Align 4-carboxy-4-hydroxy-2-oxoadipic acid aldolase; CHA aldolase; Gallate degradation protein C; EC 4.1.3.17 (characterized)
to candidate AZOBR_RS25265 AZOBR_RS25265 4-hydroxy-4-methyl-2-oxoglutarate aldolase
Query= SwissProt::Q88JX9 (238 letters) >FitnessBrowser__azobra:AZOBR_RS25265 Length = 224 Score = 182 bits (461), Expect = 6e-51 Identities = 94/213 (44%), Positives = 133/213 (62%) Query: 14 NIPRVEPHMIDALGRLGVATVHEAQGRKGLLNTAVRPIQQGVAVAGSAVTVLVAPGDNWM 73 + PR P + A +G ATVHEA GR+G +++A++PI G+ + G+A + PGDN Sbjct: 7 DFPRPTPEQVAAFATIGAATVHEALGRRGAVDSAIKPIWPGLRIVGAAFPLKTQPGDNLT 66 Query: 74 FHVAVEQCRPGDVLVVAPSSPCSDGYFGDLLATSLQARGVLGLVIDAGVRDSQTLRDMGF 133 H A++ RPGDVLVV G FGD++ATS Q+ G+ GLV + GVRD+ +RD+GF Sbjct: 67 IHAAMKLARPGDVLVVDAGDYTEQGSFGDVMATSAQSLGLAGLVTNGGVRDAAAIRDIGF 126 Query: 134 AVWSRAINAQGTVKEVLGSVNLPLLCAGQLVNAGDIVVADDDGVVVVRHGEAQAVLEAAT 193 ++SRAI+ +GTVK LG + P++ G V+ GD++V DDDG+VVV E +AVL A+ Sbjct: 127 PIFSRAISIKGTVKATLGPIAQPIVVGGVTVHPGDLIVGDDDGLVVVPLDEVEAVLTASR 186 Query: 194 QRADLEERKRLRLAAGELGLDIYEMRPRLAAKG 226 R + EER R L +G+ DI LA G Sbjct: 187 ARLEKEERLRADLQSGKTTWDIGNYDALLAQTG 219 Lambda K H 0.320 0.138 0.400 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: 162 Number of extensions: 3 Number of successful extensions: 1 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: 238 Length of database: 224 Length adjustment: 23 Effective length of query: 215 Effective length of database: 201 Effective search space: 43215 Effective search space used: 43215 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: 46 (22.3 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