Align 4-hydroxy-4-methyl-2-oxoglutarate aldolase/4-carboxy-4-hydroxy-2-oxoadipate aldolase; HMG/CHA aldolase; 4-hydroxy-2-oxoglutarate aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.3.16; EC 4.1.3.17; EC 4.1.1.112 (characterized)
to candidate PfGW456L13_3472 Bll0377 protein
Query= SwissProt::Q9AQI0 (227 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3472 Length = 270 Score = 88.2 bits (217), Expect = 1e-22 Identities = 52/163 (31%), Positives = 86/163 (52%), Gaps = 2/163 (1%) Query: 44 MRPIYAGKQVSGTAVTVLLQPGDNWMMHVAAEQIQPGDIVVAAVTAECTDGYFGDLLATS 103 MR I A + + T T+ +P N + EQIQPGD++V + G++L T Sbjct: 71 MRFIPAREDID-TYGTMTTKPNHNNLQWQGVEQIQPGDVLVIDSQNDPRAASAGNILVTR 129 Query: 104 FQARGARALIIDAGVRDVKTLQEMDFPVWSKAISSKGTIKAT-LGSVNIPIVCAGMLVTP 162 ARGARA++ D +RD + + P +++ +++ I + + +PI CAG+ V P Sbjct: 130 LLARGARAIVTDGALRDGSEIAALPLPAFAREVTATTRISYHHVADLQVPIGCAGVAVYP 189 Query: 163 GDVIVADDDGVVCVPAARAVEVLAAAQKRESFEGEKRAKLASG 205 GD+IV D DG+ +PA A E+ ++ EG ++A+G Sbjct: 190 GDIIVGDGDGLTVIPAHLAEELADYCTVQDDLEGYLAMRIAAG 232 Lambda K H 0.319 0.135 0.388 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: 125 Number of extensions: 5 Number of successful extensions: 3 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: 227 Length of database: 270 Length adjustment: 24 Effective length of query: 203 Effective length of database: 246 Effective search space: 49938 Effective search space used: 49938 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