Align 4-carboxy-4-hydroxy-2-oxoadipate aldolase; CHA aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.3.17; EC 4.1.1.112 (characterized)
to candidate HSERO_RS22295 HSERO_RS22295 4-hydroxy-4-methyl-2-oxoglutarate aldolase
Query= SwissProt::G2IQQ8 (228 letters) >FitnessBrowser__HerbieS:HSERO_RS22295 Length = 212 Score = 155 bits (392), Expect = 6e-43 Identities = 82/207 (39%), Positives = 125/207 (60%) Query: 19 EVIDGLAACGVATVHEAQGRTGLLASYMRPIYRGARVAGSALTISAPPGDNWMVHVAIEQ 78 E I L A G ATV+EAQG G L M+PI +R+AG ALT+ A PGDN ++H A+ Q Sbjct: 5 EQIQQLRALGSATVYEAQGAKGALDHGMKPIDPASRLAGPALTVDARPGDNLVLHYAVLQ 64 Query: 79 LKAGDILLLAPTSPCEDGYFGDLLATSAQARGCRGLVIDAGVRDVRDLTEMNFPVWSKAI 138 K GD+L++ + E G +GD+L A +G GLV++ VRD + ++ FPV+ + + Sbjct: 65 AKPGDVLVVDAKAFMEAGPWGDVLTVLAMKKGIAGLVVNGCVRDANTIIDLGFPVFCRGL 124 Query: 139 YAQGTVKNTLGSVNVPVVCANALVNPGDVIVADDDGVCVVPLANAEKVLEAARAREANEG 198 +GT K+ G VNVP+V + L++PGD+IV D DG+ VV + E + ++ RE E Sbjct: 125 SIKGTGKHQPGKVNVPIVIGDVLIHPGDIIVGDRDGLAVVAQSEVEMTIASSMVREEKEQ 184 Query: 199 DKREKMANGVLGLDLYKMRERLEKEGL 225 RE + NG ++L ++ L++ G+ Sbjct: 185 KMREAIENGASTVELMQLDTILKQYGM 211 Lambda K H 0.318 0.136 0.397 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: 173 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: 228 Length of database: 212 Length adjustment: 22 Effective length of query: 206 Effective length of database: 190 Effective search space: 39140 Effective search space used: 39140 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: 45 (21.9 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