Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate 3608350 Dshi_1752 3-hydroxyisobutyrate dehydrogenase (RefSeq)
Query= SwissProt::P0ABQ2 (294 letters) >FitnessBrowser__Dino:3608350 Length = 291 Score = 148 bits (373), Expect = 2e-40 Identities = 94/288 (32%), Positives = 146/288 (50%), Gaps = 16/288 (5%) Query: 1 MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVI 60 MK+GF+GLG MG PM++NL AG+++ D + + G A++A A +V+ Sbjct: 1 MKIGFVGLGNMGAPMARNLAAAGHAVTGFD-----LTAPVPEGVTGAASAAEAAAGAEVV 55 Query: 61 ITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPV 120 ITMLPN ++ VA +I PG VL+D S++ ++R ++ +A G+ LDAPV Sbjct: 56 ITMLPNGAILRSVAAE---LIPAMAPGAVLLDCSTVDVESARAVAAQAEAAGLGALDAPV 112 Query: 121 SGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIVALN 180 SGG A GTL+ MVGG A F L M VH G G G K+ N +I+ + Sbjct: 113 SGGTGGAEAGTLTFMVGGSDAAFATARPLFDIMGQKAVHCGGAGNGQAAKICNNMILGVT 172 Query: 181 IAAMSEALTLATKAGVNPDLVYQAI--RGGLAGSTVLDAKAPMV-----MDRNFKPGFRI 233 + A E LA K G++ ++ + G + S + AP + DR++ PGF Sbjct: 173 MVATCEGFALADKLGLDRQALFDVVSTSSGYSWSMNVYCPAPGIGPESPADRDYAPGFAA 232 Query: 234 DLHIKDLANALDTSHGVGAQLPLTAAVMEMMQA-LRADGLGTADHSAL 280 +L +KDL + + V A P A + + + +G+G D +A+ Sbjct: 233 ELMLKDLRLSQQAAEAVDADTPTGATATALFETFVETEGMGKKDFTAI 280 Lambda K H 0.316 0.133 0.366 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: 225 Number of extensions: 13 Number of successful extensions: 4 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: 294 Length of database: 291 Length adjustment: 26 Effective length of query: 268 Effective length of database: 265 Effective search space: 71020 Effective search space used: 71020 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