K A++ GYR D A Y+NE VG Sbjct: 9 LKRIALNHGGGSMPAIGFGTL-IADAAITISATKDALEAGYRHFDCAERYRNEREVGDAL 67 Query: 62 -IGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWP------ 114 G+ G+ARE++F+T+K+WN + E AF+ SLERL+LDYLDLYLIH P Sbjct: 68 QAGLAAGGIAREDIFVTTKLWNSNHRPERVKPAFDASLERLRLDYLDLYLIHTPFAFQAG 127 Query: 115 ---------GKDKYK------DTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKP 159 G Y DTWRA+E L G+ RAIG+S+ + L L + A IKP Sbjct: 128 DEQDPRDANGNVLYDEGVTLLDTWRAMEDLVDGGRCRAIGLSDIGLDDLVPLYESARIKP 187 Query: 160 MVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQG---QLLDNEVLTQIAEKHNKSVAQ 216 V QVE HP L + EL ++CK + I A++PL G L++ V+++IA + K+ AQ Sbjct: 188 AVVQVEAHPYLPESELLEFCKKKEIVFLAFAPLGHGIRPGPLEDPVVSRIAARIGKTPAQ 247 Query: 217 VILRWDLQHG--VVTIPKSIKEHRIIENADIFDFELSQEDMDKIDALNKDE 265 V+L W +Q G V+T PK+ R EN F++S D D +N+ E Sbjct: 248 VLLAWAVQRGTAVLTTPKTAARAR--EN-----FDISALPADAFDEINRIE 291 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: 208 Number of extensions: 12 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: 312 Length adjustment: 26 Effective length of query: 250 Effective length of database: 286 Effective search space: 71500 Effective search space used: 71500 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