Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate 206498 DVU1064 aconitate hydratase, putative
Query= curated2:Q8ZW36 (161 letters) >MicrobesOnline__882:206498 Length = 642 Score = 87.8 bits (216), Expect = 3e-22 Identities = 66/165 (40%), Positives = 93/165 (56%), Gaps = 14/165 (8%) Query: 11 GDKIDTDVIIPAKYLVY---TDPALLGQHAMEPLDPEFPKKAKGA---VLVAGRAFGMGS 64 GD I TD I+PA + ++ + +H +D +F K+A+ A V+VAG +G GS Sbjct: 475 GDDITTDHIMPAGAEITALRSNVPAISRHVFGRVDADFVKRAEAAANGVIVAGENYGQGS 534 Query: 65 SREQAALALKGAGVLAVVAESFARIFFRNAINVG-LP-VLQAPGIREKVKDGDEVELDV- 121 SRE AALA + G+ AV+A+S ARI N +N G LP +L G E+++ G V + V Sbjct: 535 SREHAALAPRHLGIRAVIAKSLARIHRANLVNFGILPLILVDKGDYERLEQGGNVTIPVA 594 Query: 122 ---EGG--IVRNITTGEVIVGKPLRGLPLEILKAGGLLNYLKNSR 161 GG V G V V L LEI++AGGLLNY++N+R Sbjct: 595 DIIAGGECAVALADGGSVRVRNDLTVDELEIIRAGGLLNYVRNAR 639 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: 269 Number of extensions: 15 Number of successful extensions: 2 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: 642 Length adjustment: 27 Effective length of query: 134 Effective length of database: 615 Effective search space: 82410 Effective search space used: 82410 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: 48 (23.1 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