Align 4-carboxy-4-hydroxy-2-oxoadipic acid aldolase; CHA aldolase; Gallate degradation protein C; EC 4.1.3.17 (characterized)
to candidate AZOBR_RS33695 AZOBR_RS33695 4-hydroxy-4-methyl-2-oxoglutarate aldolase
Query= SwissProt::Q88JX9 (238 letters) >FitnessBrowser__azobra:AZOBR_RS33695 Length = 222 Score = 170 bits (430), Expect = 2e-47 Identities = 94/218 (43%), Positives = 129/218 (59%), Gaps = 1/218 (0%) Query: 11 VVRNIPRVEPHMIDALGRLGVATVHEAQGRKGLLNTAVRPIQQGVAVAGSAVTVLVAPGD 70 VV+ PR P ++ A AT+HEA G+KG ++ ++P+ QG+ + G+AVTV P D Sbjct: 3 VVKEFPRPAPDLVAAFRGQSPATLHEAMGKKGAMSFPIKPLYQGMTLFGTAVTVSGGPTD 62 Query: 71 NWMFHVAVEQCRPGDVLVVAPSSPCSDGYFGDLLATSLQARGVLGLVIDAGVRDSQTLRD 130 N M H A+ RPGDVLVV G +GD+L + RG+ GLVID VRD+ +R+ Sbjct: 63 NLMIHAAMALTRPGDVLVVDFKGMTEAGPWGDVLTEAAIQRGLAGLVIDGCVRDAAAIRN 122 Query: 131 MGFAVWSRAINAQGTVK-EVLGSVNLPLLCAGQLVNAGDIVVADDDGVVVVRHGEAQAVL 189 MGF V+ R + +GT K + G VN P++C G +V GDI+V DDDGVVVV EA A L Sbjct: 123 MGFPVFCRGTSMKGTTKTQPTGDVNTPIVCGGVMVMPGDILVGDDDGVVVVPQAEAAATL 182 Query: 190 EAATQRADLEERKRLRLAAGELGLDIYEMRPRLAAKGL 227 A +R +EE R +L AG + + P L A G+ Sbjct: 183 AKAAERERMEEGLREQLRAGRTTVQALTLEPYLEAGGI 220 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: 155 Number of extensions: 7 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: 238 Length of database: 222 Length adjustment: 23 Effective length of query: 215 Effective length of database: 199 Effective search space: 42785 Effective search space used: 42785 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