Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate BWI76_RS05410 BWI76_RS05410 2,5-didehydrogluconate reductase B
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__Koxy:BWI76_RS05410 Length = 267 Score = 176 bits (445), Expect = 6e-49 Identities = 100/262 (38%), Positives = 156/262 (59%), Gaps = 6/262 (2%) Query: 17 MPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREELFI 76 +P FGLG F++++ T SVK A++ GYR+IDTA IY NE VG I ESGVAR ELFI Sbjct: 3 IPVFGLGTFRLKDDVVIT-SVKTALELGYRTIDTAQIYDNEAAVGQAIAESGVARNELFI 61 Query: 77 TSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKD---KYKDTWRALEKLYKDG 133 T+K+W E+ E +A+ ++SL++L+ DY+DL LIHWP + ++ AL + K G Sbjct: 62 TTKIWIENLNKEKLIASLKESLQKLRTDYVDLTLIHWPSPNDAVAVEEFMAALLEAKKQG 121 Query: 134 KIRAIGVSNFQVHHLEELLKDAEIKPM-VNQVEFHPRLTQKELRDYCKGQGIQLEAWSPL 192 R IG+SNF + +E + + + NQ+E P L +++ ++ + GI + ++ L Sbjct: 122 LTRQIGISNFTIPLMERAIAAVGAENIATNQIELSPYLQNRKVVNWAREHGIHITSYMTL 181 Query: 193 MQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQ 252 G+ L +E + +IA K++ + AQVIL W + G IP S K + N D +L + Sbjct: 182 AYGKALKDEAIARIAAKYDATPAQVILAWAMGEGYAVIPSSTKRENLASNLKAQDLQLDE 241 Query: 253 EDMDKIDALNKDERVGPNPDEL 274 +D I AL+ ++R+ +PD L Sbjct: 242 DDRQAIAALDCNDRL-VSPDGL 262 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: 184 Number of extensions: 10 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: 267 Length adjustment: 25 Effective length of query: 251 Effective length of database: 242 Effective search space: 60742 Effective search space used: 60742 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