Align 3-isopropylmalate dehydratase small subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate WP_020562793.1 A3OW_RS0107395 aconitate hydratase
Query= curated2:Q9WYC8 (166 letters) >NCBI__GCF_000372865.1:WP_020562793.1 Length = 646 Score = 78.2 bits (191), Expect = 2e-19 Identities = 54/169 (31%), Positives = 92/169 (54%), Gaps = 18/169 (10%) Query: 8 KFGDNISTDHIAPG--RYFHLRNNLEELAKHVLEDAMEDFAKKV----QKGDIIVAGKNF 61 K GDN+STD I P + R+N+ +++ V F ++ ++G +V G+N+ Sbjct: 473 KVGDNVSTDEIMPAGAKVLPFRSNIPAISEFVFAQIDTGFYQRTLPYREQGFFVVGGENY 532 Query: 62 GLGSSREHAARIIKIAGVSCIVAKSFARIFYRNAINVGL-PVIEL--KEVDEINQGDELE 118 G GSSREHAA + G+ ++AKSFARI + N +N G+ P++ L + +I Q D L Sbjct: 533 GQGSSREHAALAPRYLGLRAVLAKSFARIHHGNLVNFGIVPLVFLDPENWGDIGQEDVLR 592 Query: 119 ID-----LENG---VLKNLTTGKEYRFT-PIPKFLLEILKEDGIVNYLK 158 I+ L G V++N+T G+ Y + + ++ + G++N +K Sbjct: 593 IESLRSALAGGASVVVENVTRGRRYEMRHGLSRRQIDAVLAGGLINSVK 641 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: 279 Number of extensions: 18 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: 166 Length of database: 646 Length adjustment: 28 Effective length of query: 138 Effective length of database: 618 Effective search space: 85284 Effective search space used: 85284 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