Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA
Query= curated2:Q5JFV7 (163 letters) >NCBI__GCF_000009985.1:WP_011386009.1 Length = 903 Score = 45.4 bits (106), Expect = 2e-09 Identities = 44/134 (32%), Positives = 61/134 (45%), Gaps = 15/134 (11%) Query: 26 LTKDPEELARIAFIEARPEFSREVKPGDVVVGGRNFGIGSSRESAALSLKAAGVAGVIAE 85 LT E + + +A + P +V G +G GSSR+ AA K GV V+A+ Sbjct: 747 LTLHQPEGSEMPIFDAASRYQEAGIPS-IVFAGTEYGTGSSRDWAAKGPKLLGVRAVVAQ 805 Query: 86 SFGRIFYRNAVNLG-LPLLVGDTSGLRDGEVVEVNWRTGEVRTENGVFHFKPLDGFLLRI 144 SF RI N V +G LPL RDGE G+ FH + L G +LR Sbjct: 806 SFERIHRSNLVGMGVLPL------QFRDGESAASLGIAGDEE-----FHVRGLSG-VLRP 853 Query: 145 VEEGGILSFIARRG 158 +E +L + R+G Sbjct: 854 RQE-VVLEIVNRQG 866 Lambda K H 0.321 0.142 0.421 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: 393 Number of extensions: 20 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 163 Length of database: 903 Length adjustment: 30 Effective length of query: 133 Effective length of database: 873 Effective search space: 116109 Effective search space used: 116109 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: 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