Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate PfGW456L13_4603 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)
Query= SwissProt::P0ABQ2 (294 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4603 Length = 298 Score = 189 bits (481), Expect = 5e-53 Identities = 104/286 (36%), Positives = 165/286 (57%), Gaps = 2/286 (0%) Query: 3 VGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVIIT 62 +GF G+G+MG PM + LL AGY L V +RNP+ ++ AGA ++ + + DV++ Sbjct: 8 LGFAGIGLMGLPMCRRLLAAGYPLAVWNRNPDKCKPLVEAGARQVASPAELCQYADVVML 67 Query: 63 MLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAK-GIDMLDAPVS 121 L ++ V+EV G G++EGAK G +L+D SS+ P A+RE++ L AK G+ LD PVS Sbjct: 68 CLADTSVVREVVFGPAGVVEGAKKGQLLVDFSSLEPNATREMAAELAAKTGMGWLDTPVS 127 Query: 122 GGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIVALNI 181 GG A G+L++MVGG+ ++ ++ ++ V H G +GAG VTK NQ+IVA N Sbjct: 128 GGVVGAEAGSLAIMVGGELQDLERVRPVLLSLGQRVTHMGGVGAGQVTKACNQMIVACNA 187 Query: 182 AAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKP-GFRIDLHIKDL 240 ++E + LA ++GV+ L+ +A+ GG A S L AP + F+P + + +KDL Sbjct: 188 LVIAEVVALAERSGVDASLIAEALAGGFADSKPLQILAPQMAQNRFEPVKWHVRTLLKDL 247 Query: 241 ANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEK 286 A+ S G+ P++ ++M+ + G D S L Y + Sbjct: 248 DTAVKFSREQGSATPISGLAAQLMRLHGSQGFLEKDPSTLVQMYRE 293 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: 215 Number of extensions: 8 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: 298 Length adjustment: 26 Effective length of query: 268 Effective length of database: 272 Effective search space: 72896 Effective search space used: 72896 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