Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate Ga0059261_3296 Ga0059261_3296 aconitate hydratase 1
Query= curated2:B4UAN1 (191 letters) >FitnessBrowser__Korea:Ga0059261_3296 Length = 890 Score = 50.1 bits (118), Expect = 1e-10 Identities = 45/142 (31%), Positives = 67/142 (47%), Gaps = 19/142 (13%) Query: 48 YAADGAPRPDFVMNRPEAQGCS-ILVAGDNFGCGSSREHAPWALVDAGVRAVISTRIADI 106 YA + P D M R +A G ++VAG +G GSSR+ A GVRAVI+ I Sbjct: 742 YAGETMPIYDAAM-RHKADGTPLVIVAGKEYGTGSSRDWAAKGTNLLGVRAVITESFERI 800 Query: 107 FRNNALKNGLVP-----------VVLDAASHAKLLAAPGASVRVDVEAQTVTLPDGSTAR 155 R+N + G++P + LD + + G R DVE + +T DGS+ Sbjct: 801 HRSNLVGMGVLPLQFAEGVTRQTLKLDGSETFTITGVAGLRPRQDVEVK-LTRADGSS-- 857 Query: 156 FPLDGFARYCLLNGVDELGFLL 177 + F C ++ V+EL + L Sbjct: 858 ---ETFLTRCRIDTVNELEYFL 876 Lambda K H 0.321 0.138 0.411 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: 383 Number of extensions: 15 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: 191 Length of database: 890 Length adjustment: 31 Effective length of query: 160 Effective length of database: 859 Effective search space: 137440 Effective search space used: 137440 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 (21.9 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