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_101443452.1 BD749_RS06200 aconitate hydratase
Query= curated2:Q9WYC8 (166 letters) >NCBI__GCF_002846395.1:WP_101443452.1 Length = 759 Score = 52.4 bits (124), Expect = 2e-11 Identities = 41/139 (29%), Positives = 64/139 (46%), Gaps = 29/139 (20%) Query: 14 STDHIA-PGRYFHLRNNLEELAKHVLEDAMEDFAKKVQK--------------------- 51 +TDHI+ G + R +L+ ++ ++L A+ F + K Sbjct: 567 TTDHISMAGPWLKYRGHLDNISNNMLIGAINAFNGEANKVYNDMTRGYDTVPATARTYKA 626 Query: 52 ---GDIIVAGKNFGLGSSREHAARIIKIAGVSCIVAKSFARIFYRNAIN---VGLPVIEL 105 G ++V +N+G GSSREHAA + GV ++ KSFARI N +GL Sbjct: 627 AGIGTVVVGDENYGEGSSREHAAMEPRHLGVRAVIVKSFARIHETNLKKQGMLGLTFANK 686 Query: 106 KEVDEINQGDELEI-DLEN 123 + D I + D ++I LEN Sbjct: 687 ADYDLIEENDTIDILGLEN 705 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: 306 Number of extensions: 17 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: 166 Length of database: 759 Length adjustment: 29 Effective length of query: 137 Effective length of database: 730 Effective search space: 100010 Effective search space used: 100010 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 Jul 26 2024. The underlying query database was built on Jul 25 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