Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate AO356_30330 AO356_30330 2-hydroxy-3-oxopropionate reductase
Query= SwissProt::P0ABQ2 (294 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30330 Length = 444 Score = 136 bits (342), Expect = 1e-36 Identities = 81/266 (30%), Positives = 133/266 (50%), Gaps = 3/266 (1%) Query: 1 MKVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVI 60 MK+G+IGLG +G +++ L +SL V D N A+ GA+ A TA +A +CDVI Sbjct: 1 MKIGYIGLGALGSQLARRFLS--HSLCVWDINTAAVDTFKKLGADVAPTAADLARRCDVI 58 Query: 61 ITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPV 120 LP S V+ G NG+ G PGT++ID +S P +R ++E L +GIDM+DA V Sbjct: 59 FLCLPRSSDVRSALFGPNGLAAGLVPGTLIIDQTSGIPGETRRMAEELAERGIDMMDAAV 118 Query: 121 SGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGE-IGAGNVTKLANQVIVAL 179 S +G ++MV G ++++ +++ + ++ GE +G G K+ N + A Sbjct: 119 SASPLVVAEGKATLMVAGPDTVYERALPVLQVITQTIYRCGERVGDGQAMKMVNNAMNAG 178 Query: 180 NIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKD 239 E + + KAG++ L+ + A + D P + F + L +KD Sbjct: 179 CRLGTLEVVAMGKKAGLSLPLMADVLNRNKARNQTTDRMLPALAQGKPSTNFALALMLKD 238 Query: 240 LANALDTSHGVGAQLPLTAAVMEMMQ 265 + A+ +PLTA V ++Q Sbjct: 239 VDQAVALGMSRDVPMPLTALVRALLQ 264 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: 276 Number of extensions: 19 Number of successful extensions: 3 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: 444 Length adjustment: 29 Effective length of query: 265 Effective length of database: 415 Effective search space: 109975 Effective search space used: 109975 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: 49 (23.5 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