Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_004511698.1 GMET_RS13850 aconitate hydratase
Query= curated2:Q8ZW36 (161 letters) >NCBI__GCF_000012925.1:WP_004511698.1 Length = 648 Score = 77.8 bits (190), Expect = 3e-19 Identities = 64/168 (38%), Positives = 87/168 (51%), Gaps = 18/168 (10%) Query: 8 LVYGDKIDTDVIIPA--KYLVYTD--PALLGQHAMEPLDPEFPKKAK---GAVLVAGRAF 60 L GD I TD I+PA K L Y PA+ Q E LDP+F K+AK V++ G + Sbjct: 476 LTVGDNISTDTIMPAGNKVLPYRSNIPAI-SQFVFEHLDPDFHKRAKEKGNGVVIGGENY 534 Query: 61 GMGSSREQAALALKGAGVLAVVAESFARIFFRNAINVG-LPV-LQAPGIREKVKDGD--- 115 G GSSRE AALA + G+ A + +SFARI N +N G LP+ + P + VK GD Sbjct: 535 GQGSSREHAALAPRYLGIRAKIVKSFARIHKANLVNFGILPLTFRNPADYDLVKQGDRLV 594 Query: 116 --EVELDVEGG---IVRNITTGEVIVGKPLRGLPLEILKAGGLLNYLK 158 +V V G I + E++ + + L AGG LN++K Sbjct: 595 FPDVRRLVASGAAEIPVRVDGREIVTILEVSDRQRQELLAGGTLNFVK 642 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: 256 Number of extensions: 12 Number of successful extensions: 3 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: 648 Length adjustment: 27 Effective length of query: 134 Effective length of database: 621 Effective search space: 83214 Effective search space used: 83214 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 10 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