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 Ga0059261_3686 Ga0059261_3686 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)
Query= BRENDA::Q9LSV0 (289 letters) >FitnessBrowser__Korea:Ga0059261_3686 Length = 295 Score = 116 bits (290), Expect = 7e-31 Identities = 88/287 (30%), Positives = 124/287 (43%), Gaps = 9/287 (3%) Query: 3 VGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTIA 62 VGF+GLG MG M+ NL K G V ++ + + G ES A + + I Sbjct: 4 VGFIGLGNMGGGMAANLAKAGHDVRAFDLSADALERAKAAGCLPVESAAAAAEGAEAVIT 63 Query: 63 MLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVSG 122 ML V D V G ID ST+D T+ ++ +A KG V+ PVSG Sbjct: 64 MLPAGKHVEQVYEDS--VFGAADTGAILIDCSTIDVATARRVADAAQAKGLAAVDAPVSG 121 Query: 123 SKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMMN 182 A G L + GD A FE + +GK + G G G K+ NM++G+ M Sbjct: 122 GIAAAAGGTLTFMVGGDAAAFERAEVFLAAMGKAVIHAGGNGAGQASKICNNMLLGATMV 181 Query: 183 AFSEGLVLADKSGLSSDTLLDILDLGA------MTNPMFKGKGP-SMNKSSYPPAFPLKH 235 A E L+LA K GL T DI + + T G GP + + Y F Sbjct: 182 ATCEALLLAQKLGLDPQTFYDIASVSSGACWSLNTYAPLPGMGPQTPADNGYQGGFAAGL 241 Query: 236 QQKDMRLALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIE 282 KD++LA+ + P+ A A E + K G +DFS +I+ Sbjct: 242 MLKDLKLAMEAAESTHSETPMGARAAELYTKFADAGNAGVDFSGIIK 288 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: 202 Number of extensions: 7 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: 289 Length of database: 295 Length adjustment: 26 Effective length of query: 263 Effective length of database: 269 Effective search space: 70747 Effective search space used: 70747 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