Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate Pf6N2E2_2301 Aconitate hydratase (EC 4.2.1.3)
Query= curated2:A4YF02 (161 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 Length = 913 Score = 50.4 bits (119), Expect = 8e-11 Identities = 45/146 (30%), Positives = 58/146 (39%), Gaps = 54/146 (36%) Query: 11 GDKIDTDIIIPARHLKYTDPA--YLAQHAMEP---------------------------- 40 GD + TD I PA ++K PA YL + +EP Sbjct: 688 GDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSRRGNHQVMMRGTFANIRIRN 747 Query: 41 --LDPE---------------------FYKKASKGVVIVAGKVFGMGSSREQAAIALKAA 77 LD E Y+ +V++AG+ +G GSSR+ AA Sbjct: 748 EMLDGEEGGNTIYIPSGERMPIYDAAMLYQAVGTPLVVIAGQEYGTGSSRDWAAKGTNLL 807 Query: 78 GVKAVIAESFARIFYRNCINNG-LPL 102 GVKAVIAESF RI N + G LPL Sbjct: 808 GVKAVIAESFERIHRSNLVGMGVLPL 833 Lambda K H 0.318 0.137 0.384 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: 295 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 161 Length of database: 913 Length adjustment: 30 Effective length of query: 131 Effective length of database: 883 Effective search space: 115673 Effective search space used: 115673 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: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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