Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate Dsui_0578 Dsui_0578 homocitrate synthase NifV
Query= BRENDA::P9WMK5 (346 letters) >FitnessBrowser__PS:Dsui_0578 Length = 384 Score = 74.3 bits (181), Expect = 5e-18 Identities = 87/289 (30%), Positives = 125/289 (43%), Gaps = 48/289 (16%) Query: 4 MWDVRITDTSLRDGSHHKRHQFTKDEVGAIVAALDAAGVPVIEVTHGDGLGGSSFNYGFS 63 M + I DT+LRDG FT E AI AL AAGVP +EV G+ Sbjct: 1 MTTITINDTTLRDGEQTAGVAFTAAEKLAIAQALAAAGVPEMEV----GIPAMG------ 50 Query: 64 KTPEQELIKLAAATAKEARIAFLMLPGVGTKDDIKEARDNGGSICRIATHCTEADV---- 119 EQE+I+ A +R LM+ G D++ R I ++ ++ + Sbjct: 51 -EQEQEVIRAIAGLGLSSR---LMVWGRMCAADLEVTRRCNAHIVNLSIPVSDQQIRHKL 106 Query: 120 ---------SIQHF-GLARELGLETV--------GFLMMAHTIAPEKLAAQARIMADAGC 161 SI+ F AR GLE L H + AAQA AG Sbjct: 107 NKDHRWVLDSIRRFVPEARAAGLEVCVGGEDSSRADLDFLHRVME---AAQA-----AGA 158 Query: 162 QCVYVVDSAGALVLDGVADRVSALVAELGEDAQVGFHGHENLGLGVANSVAAVRAGAKQI 221 + D+ G L R++AL A D ++ H H++LGL AN++AAV AGA I Sbjct: 159 RRFRFADTLGVLDPFITHQRIAALRAR--SDLEIEIHAHDDLGLATANTLAAVTAGATHI 216 Query: 222 DGSCRRFGAGAGNAPV-EALIGVFDKIGVKTGIDFFDIADAAEDVVRPA 269 + + G AGNAP+ E++I + + +G+D + A D+V A Sbjct: 217 NTTVNGLGERAGNAPLEESVIALRHLYDIDSGVDPLQL-PAISDLVAKA 264 Lambda K H 0.320 0.136 0.393 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: 335 Number of extensions: 27 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: 346 Length of database: 384 Length adjustment: 29 Effective length of query: 317 Effective length of database: 355 Effective search space: 112535 Effective search space used: 112535 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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