Align 4-hydroxy-2-oxohexanoate aldolase (EC 4.1.3.43) (characterized)
to candidate PP_1791 PP_1791 putative Aldolase/synthase
Query= BRENDA::Q53WI0 (347 letters) >FitnessBrowser__Putida:PP_1791 Length = 534 Score = 88.2 bits (217), Expect = 4e-22 Identities = 74/240 (30%), Positives = 109/240 (45%), Gaps = 12/240 (5%) Query: 14 VDTTLRDGSHAHRHQYTVEEARAIAQALDEAGVYAIEVSHGDGLGGSSLQYGFSRTDE-- 71 +D TLRDG + + ++ A+ AG+ IE+ L SS + T + Sbjct: 4 LDCTLRDGGYYNNWNFSEALIAQYITAMQAAGIQTIELGLRS-LKNSSFSGACAYTTDAF 62 Query: 72 MELIRAVRETVRRAKVAALLLPGIGTRKELKE------AVEAGIQMVRIATQCTEADISE 125 + + V L G ++ + A E+ + +VRIA E + Sbjct: 63 LSTLDLPPSMTIGVMVNGSELVGKNAGQQALQLLFPSPASESPVDLVRIACHVHEFAEAL 122 Query: 126 QHFGMAKEMGLEAVGFLMMSHMRPPEF-LAEQARLMEGYGADVVYIVDSAGAMLPEDAYA 184 KE G + VGF +M E + A+L Y DV+Y DS G+M P+DA Sbjct: 123 PAASWLKERGYD-VGFNLMQIANCSESEIKALAKLANNYPLDVLYFADSMGSMSPDDAAQ 181 Query: 185 RVKALKEALSRAKVGFHAHNNLGLAIGNTLAALAAGADWVDATLRGYGAGAGNAPLEVLA 244 ++ L+ A +G H H+NLGLA+ NTL A+ G WVD+T+ G G G GNA E LA Sbjct: 182 IIQWLRSEWQGA-LGIHTHDNLGLALSNTLRAMDEGVTWVDSTVTGMGRGPGNARTEELA 240 Lambda K H 0.319 0.135 0.386 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: 428 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 347 Length of database: 534 Length adjustment: 32 Effective length of query: 315 Effective length of database: 502 Effective search space: 158130 Effective search space used: 158130 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 (21.7 bits) S2: 51 (24.3 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