Align 3-isopropylmalate dehydratase small subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate Echvi_4039 Echvi_4039 aconitate hydratase 1
Query= curated2:Q9WYC8 (166 letters) >FitnessBrowser__Cola:Echvi_4039 Length = 925 Score = 49.3 bits (116), Expect = 2e-10 Identities = 30/99 (30%), Positives = 55/99 (55%), Gaps = 7/99 (7%) Query: 46 AKKVQKGD---IIVAGKNFGLGSSREHAARIIKIAGVSCIVAKSFARIFYRNAINVGLPV 102 ++K QK D +++AGK +G GSSR+ AA+ + G+ ++A+S+ RI N + +G+ Sbjct: 785 SEKYQKDDTPLVVLAGKEYGSGSSRDWAAKGTTLLGIHAVIAESYERIHRSNLVGMGVLP 844 Query: 103 IELKE---VDEINQGDELEIDLENGVLKNLTTGKEYRFT 138 ++ E + + EI +E G+ + LT K + T Sbjct: 845 LQFAEGQSASSLGLDGKEEITIE-GITEGLTPLKNLKAT 882 Lambda K H 0.321 0.141 0.408 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: 417 Number of extensions: 21 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: 166 Length of database: 925 Length adjustment: 30 Effective length of query: 136 Effective length of database: 895 Effective search space: 121720 Effective search space used: 121720 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: 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