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_086508286.1 BZY95_RS01750 aconitate hydratase
Query= curated2:Q9WYC8 (166 letters) >NCBI__GCF_002151265.1:WP_086508286.1 Length = 656 Score = 72.8 bits (177), Expect = 1e-17 Identities = 55/171 (32%), Positives = 86/171 (50%), Gaps = 24/171 (14%) Query: 10 GDNISTDHIAPG--RYFHLRNNLEELAKHVLEDAMEDFAKKVQK-----GDIIVAGKNFG 62 GDN+STD I P R +++ A E D+A++ + G IV G N+G Sbjct: 477 GDNVSTDDIMPAGQRVMPYWSSVYASAPFTFEAVDADYARRAENTRTLGGHAIVGGHNYG 536 Query: 63 LGSSREHAARIIKIAGVSCIVAKSFARIFYRNAINVG---LPVIELKEVDEINQGDELEI 119 GSSRE+AA + + G+ ++AKSFARI ++N I G L I+ ++ D + QGD L I Sbjct: 537 QGSSRENAALVPRYLGLQAVLAKSFARIHWQNLICFGALPLSFIDAQDYDRLEQGDSLVI 596 Query: 120 DLENGVLKNLTTGKEYRFTPIPK--FLL---------EILKEDGIVNYLKK 159 + + L G E + K F L E+L G++N++++ Sbjct: 597 ---HDLHAQLAAGAELTAEVVGKGAFRLHHGLTPRQRELLACGGVINHIRR 644 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: 270 Number of extensions: 13 Number of successful extensions: 2 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: 656 Length adjustment: 28 Effective length of query: 138 Effective length of database: 628 Effective search space: 86664 Effective search space used: 86664 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 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