Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate PP_3376 PP_3376 putative phosphonate dehydrogenase
Query= curated2:B1L765 (332 letters) >FitnessBrowser__Putida:PP_3376 Length = 320 Score = 263 bits (671), Expect = 6e-75 Identities = 147/324 (45%), Positives = 207/324 (63%), Gaps = 9/324 (2%) Query: 1 MKPRVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALVSLLTDP---I 57 MK R+ + + + + ++++++ E+ W D P + R++D L + Sbjct: 1 MKKRIVLYKRLSDDLMARLQDRVEVT-WVDTTQPDA---LARLRDALPGAHGLLGASLRL 56 Query: 58 DAEVFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAAR 117 DA + + AP+L +V+ +VG DN D+ E ++RG+ +TNTP VLTETTAD FAL++A AR Sbjct: 57 DASLLDLAPQLEVVSSVSVGVDNYDIAELSRRGVMLTNTPDVLTETTADTGFALILATAR 116 Query: 118 RVVEADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAK-GFGMRILYY 176 RVVE +VR+G+W+ P G DV+G+TLGIVGMGRIG A+ARRA GFGMR+LY+ Sbjct: 117 RVVELANWVRDGRWQANLGPAHF-GSDVHGKTLGIVGMGRIGEALARRAAAGFGMRVLYH 175 Query: 177 DSIRREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNT 236 + + E L++LL+++DFV L VPL+ T +IG +L MK AILVN Sbjct: 176 SQRAKPEVEARYAACQCSLDELLQQADFVCLTVPLSASTEGLIGARELALMKPDAILVNI 235 Query: 237 SRGKVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASHETRS 296 SRG+VVD++AL +AL+ I GAGLDVF EP+P D PLL+L+NVV PH SA+ ETR Sbjct: 236 SRGRVVDEQALIEALRARRIRGAGLDVFVHEPLPIDSPLLQLDNVVATPHIGSATEETRQ 295 Query: 297 RMAEMVAENLIAFKRGEIPPNLVN 320 MA +NL++ GE P NLVN Sbjct: 296 AMARCAVDNLLSALAGERPVNLVN 319 Lambda K H 0.319 0.137 0.398 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: 258 Number of extensions: 11 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: 332 Length of database: 320 Length adjustment: 28 Effective length of query: 304 Effective length of database: 292 Effective search space: 88768 Effective search space used: 88768 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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