Align 3-isopropylmalate dehydratase small subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate Echvi_2531 Echvi_2531 aconitate hydratase, mitochondrial
Query= curated2:Q8TW31 (168 letters) >FitnessBrowser__Cola:Echvi_2531 Length = 757 Score = 49.3 bits (116), Expect = 1e-10 Identities = 39/124 (31%), Positives = 60/124 (48%), Gaps = 14/124 (11%) Query: 54 VIVAGKNFGCGSSREQAVMALQQAGVACVVARSFARIFYRNAINRGL--PTVEAEEDPTE 111 ++V N+G GSSRE A M + GV V+ +SFARI N +G+ T + E D + Sbjct: 632 IVVGDHNYGEGSSREHAAMEPRHLGVKAVLVKSFARIHETNLKKQGMLALTFDNEADYDK 691 Query: 112 VVEDGNRVTVDLD----------ELVLRAGSEEVPLREPP--EFALQAWREGGLLELVKK 159 V ED +DLD E V GS++V + + ++ ++ G L L+K+ Sbjct: 692 VQEDDTINFLDLDQFAPDKPLTLEFVHADGSKDVIVANHSYNDAQIKWFKAGSALNLIKE 751 Query: 160 NPDK 163 K Sbjct: 752 EQKK 755 Lambda K H 0.318 0.138 0.419 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: 335 Number of extensions: 15 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: 168 Length of database: 757 Length adjustment: 29 Effective length of query: 139 Effective length of database: 728 Effective search space: 101192 Effective search space used: 101192 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