Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate PP_1143 PP_1143 3-hydroxyisobutyrate dehydrogenase family protein
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__Putida:PP_1143 Length = 295 Score = 197 bits (500), Expect = 3e-55 Identities = 109/284 (38%), Positives = 168/284 (59%), Gaps = 2/284 (0%) Query: 5 VGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVIIT 64 +GF G+G+MG PM + LL AGY L V +R+P+ A ++AAGA AS+ + D+++ Sbjct: 8 LGFAGIGLMGLPMCRRLLAAGYPLTVWNRSPDKCAALVAAGARLASSPAELCRDSDMVLL 67 Query: 65 MLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAK-GVEMLDAPVS 123 L ++ V+EV GE GI +G + G +LID SS+ P A+RE++ L A G+ LDAPVS Sbjct: 68 CLADTAVVREVVFGEQGIAQGGRSGQLLIDFSSLEPTATREMAAELAALCGMAWLDAPVS 127 Query: 124 GGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALNI 183 GG P A GTL++MVGG+ A + +++ + V H G +GAG VTK NQ+IVA N Sbjct: 128 GGTPGAEAGTLAIMVGGEAADLQRARPVLQVLGQRVTHMGAVGAGQVTKACNQMIVACNA 187 Query: 184 AAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKP-GFRIDLHIKDL 242 ++E + LA ++GV+ L+ +A+ GG A S L AP + + F+P + + +KDL Sbjct: 188 LVIAEVVALAEQSGVDATLIAEALAGGFADSKPLQILAPQMAESRFEPIKWHVRTLLKDL 247 Query: 243 ANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSALACYY 286 A+ S G+ PL+ ++M+ + G+ D + L Y Sbjct: 248 DGAVKFSREQGSATPLSGLAAQLMRLHGSQGYLQKDPATLVELY 291 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: 193 Number of extensions: 8 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