Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate 7026457 Shewana3_3599 aldo/keto reductase (RefSeq)
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__ANA3:7026457 Length = 280 Score = 159 bits (403), Expect = 5e-44 Identities = 95/260 (36%), Positives = 139/260 (53%), Gaps = 6/260 (2%) Query: 17 MPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFI 76 MP G G F++++ N A ++V A++ G R IDTA IY NE+ VG I SG+ REELFI Sbjct: 17 MPMLGTGTFRLKD-NAAFDAVLMALEEGSRHIDTAQIYGNEQAVGDAINTSGIPREELFI 75 Query: 77 TSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWP---GKDKYKDTWRALEKLYKDG 133 T+KVW E+ E + SL LQ YLDL LIHWP + + L+ + G Sbjct: 76 TTKVWTENLTKERFETSVIDSLTALQTKYLDLLLIHWPLNSDEPSMVEYLSELKAVLDKG 135 Query: 134 KIRAIGVSNFQVHHLEELLKD-AEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPL 192 R IGVSNF L + + E NQVE HP L +++ D+C+ + + + P Sbjct: 136 LTRRIGVSNFTNAQLAQAIAILGEGVIYTNQVEVHPYLINRKVTDFCRQHNVLVTGYMPF 195 Query: 193 MQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQ 252 G +L +E + +A H + AQ++L W Q G TIP S K + N L+ Sbjct: 196 AYGAVLQDETIVNLASVHQATPAQIVLAWLRQLGFATIPSSTKRDNVRSNLAAASINLTP 255 Query: 253 EDMDKIDALNKDERVGPNPD 272 ++++I+ L+++ RV NPD Sbjct: 256 AEIEQINQLDRNHRVA-NPD 274 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: 180 Number of extensions: 9 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: 280 Length adjustment: 25 Effective length of query: 251 Effective length of database: 255 Effective search space: 64005 Effective search space used: 64005 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