Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_027178549.1 G496_RS0106385 aconitate hydratase
Query= BRENDA::Q58673 (168 letters) >NCBI__GCF_000429985.1:WP_027178549.1 Length = 637 Score = 84.3 bits (207), Expect = 3e-21 Identities = 61/166 (36%), Positives = 92/166 (55%), Gaps = 15/166 (9%) Query: 11 KFGNNVDTDAILPARYLVYTKPEEL---AQFVMTGADPDFPKKVKPGD--IIVGGKNFGC 65 K G+N+ TD ILPA + + ++++ + D +F ++K + II+GG+N+G Sbjct: 473 KVGDNITTDHILPAGPQITALRSNIPAISEYIFSRVDENFVSRMKAAESGIILGGENYGQ 532 Query: 66 GSSREHAPLGLKGAGISCVIAESFARIFYRNAINVG-LPLIEC-KGISEKVNEGDELEVN 123 GSSREHA LG + G+ VI +S ARI N +N G LPL+ K E++ EG EL ++ Sbjct: 533 GSSREHAALGPRHLGVVAVITKSLARIHRANLVNFGILPLVLVDKSDYERLAEGSELTID 592 Query: 124 LE------TGEIKNLTTGEVLK-GQKLPEFMMEILEAGGLMPYLKK 162 T EI ++ GE K L + +EI+ AGGL+ Y K Sbjct: 593 TSTITPGGTSEI-SVAGGESFKVSNDLSKNELEIIRAGGLLNYAGK 637 Lambda K H 0.317 0.139 0.405 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: 279 Number of extensions: 17 Number of successful extensions: 3 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: 168 Length of database: 637 Length adjustment: 28 Effective length of query: 140 Effective length of database: 609 Effective search space: 85260 Effective search space used: 85260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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