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_020174411.1 A3OQ_RS0105720 aconitate hydratase AcnA
Query= curated2:Q9RTY5 (177 letters) >NCBI__GCF_000385335.1:WP_020174411.1 Length = 910 Score = 48.1 bits (113), Expect = 4e-10 Identities = 36/124 (29%), Positives = 54/124 (43%), Gaps = 19/124 (15%) Query: 52 VLIGGRNWGLGSSREYAPQALKKLHIGGIVAPSFARIHYRNLLNLGIPAFEYDL----TE 107 V+ G +G GSSR++A + K L + ++A SF RIH NL+ +G+ ++ Sbjct: 782 VIFAGAEYGNGSSRDWAAKGTKLLGVRAVIAESFERIHRSNLVGMGVLPLTFEAGTTWAS 841 Query: 108 LLEDGDEVTL-----------DAQTGLLTYADGTVQLPPPPEFLREALKEGSILEFFKKH 156 L GDE+ + YADG V+ P L + LE+FK Sbjct: 842 LGLKGDEIVTIHGLGEGLKPRQMMEAEIKYADGGVKTVP----LLCRIATEDELEYFKNG 897 Query: 157 GRFP 160 G P Sbjct: 898 GILP 901 Lambda K H 0.318 0.139 0.423 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: 394 Number of extensions: 24 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: 177 Length of database: 910 Length adjustment: 30 Effective length of query: 147 Effective length of database: 880 Effective search space: 129360 Effective search space used: 129360 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 (21.7 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