Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate HSERO_RS21160 HSERO_RS21160 3-hydroxyisobutyrate dehydrogenase
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__HerbieS:HSERO_RS21160 Length = 298 Score = 190 bits (483), Expect = 3e-53 Identities = 99/283 (34%), Positives = 161/283 (56%), Gaps = 1/283 (0%) Query: 1 MTMKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCD 60 M+ VG IGLG MG ++ +LL+AG+++ D E + AAG + +A + D Sbjct: 1 MSRNVGVIGLGAMGYGVASSLLRAGFNVHACDVRKEVLDKFAAAGGVACANPAELAGKVD 60 Query: 61 VIITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDA 120 V+IT++ N+ + V G+NG + KPG+V+I +++AP + E+ L KG+ +LDA Sbjct: 61 VVITLVVNAAQTETVLFGDNGAVSAMKPGSVVISSATVAPDFAIELGKRLVEKGLLLLDA 120 Query: 121 PVSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDI-GAGNVTKLANQVIV 179 PVSGG +A G +++M G ++ K D++ MAG V GD G G+ K+ NQ++ Sbjct: 121 PVSGGAARAASGEMTMMTSGPAEVYAKIEDVLAGMAGKVYRLGDTHGIGSKVKIINQLLA 180 Query: 180 ALNIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHI 239 ++IAA +EA+ L + GVNPD +Y+ I S + + + P ++ ++ P +D+ + Sbjct: 181 GVHIAASAEAMALGLREGVNPDALYEVITHSAGNSWMFENRVPHILSGDYTPLSAVDIFV 240 Query: 240 KDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSAL 282 KDL LDT+ LPL+AA +M GHG +D SA+ Sbjct: 241 KDLGLVLDTARRSKFPLPLSAAAHQMFMMASTAGHGGEDDSAV 283 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: 236 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: 296 Length of database: 298 Length adjustment: 26 Effective length of query: 270 Effective length of database: 272 Effective search space: 73440 Effective search space used: 73440 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