Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate WP_057507560.1 ABB28_RS04900 3-hydroxyisobutyrate dehydrogenase
Query= SwissProt::P0ABQ2 (294 letters) >NCBI__GCF_001431535.1:WP_057507560.1 Length = 296 Score = 181 bits (459), Expect = 2e-50 Identities = 103/286 (36%), Positives = 165/286 (57%), Gaps = 7/286 (2%) Query: 2 KVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVII 61 ++ FIGLG MG PM+ NL KAG+++ V D P A+ + AGA AS+A +V+I Sbjct: 3 RIAFIGLGNMGGPMAANLAKAGHAVRVFDLVPAAVQAAVDAGATAASSALDTLADAEVVI 62 Query: 62 TMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPVS 121 +MLP S HV+ V LG++G++ G ++ID S+IAP +R+++EA A+G+ MLDAPVS Sbjct: 63 SMLPASRHVEGVYLGDDGLLADIPGGALVIDCSTIAPATARKVAEAAAARGLQMLDAPVS 122 Query: 122 GGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIVALNI 181 GG A GTL+ +VGG++ ++ ++AM ++ H G GAG V KL N + + + + Sbjct: 123 GGTAGATAGTLTFIVGGEEDALERARPYLQAMGRNIFHVGASGAGQVAKLCNNMALGVIM 182 Query: 182 AAMSEALTLATKAGVNPDLVYQ--AIRGGLAGSTVLDAKAPMVMD-----RNFKPGFRID 234 A E++ L G++P ++ Q A+ G + +T + P V++ R + GF D Sbjct: 183 AVTGESIALGVAHGLDPKVLSQMMAVSTGRSWATEVCNPWPGVLENAPASRGYSGGFGSD 242 Query: 235 LHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSAL 280 L +KD+ A++ + VGA +PL + G G D S++ Sbjct: 243 LMLKDMGLAVEAAMSVGASIPLGELARNLYSMNHQAGRGKLDFSSV 288 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: 206 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: 294 Length of database: 296 Length adjustment: 26 Effective length of query: 268 Effective length of database: 270 Effective search space: 72360 Effective search space used: 72360 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 24 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