Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_011779960.1 MVAN_RS13785 aconitate hydratase
Query= curated2:C3N1A2 (165 letters) >NCBI__GCF_000015305.1:WP_011779960.1 Length = 954 Score = 47.8 bits (112), Expect = 5e-10 Identities = 32/97 (32%), Positives = 45/97 (46%), Gaps = 2/97 (2%) Query: 46 YKKASKGVIIVAGKVFGMGSSREQAAIALKAAGVKAVVAESFARIFYRNAINNGLPVITL 105 Y K ++++ GK +G GSSR+ AA GV+AV+ ESF RI N I G+ + Sbjct: 811 YAKEGIPLVVLGGKEYGSGSSRDWAAKGTTLLGVRAVITESFERIHRSNLIGMGVIPLQF 870 Query: 106 P--NSTKEIDESSYVKIDVETGEILVGNKVLKGKGIT 140 P S + D+E E L K K +T Sbjct: 871 PKGESAASLKLDGTETFDIEGIEALNEGKTPKTVKVT 907 Score = 31.2 bits (69), Expect = 5e-05 Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 2/34 (5%) Query: 11 GDKIDTDIIIPARYLKYTDP--QYLAQHAMEPLD 42 GD + TD I PA +K P QYL +H +EP D Sbjct: 721 GDSVTTDHISPAGSIKKGTPAAQYLEEHGVEPKD 754 Lambda K H 0.318 0.137 0.376 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: 367 Number of extensions: 18 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: 2 Length of query: 165 Length of database: 954 Length adjustment: 30 Effective length of query: 135 Effective length of database: 924 Effective search space: 124740 Effective search space used: 124740 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 (21.7 bits) S2: 50 (23.9 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