Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate Ac3H11_1140 Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
Query= curated2:Q9WYC7 (418 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1140 Length = 980 Score = 89.4 bits (220), Expect = 5e-22 Identities = 65/202 (32%), Positives = 94/202 (46%), Gaps = 26/202 (12%) Query: 60 LFIDHASPSPRKELSNSQKMMR-----EFGKEMGVKVFDA------GDGISHQILAEKYV 108 + IDH +L+ + R EF K G++ FD G GI HQ+ E Y+ Sbjct: 142 IMIDHYGKKNSLDLNMKLEFQRNRERYEFMK-WGMQAFDTFGVVPPGFGIVHQVNLE-YL 199 Query: 109 KPG-----------DLVAGADSHTCTAGGLGAFGTGMGSTDVAIIFGLGQN-WFKVPETI 156 G D + G DSHT G+G G G+G + LGQ +F P+ + Sbjct: 200 ARGVHKRKDGVFYPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAAM-LGQPVYFLTPDVV 258 Query: 157 KVVVNGKLQDGVYAKDIILEIARILGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEV 216 + G+L++GV A D++L + +L K +EF G + + DR TI NMA E Sbjct: 259 GFEMTGRLREGVTATDLVLTVTELLRKHKVVGKFVEFFGEGTRTLALPDRATIGNMAPEY 318 Query: 217 GAKAGLMPSDEKTREFLKKMGR 238 GA G P DEKT ++ + GR Sbjct: 319 GATMGFFPVDEKTIDYFQGTGR 340 Score = 40.8 bits (94), Expect = 2e-07 Identities = 38/135 (28%), Positives = 59/135 (43%), Gaps = 20/135 (14%) Query: 295 IGTCTNGRLQDLEIALKILEKHGKH------PDVRLIVGPASRKVYMDALEKGIIKKFVE 348 I +CTN + +A +L K P ++ + P SR V E G++ + Sbjct: 494 ITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPHIKTSLAPGSRIVTEYLSETGLLPYLEK 553 Query: 349 LGAAVIPPGCGPCVGIHMGVLGDGERVLSTQ-----------NRNFKGRMGNPNAEI-YL 396 LG ++ GC C+G + G L TQ NRNF+ R+ +PN + +L Sbjct: 554 LGFSIAGYGCTTCIG-NAGDLTPELNEAITQNDLVCAAVLSGNRNFEARI-HPNLKANFL 611 Query: 397 ASPATAAATAVTGYI 411 ASP A A+ G + Sbjct: 612 ASPPLVVAYAIAGTV 626 Lambda K H 0.318 0.137 0.395 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: 845 Number of extensions: 36 Number of successful extensions: 3 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: 418 Length of database: 980 Length adjustment: 38 Effective length of query: 380 Effective length of database: 942 Effective search space: 357960 Effective search space used: 357960 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: 54 (25.4 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