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 WP_011937525.1 GURA_RS02990 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q9LSV0 (289 letters) >NCBI__GCF_000016745.1:WP_011937525.1 Length = 287 Score = 329 bits (844), Expect = 4e-95 Identities = 165/282 (58%), Positives = 209/282 (74%) Query: 4 GFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTIAM 63 GFLGLGIMG AM+ NLLK GF VTVWNR+ KC+EL GA +P +V++ C T AM Sbjct: 5 GFLGLGIMGSAMAKNLLKAGFDVTVWNRSPEKCEELAALGARSAATPRQVVESCGITFAM 64 Query: 64 LSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVSGS 123 LSDP A +V F GVLE I GKGY+DMSTVDA T+ KI A+T KGGRF+E PVSGS Sbjct: 65 LSDPAADEAVCFGTDGVLEGIGAGKGYVDMSTVDATTAQKIGAAVTDKGGRFLEAPVSGS 124 Query: 124 KKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMMNA 183 +KPAEDG LIIL AGDK+L+ E++PAF+ +GK+ +LG+VG GA+MKL+VNM+MG MM+ Sbjct: 125 RKPAEDGTLIILTAGDKSLYNEAMPAFERMGKKVLFLGEVGKGAEMKLVVNMVMGGMMSI 184 Query: 184 FSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMRLA 243 F EGL L K+GL +LD++D GA+ NPMFK KG + ++ AFPLKH QKD+RLA Sbjct: 185 FCEGLALGAKAGLEVTDMLDVMDAGAVANPMFKLKGGLIAAGNFTTAFPLKHMQKDLRLA 244 Query: 244 LALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEAVK 285 + LGD + AAAANEAFK+A++LG GD DFSA+ +A++ Sbjct: 245 VGLGDWLGQPLFTAAAANEAFKRAKALGFGDEDFSALFKAIE 286 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: 293 Number of extensions: 9 Number of successful extensions: 1 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: 287 Length adjustment: 26 Effective length of query: 263 Effective length of database: 261 Effective search space: 68643 Effective search space used: 68643 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 Apr 09 2024. 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