Align 3-isopropylmalate dehydratase small subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate Ac3H11_1140 Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
Query= curated2:Q9V1I9 (163 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1140 Length = 980 Score = 46.6 bits (109), Expect = 1e-09 Identities = 39/124 (31%), Positives = 58/124 (46%), Gaps = 20/124 (16%) Query: 54 VVVGGKNFGIGSSRESAALALKAAGVSGIIAKSFGRIFYRNAVNLGI-PLLI--GDTDE- 109 VV G+ +G GSSR+ AA + G+ ++A+SF RI N V +G+ PL GD+ E Sbjct: 853 VVFAGEEYGTGSSRDWAAKGTQLLGIKAVVARSFERIHRSNLVGMGVLPLQFKAGDSWET 912 Query: 110 --LEDGDVITVNWETGEVRKNGQTLQFEPLPGFLLEIV--------------REGGILEF 153 L +VI V + ++ L G + E+V R GGIL F Sbjct: 913 LGLTGNEVIDVLPDPALTPQSDARLVIRRADGTVREVVVTLRIDTPIEVDYYRAGGILPF 972 Query: 154 IRRR 157 + R+ Sbjct: 973 VLRQ 976 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: 339 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: 163 Length of database: 980 Length adjustment: 30 Effective length of query: 133 Effective length of database: 950 Effective search space: 126350 Effective search space used: 126350 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