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 AZOBR_RS26815 AZOBR_RS26815 3-hydroxyisobutyrate dehydrogenase
Query= BRENDA::Q9LSV0 (289 letters) >FitnessBrowser__azobra:AZOBR_RS26815 Length = 299 Score = 129 bits (324), Expect = 8e-35 Identities = 86/289 (29%), Positives = 132/289 (45%), Gaps = 7/289 (2%) Query: 3 VGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTIA 62 + F+GLG MG+ M NL K G V ++ + D G V + AE + I+ Sbjct: 4 IAFIGLGNMGRPMCDNLTKAGHDVVGYDVVPAARDAYAAAGGRVASTLAEALADADTVIS 63 Query: 63 MLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVSG 122 M+ + D+GGVL G ID ST+D E++ +++A G V+ PVSG Sbjct: 64 MIPTGKHVRAAYEDEGGVLAHARPGTMLIDCSTIDVESARAVSKAAADAGFVMVDAPVSG 123 Query: 123 SKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMMN 182 + A+ G L + G FE + P +G + F++G GNG +K+ NM+ G M Sbjct: 124 AVPAAQAGTLTFMVGGTAEGFERARPVLTAMGPKIFHVGASGNGVALKICNNMMAGMSMV 183 Query: 183 AFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGP-------SMNKSSYPPAFPLKH 235 A SE LA+K GL T+ D++ + + + P S Y P F Sbjct: 184 AISEVFALAEKLGLDHQTVYDVMTVSSGNCWALQSYCPVPGPVPASPANRDYQPGFAAAM 243 Query: 236 QQKDMRLALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEAV 284 KDMRL+ + + P+A +A ++ G G+ DFSAV + Sbjct: 244 MLKDMRLSQNAAATSGAATPLAGSAAALYQMLVEHGHGNKDFSAVFALI 292 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: 187 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: 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