Align 3-isopropylmalate dehydratase small subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate PP_2336 PP_2336 aconitate hydratase 1
Query= curated2:Q9RTI0 (208 letters) >FitnessBrowser__Putida:PP_2336 Length = 862 Score = 55.1 bits (131), Expect = 4e-12 Identities = 43/106 (40%), Positives = 59/106 (55%), Gaps = 7/106 (6%) Query: 27 VESELAKYAMEDYDKDFVRRVQPGDIIVAGADFGCGSSREHAVWALRGAGVSAVIAPNFA 86 +E E M + + +++R QP IIVAGAD+G GSSR+ A +R AGV A++A F Sbjct: 711 IEPEGKVTRMWEAIETYMQRKQPL-IIVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFE 769 Query: 87 RIYYRNSINNGFLALECEGITE---LFQDGEEAELDLKGGTIRNPR 129 RI+ N + G L LE + T+ L DG E D+ G R PR Sbjct: 770 RIHRTNLVGMGVLPLEFKPGTDRKTLGLDGSET-YDVLGA--RTPR 812 Lambda K H 0.315 0.135 0.406 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: 429 Number of extensions: 24 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: 208 Length of database: 862 Length adjustment: 31 Effective length of query: 177 Effective length of database: 831 Effective search space: 147087 Effective search space used: 147087 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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