Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate GFF4113 PS417_21070 aconitate hydratase
Query= curated2:B1YDA5 (162 letters) >FitnessBrowser__WCS417:GFF4113 Length = 864 Score = 48.5 bits (114), Expect = 3e-10 Identities = 41/135 (30%), Positives = 69/135 (51%), Gaps = 19/135 (14%) Query: 45 FPKKAKGAVLVAGRAFGMGSSREQAAIALKGAGVLAVVAESFARIFFRNAINVG-LPVLQ 103 + ++ + +++AG +G GSSR+ AA ++ AGV A+ AE F RI N + +G LP+ Sbjct: 727 YMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLVGMGVLPLEF 786 Query: 104 VPDVTKRVREGDELEV-DIEGG--------YLLNLTTGERLEGKPLRGLPLA----ILKA 150 +P + + D E D+ G ++N GER+E L A I +A Sbjct: 787 LPGTDRHTLKIDGSETYDVVGARTPRAQLTLVINRKNGERVEVPVTCRLDTAEEVSIYEA 846 Query: 151 GGLV-----NFLKTA 160 GG++ +FL++A Sbjct: 847 GGVLQRFAQDFLESA 861 Lambda K H 0.320 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: 281 Number of extensions: 11 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: 162 Length of database: 864 Length adjustment: 29 Effective length of query: 133 Effective length of database: 835 Effective search space: 111055 Effective search space used: 111055 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: 49 (23.5 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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