Align 3-isopropylmalate dehydratase small subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate BPHYT_RS23060 BPHYT_RS23060 3-isopropylmalate dehydratase large subunit
Query= curated2:Q9V1I9 (163 letters) >FitnessBrowser__BFirm:BPHYT_RS23060 Length = 655 Score = 68.6 bits (166), Expect = 2e-16 Identities = 56/152 (36%), Positives = 78/152 (51%), Gaps = 24/152 (15%) Query: 12 DNVSTDEITPGRYNLTKDPQELARIAFI-----EVRPEFAEKVRRG--DVVVGGKNFGIG 64 DNVSTDEITP LT D + L + ++ E P V+ G V V GK +G G Sbjct: 40 DNVSTDEITPVTVMLTYD-ERLGQFPYVGFKAGERMPIGRNAVKNGGFQVTVAGKRYGKG 98 Query: 65 SSRESAALALKAAGVSGIIAKSFGRIFYRNAVNLGIPLLIGD---TDELEDGDVITVNWE 121 SSRES+ LA +AG+ I+A+SF RI+ +N N+GI L D D L G+ + ++ Sbjct: 99 SSRESSPLAELSAGIRLIVAESFERIYQQNCDNIGI-LTTTDFSVLDRLSAGEAVPID-- 155 Query: 122 TGEVRKNGQTLQFEPLPGFLLEIVREGGILEF 153 E K L +I+R GG+L + Sbjct: 156 --EFLKGRDAL--------TQQIIRSGGLLAY 177 Lambda K H 0.321 0.142 0.425 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: 210 Number of extensions: 10 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: 163 Length of database: 655 Length adjustment: 28 Effective length of query: 135 Effective length of database: 627 Effective search space: 84645 Effective search space used: 84645 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: 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