Align 2-hydroxy-3-oxopropionate reductase; EC 1.1.1.60; Tartronate semialdehyde reductase; TSAR (uncharacterized)
to candidate CCNA_01645 CCNA_01645 3-hydroxyisobutyrate dehydrogenase
Query= curated2:P77161 (292 letters) >FitnessBrowser__Caulo:CCNA_01645 Length = 286 Score = 151 bits (382), Expect = 1e-41 Identities = 97/286 (33%), Positives = 149/286 (52%), Gaps = 5/286 (1%) Query: 1 MKLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVADELLSL--GAVSVETARQVTEASDI 58 MK FIG+G+MG PMA +L AGH++ V P + G + ET + +++ Sbjct: 1 MKTAFIGMGVMGFPMAGHLKAAGHEVAVYNRSPEKARRWAEKHGGAAFETIAEAVAGAEV 60 Query: 59 IFIMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAP 118 + + V + V +++ A +G IVD ++ S + A + G ++DAP Sbjct: 61 VLLCVGNDDDVRDLVAQ---VLPAMGEGGVIVDHTTTSAKVAREMAALAAQSGRAFVDAP 117 Query: 119 VSGGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVAL 178 VSGG+ GA G L+IM GGD+A ++RV P+ E+ K + +G G GQ K+ NQI +A Sbjct: 118 VSGGQAGAESGQLTIMAGGDQAAYDRVLPVIEVYAKAVRRIGEVGAGQLTKMCNQIAIAG 177 Query: 179 NIEAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKD 238 ++ V+EAL FA +A V A+ G A S +E M + F+ GF + +KD Sbjct: 178 VVQGVAEALHFAKRACLPTDDVLAAISKGAAQSWQMENRWPTMAQGKFDFGFAVDWMRKD 237 Query: 239 LNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALE 284 L +AL A+ LP TA + + A GG++ D S+LV LE Sbjct: 238 LGIALDEARTNGAKLPATALIDQFYAEVQAMGGNRWDTSSLVARLE 283 Lambda K H 0.318 0.135 0.376 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: 175 Number of extensions: 10 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: 292 Length of database: 286 Length adjustment: 26 Effective length of query: 266 Effective length of database: 260 Effective search space: 69160 Effective search space used: 69160 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 (21.7 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