Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate N515DRAFT_1074 N515DRAFT_1074 3-hydroxyisobutyrate dehydrogenase
Query= SwissProt::P0ABQ2 (294 letters) >FitnessBrowser__Dyella79:N515DRAFT_1074 Length = 292 Score = 148 bits (374), Expect = 1e-40 Identities = 96/283 (33%), Positives = 154/283 (54%), Gaps = 4/283 (1%) Query: 1 MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVI 60 MKVGFIGLG MG M+ NLLKAG+S+ V +R+PEA A + + GA+ AST + A Q + + Sbjct: 1 MKVGFIGLGAMGSAMASNLLKAGHSVTVWNRSPEATAPLASLGAKVASTPQR-AAQGEAL 59 Query: 61 ITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPV 120 +ML N V+EV L ++G++E GTV ++ ++++ +RE++ A +G+D + APV Sbjct: 60 FSMLSNDQAVREVVL-DSGLLEEMDKGTVHVNHATVSVALARELASAHAQRGLDYVAAPV 118 Query: 121 SGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTG-EIGAGNVTKLANQVIVAL 179 G A G L+++V G A+ ++ L++AM ++ G E NV K+A ++ Sbjct: 119 FGRPDVAAAGRLNIVVAGKPAVLERVRPLLEAMGSAIWPMGEEAERANVVKIAGNFMLGA 178 Query: 180 NIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKP-GFRIDLHIK 238 I +M+EA L GV+ + L + A ++ ++ FKP GF + L K Sbjct: 179 AIESMAEASALTRAHGVSAGDFLHVMTSTLFAAPPYQGYAKLIAEQRFKPAGFALPLGYK 238 Query: 239 DLANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALA 281 D+ AL + LP + + + + A G D SALA Sbjct: 239 DINLALSAADATRVPLPFASVLRDSLLETLALGDEDVDWSALA 281 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: 194 Number of extensions: 8 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: 292 Length adjustment: 26 Effective length of query: 268 Effective length of database: 266 Effective search space: 71288 Effective search space used: 71288 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