Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate AZOBR_RS19710 AZOBR_RS19710 2 5-didehydrogluconate reductase
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__azobra:AZOBR_RS19710 Length = 274 Score = 173 bits (438), Expect = 4e-48 Identities = 100/264 (37%), Positives = 152/264 (57%), Gaps = 3/264 (1%) Query: 13 NGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVARE 72 NG +P G G F++ +G + V A+K G+R IDTA IY NE VG IK S + R Sbjct: 7 NGASIPALGFGTFRM-SGPDVLRMVPEALKLGFRHIDTAQIYGNESEVGEAIKASNLPRG 65 Query: 73 ELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKD-KYKDTWRALEKLYK 131 E+F+T+KVW + + + ++SL +L+ DY+DL L+HWP + + +L + Sbjct: 66 EVFLTTKVWVSNYKADDFRRSVDESLAKLRTDYVDLLLLHWPNEAVPLAEQIESLNAVRA 125 Query: 132 DGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSP 191 GK R IGVSNF L+E ++ ++ + NQ+E+HP L Q + + + G + A+ Sbjct: 126 AGKTRHIGVSNFNRTLLDESVRLSKAPIVTNQIEYHPYLDQSVMLEAARRHGQSITAYYA 185 Query: 192 LMQGQLLDNEVLTQIAEKHNKSVAQVILRWDL-QHGVVTIPKSIKEHRIIENADIFDFEL 250 + G++ + VLT IA + KS AQV+LRW + Q GV+ + K++ E R EN IFDFEL Sbjct: 186 MADGKVFKDPVLTDIAARLGKSAAQVVLRWLVQQEGVIALSKTVGEKRAAENLAIFDFEL 245 Query: 251 SQEDMDKIDALNKDERVGPNPDEL 274 S+ DM I L + + +PD L Sbjct: 246 SEADMAAIHGLARPDGRIVSPDGL 269 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: 164 Number of extensions: 9 Number of successful extensions: 3 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: 274 Length adjustment: 25 Effective length of query: 251 Effective length of database: 249 Effective search space: 62499 Effective search space used: 62499 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 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