Align glyoxylate reductase (EC 1.1.1.26); 4-hydroxybutyrate dehydrogenase (EC 1.1.1.61); glyoxylate reductase (NADP+) (EC 1.1.1.79) (characterized)
to candidate Dsui_3438 Dsui_3438 beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
Query= BRENDA::Q9LSV0 (289 letters) >FitnessBrowser__PS:Dsui_3438 Length = 299 Score = 136 bits (342), Expect = 6e-37 Identities = 90/290 (31%), Positives = 143/290 (49%), Gaps = 6/290 (2%) Query: 1 MEVGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYT 60 ME+GF+GLGIMG+ M++NLLK G V VW R L+E GA C SPA V + + Sbjct: 1 MEIGFIGLGIMGRPMALNLLKGGHGVHVWARRPESMAPLLEAGAVGCSSPAAVAGQVEVV 60 Query: 61 IAMLSDPCAALSVVFDKGGVLEQICEGKGY-----IDMSTVDAETSLKINEAITGKGGRF 115 I+M++D V+ GV EG G +DMST+ + + + +G F Sbjct: 61 ISMVADAPDVAQVMLGPDGVAAG-AEGAGKHGLVAVDMSTIAPAAARDLAARLQARGVDF 119 Query: 116 VEGPVSGSKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNM 175 V+ PVSG + A G L I+A G F +++PAF LG+ ++G G G K + Sbjct: 120 VDAPVSGGEVGAIAGSLSIMAGGSAEAFAKALPAFLCLGQNVVHVGAAGAGQVAKACNQI 179 Query: 176 IMGSMMNAFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKH 235 + G + A +E A ++G+ + + L G + + + G M + ++ P F Sbjct: 180 VTGMGVLAVAEAFNFARQAGVDPAKVREALLGGFAYSRILENHGQRMLERNFKPGFKSWM 239 Query: 236 QQKDMRLALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEAVK 285 QKD+ + + E + +P AAA + F GL + D AV++ ++ Sbjct: 240 HQKDLNIVMQSAHELGLCLPGAAATAQMFNAMVGSGLEEEDSVAVLKLLE 289 Lambda K H 0.317 0.134 0.379 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: 203 Number of extensions: 5 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: 289 Length of database: 299 Length adjustment: 26 Effective length of query: 263 Effective length of database: 273 Effective search space: 71799 Effective search space used: 71799 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: 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