Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate H281DRAFT_02981 H281DRAFT_02981 aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming)
Query= curated2:Q8ZW36 (161 letters) >FitnessBrowser__Burk376:H281DRAFT_02981 Length = 865 Score = 46.2 bits (108), Expect = 1e-09 Identities = 24/64 (37%), Positives = 40/64 (62%), Gaps = 1/64 (1%) Query: 45 FPKKAKGAVLVAGRAFGMGSSREQAALALKGAGVLAVVAESFARIFFRNAINVG-LPVLQ 103 + ++ + +++AG +G GSSR+ AA ++ AG A+VAE F RI N + +G LP+ Sbjct: 727 YMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGAEAIVAEGFERIHRTNLVGMGVLPLEF 786 Query: 104 APGI 107 PG+ Sbjct: 787 KPGV 790 Lambda K H 0.319 0.141 0.398 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: 304 Number of extensions: 17 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: 161 Length of database: 865 Length adjustment: 29 Effective length of query: 132 Effective length of database: 836 Effective search space: 110352 Effective search space used: 110352 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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