Align 3-isopropylmalate dehydratase small subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate PfGW456L13_4116 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)
Query= curated2:Q8TW31 (168 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 Length = 864 Score = 41.2 bits (95), Expect = 5e-08 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 7/71 (9%) Query: 54 VIVAGKNFGCGSSREQAVMALQQAGVACVVARSFARIFYRNAINRGLPTVEAEEDPTEVV 113 +I+AG ++G GSSR+ A ++ AGV + A F RI N + G+ P E Sbjct: 734 IIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLVGMGVL-------PLEFK 786 Query: 114 EDGNRVTVDLD 124 NR T+ +D Sbjct: 787 PGTNRHTLAID 797 Lambda K H 0.318 0.138 0.419 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: 339 Number of extensions: 15 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: 168 Length of database: 864 Length adjustment: 30 Effective length of query: 138 Effective length of database: 834 Effective search space: 115092 Effective search space used: 115092 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: 49 (23.5 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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