Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate AO353_26885 AO353_26885 bifunctional glyoxylate/hydroxypyruvate reductase B
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26885 Length = 328 Score = 259 bits (662), Expect = 6e-74 Identities = 141/272 (51%), Positives = 181/272 (66%), Gaps = 6/272 (2%) Query: 56 KVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAV 115 K+D ELL+ AP+L+ IA +VG DN DI+ +R I ++NTP VLT+ TAD FAL+LA Sbjct: 55 KLDAELLDLAPRLEAIASVSVGVDNYDIDYLNRRQILLSNTPDVLTETTADTGFALILAT 114 Query: 116 ARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAK-GFGM 174 ARR+VE VR+G+W ++ H G + GKTLGI+G GRIG+ALA+R GFGM Sbjct: 115 ARRVVELANLVRAGQWNRNIGPAH----FGTDVHGKTLGIIGMGRIGEALAQRGHFGFGM 170 Query: 175 KIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNA 234 I+Y+S + KP E+ A+Y LL+++DFI L +PLT ET +IG ++ LM+P + Sbjct: 171 PILYHSHSVKPAVEQRFNAQYRSLPALLQQADFICLTLPLTAETEGLIGAEQFALMRPES 230 Query: 235 ILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPY-YNEELFKLKNVVLAPHIGSAT 293 I IN SRG VVD ALI+AL++G I AGLDVFE EP Y+ L +L NVV PHIGSAT Sbjct: 231 IFINISRGKVVDETALIEALRQGQIRAAGLDVFEREPLAYDSPLLQLNNVVATPHIGSAT 290 Query: 294 HEAREGMAELVAKNLIAFAKGEIPPNLVNKDV 325 HE RE MA NL+A GE P NLVN V Sbjct: 291 HETREAMARCAVDNLLAALAGERPANLVNGQV 322 Lambda K H 0.317 0.137 0.392 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: 251 Number of extensions: 13 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: 331 Length of database: 328 Length adjustment: 28 Effective length of query: 303 Effective length of database: 300 Effective search space: 90900 Effective search space used: 90900 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: 49 (23.5 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