Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate SMc00133 SMc00133 oxidoreductase
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__Smeli:SMc00133 Length = 289 Score = 164 bits (415), Expect = 2e-45 Identities = 102/287 (35%), Positives = 154/287 (53%), Gaps = 2/287 (0%) Query: 4 KVGFIGLGIMGKPMSKNL-LKAGYSLVVSDRNPEAIADVIAA-GAETASTAKAIAEQCDV 61 KV FIGLG+MG PM+ +L + G+ + V +R AA G TA+T A+ D Sbjct: 3 KVAFIGLGVMGYPMAGHLKARGGHDVTVYNRTAAKAEQWAAAFGGRTAATPAGAAKDQDF 62 Query: 62 IITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAP 121 + + N ++ V GENG E PG+V ID ++ + +RE+ A AKG +DAP Sbjct: 63 VFACVGNDDDLRSVTTGENGAFETMAPGSVFIDNTTASAAVARELYAAAAAKGAHFIDAP 122 Query: 122 VSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVAL 181 VSGG+ A +G L+VM GGD FDK +++A A V G GAG +TK+ NQ+ +A Sbjct: 123 VSGGQAGAENGVLTVMCGGDAGAFDKAKPVIEAYARMVGLMGPAGAGQLTKMINQICIAG 182 Query: 182 NIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKD 241 + ++E + KAG++ + V + I G AGS ++ + + + + GF +D KD Sbjct: 183 LVQGLAEGIHFGKKAGLDIEKVIEVISKGAAGSWQMENRHKTMNEGKYDFGFAVDWMRKD 242 Query: 242 LANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSALACYYEK 288 L L + GA+LP+TA V + ++A G D S+L EK Sbjct: 243 LDIVLAEARHNGAKLPVTALVDQFYGDIQALGGNRWDTSSLLARLEK 289 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: 203 Number of extensions: 6 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: 289 Length adjustment: 26 Effective length of query: 270 Effective length of database: 263 Effective search space: 71010 Effective search space used: 71010 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