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 Pf1N1B4_5069 Demethylmenaquinone methyltransferase
Query= SwissProt::Q9AQI0 (227 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5069 Length = 144 Score = 99.0 bits (245), Expect = 4e-26 Identities = 52/138 (37%), Positives = 77/138 (55%) Query: 79 PGDIVVAAVTAECTDGYFGDLLATSFQARGARALIIDAGVRDVKTLQEMDFPVWSKAISS 138 P V+ T GY+G++L + +A G L+ID GVRD+ L++ FPV+++ IS Sbjct: 2 PRGSVLVVGTGGFIAGYWGEVLTVAAEAAGVVGLVIDGGVRDIAALKKRQFPVFARGISV 61 Query: 139 KGTIKATLGSVNIPIVCAGMLVTPGDVIVADDDGVVCVPAARAVEVLAAAQKRESFEGEK 198 KGT+KA+ SV P G V GD++VADDDGV+ +P A A LA + R + E + Sbjct: 62 KGTVKASAPSVGQPFNFNGAFVAQGDLVVADDDGVIIIPKADAARTLAEGEARANKEAQM 121 Query: 199 RAKLASGVLGLDMYKMRE 216 L G L++ + E Sbjct: 122 MQALTEGRSTLELMNLTE 139 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: 70 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: 227 Length of database: 144 Length adjustment: 19 Effective length of query: 208 Effective length of database: 125 Effective search space: 26000 Effective search space used: 26000 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: 44 (21.6 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