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_089322123.1 CHB58_RS00430 aconitate hydratase
Query= curated2:Q9WYC8 (166 letters) >NCBI__GCF_900188395.1:WP_089322123.1 Length = 650 Score = 99.0 bits (245), Expect = 1e-25 Identities = 66/167 (39%), Positives = 99/167 (59%), Gaps = 16/167 (9%) Query: 8 KFGDNISTDHIAPG--RYFHLRNNLEELAKHVLEDAMEDFAKKVQK--GDIIVAGKNFGL 63 K GDNI+TDHI PG + LR+N+ ++++V E+FAK+ ++ G IV G+N+G Sbjct: 476 KVGDNITTDHIIPGGAKILPLRSNIPAISEYVYSVVDENFAKRAKEKGGGFIVGGENYGQ 535 Query: 64 GSSREHAARIIKIAGVSCIVAKSFARIFYRNAINVG-LPVIEL--KEVDEINQGDELEID 120 GSSREHAA G+ ++AKS+ARI N IN G LP+I + ++ D+I+QGD LEID Sbjct: 536 GSSREHAAIGPMYLGIKAVIAKSYARIHRANLINFGILPLIFVNPEDYDKIDQGDILEID 595 Query: 121 LEN---GVLKNLTTGKEYRFTPIP------KFLLEILKEDGIVNYLK 158 N G +T + IP + ++I+K G++ Y+K Sbjct: 596 TSNFAPGEDNIITVINRTKGISIPTKHGLNERQVKIIKAGGVLKYVK 642 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: 288 Number of extensions: 20 Number of successful extensions: 4 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: 650 Length adjustment: 28 Effective length of query: 138 Effective length of database: 622 Effective search space: 85836 Effective search space used: 85836 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