Align 2-hydroxy-3-oxopropionate reductase; EC 1.1.1.60; Tartronate semialdehyde reductase; TSAR (uncharacterized)
to candidate Ac3H11_4470 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)
Query= curated2:P77161 (292 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4470 Length = 304 Score = 157 bits (396), Expect = 4e-43 Identities = 93/289 (32%), Positives = 148/289 (51%), Gaps = 6/289 (2%) Query: 2 KLGFIGLGIMGTPMAINLARAGHQLHV------TTIGPVADELLSLGAVSVETARQVTEA 55 K+ F+GLG+MG PMA +LA AGH++ V ++ A+ + T R+ Sbjct: 16 KVAFLGLGVMGYPMAGHLALAGHEVTVYNRTATKSVAWCAEYAGAKAPKHATTPREAAAG 75 Query: 56 SDIIFIMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYL 115 +DI+F V + + V G +G G VD ++ S + LG ++ Sbjct: 76 ADIVFCCVGNDNDLRSVTLGADGAFAGMQPGAIFVDHTTASAEVARELYAAAKALGLQFV 135 Query: 116 DAPVSGGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQII 175 DAPVSGG+ GA+ G L++M GGD A F+ +P+ + TL+G +G GQ K+ NQI Sbjct: 136 DAPVSGGQAGAQNGQLTVMCGGDAAAFDAAQPVATAFSRAFTLLGESGSGQLAKMVNQIC 195 Query: 176 VALNIEAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALH 235 +A ++ +SEA+ F AG D +V + G A S ++ G+ M+ F+ GF + Sbjct: 196 IAGLVQGLSEAVAFGQNAGLDMKQVLDVIGKGAAQSWQMDNRGKTMVDGKFDFGFAVDWM 255 Query: 236 QKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALE 284 +KDL L L AK +P TA + + GG++ D S+L++ L+ Sbjct: 256 RKDLGLVLDEAKRNGSRVPVTALVDQFYADVQQMGGNRWDTSSLIKRLK 304 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: 229 Number of extensions: 12 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: 304 Length adjustment: 26 Effective length of query: 266 Effective length of database: 278 Effective search space: 73948 Effective search space used: 73948 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