Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate Ga0059261_3686 Ga0059261_3686 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__Korea:Ga0059261_3686 Length = 295 Score = 171 bits (432), Expect = 2e-47 Identities = 101/286 (35%), Positives = 151/286 (52%), Gaps = 9/286 (3%) Query: 4 KVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVII 63 +VGFIGLG MG M+ NL KAG+ + D + +A+ AAG +A A AE + +I Sbjct: 3 RVGFIGLGNMGGGMAANLAKAGHDVRAFDLSADALERAKAAGCLPVESAAAAAEGAEAVI 62 Query: 64 TMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAPVS 123 TMLP HV++V E+ + A G +LID S+I +R ++DA +AKG+ +DAPVS Sbjct: 63 TMLPAGKHVEQVY--EDSVFGAADTGAILIDCSTIDVATARRVADAAQAKGLAAVDAPVS 120 Query: 124 GGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALNI 183 GG A GTL+ MVGGD A F++ + AM +V+H G GAG +K+ N +++ + Sbjct: 121 GGIAAAAGGTLTFMVGGDAAAFERAEVFLAAMGKAVIHAGGNGAGQASKICNNMLLGATM 180 Query: 184 AAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPM-------VMDRNFKPGFRID 236 A EAL LA K G++P Y L+ AP+ D ++ GF Sbjct: 181 VATCEALLLAQKLGLDPQTFYDIASVSSGACWSLNTYAPLPGMGPQTPADNGYQGGFAAG 240 Query: 237 LHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSAL 282 L +KDL A++ + ++ P+ A E+ G+ D S + Sbjct: 241 LMLKDLKLAMEAAESTHSETPMGARAAELYTKFADAGNAGVDFSGI 286 Lambda K H 0.316 0.132 0.367 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: 210 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: 296 Length of database: 295 Length adjustment: 26 Effective length of query: 270 Effective length of database: 269 Effective search space: 72630 Effective search space used: 72630 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