Align 4-carboxy-4-hydroxy-2-oxoadipic acid aldolase; CHA aldolase; Gallate degradation protein C; EC 4.1.3.17 (characterized)
to candidate RR42_RS28420 RR42_RS28420 4-hydroxy-4-methyl-2-oxoglutarate aldolase
Query= SwissProt::Q88JX9 (238 letters) >FitnessBrowser__Cup4G11:RR42_RS28420 Length = 220 Score = 147 bits (370), Expect = 2e-40 Identities = 82/207 (39%), Positives = 121/207 (58%), Gaps = 2/207 (0%) Query: 12 VRNIPRVEPHMIDALGRLGVATVHEAQGRKGLLNTAVRPIQQGVAVAGSAVTVLVAPGDN 71 +R RV P +++A L AT+HEA G+ G++ A++P+ G + G A+TV GDN Sbjct: 11 IREFVRVSPKVVEAARALPTATLHEAGGKIGVIPPAIKPVAPGFRICGPALTVHSPGGDN 70 Query: 72 WMFHVAVEQCRPGDVLVVAPSSPCSDGYFGDLLATSLQARGVLGLVIDAGVRDSQTLRDM 131 H A++ +PGDVLVV S GY+G+++ T+ + + + GLVID VRD L ++ Sbjct: 71 LWLHRALDIAQPGDVLVVHVSGAYEHGYWGEIMTTAAKVKQLGGLVIDGCVRDGVLLEEI 130 Query: 132 GFAVWSRAINAQGTVKE--VLGSVNLPLLCAGQLVNAGDIVVADDDGVVVVRHGEAQAVL 189 GF V++R + +GT K+ +G +N P+L G V AGD+VV D DGVVVV A V+ Sbjct: 131 GFPVFARGLCIRGTGKDYGAIGWLNAPVLIGGARVEAGDLVVGDRDGVVVVSRARAGEVV 190 Query: 190 EAATQRADLEERKRLRLAAGELGLDIY 216 + A R E R+ AGE + IY Sbjct: 191 DKAQDREATEAAILKRVGAGEATMRIY 217 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: 151 Number of extensions: 8 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: 220 Length adjustment: 23 Effective length of query: 215 Effective length of database: 197 Effective search space: 42355 Effective search space used: 42355 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