Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate N515DRAFT_2996 N515DRAFT_2996 3-hydroxyisobutyrate dehydrogenase
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__Dyella79:N515DRAFT_2996 Length = 286 Score = 152 bits (383), Expect = 1e-41 Identities = 98/283 (34%), Positives = 146/283 (51%), Gaps = 5/283 (1%) Query: 1 MTMKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAG-AETASTAKAIAEQC 59 MT K F+GLG MG PM+ +L G V++R +A AD +A A + +A QC Sbjct: 1 MTFKAAFVGLGAMGAPMAGHLKSKGLLHAVANRT-QAKADALARELGVVAPPLEQLAAQC 59 Query: 60 DVIITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLD 119 +VI + V + ++ K G V++D S++AP ++ + L GV+ LD Sbjct: 60 EVIALCVTADADVLATI---DTMLPHLKRGAVVVDHSTVAPDTAKRAAARLATAGVDFLD 116 Query: 120 APVSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIV 179 APVSGG A +G LSVMVGGD A+ ++ +++A A V H GD+GAG TK NQV+V Sbjct: 117 APVSGGVEGAKNGKLSVMVGGDAAVLERARPVLEAYALRVTHLGDVGAGQATKAVNQVLV 176 Query: 180 ALNIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHI 239 A A+ E L L G+ + + + G AGS L+ + ++ F GF++ L Sbjct: 177 AGIAQAVCEGLALGEALGLEAERLLPTLGAGAAGSWFLEKRGATMLRDEFSVGFKLALLH 236 Query: 240 KDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSAL 282 KDL + G G + + L + G+G+DD SAL Sbjct: 237 KDLGIVKRIAEGAGTDRTVIEKSLADYAELMSQGYGDDDISAL 279 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: 216 Number of extensions: 7 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: 286 Length adjustment: 26 Effective length of query: 270 Effective length of database: 260 Effective search space: 70200 Effective search space used: 70200 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