Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate PP_2112 PP_2112 aconitate hydratase 1
Query= curated2:Q9WYC7 (418 letters) >FitnessBrowser__Putida:PP_2112 Length = 913 Score = 94.4 bits (233), Expect = 1e-23 Identities = 78/247 (31%), Positives = 109/247 (44%), Gaps = 43/247 (17%) Query: 25 LARVDIAMAQDGTGPLMINEFRELGFKEVKVPKAFLFIDHASP-----SPRKELSNSQKM 79 LA + AMA+ G P IN + L IDH+ +P+ N Sbjct: 100 LAAMRAAMAKAGGDPQRINPLSPVD----------LVIDHSVMVDRYGTPQAFAENVDIE 149 Query: 80 MREFGKEM-----GVKVFD------AGDGISHQILAE--------------KYVKPGDLV 114 M+ G+ G FD G GI HQ+ E Y P LV Sbjct: 150 MQRNGERYAFLRWGQSAFDNFRVVPPGTGICHQVNLEYLGRTVWTREADGRTYAFPDTLV 209 Query: 115 AGADSHTCTAGGLGAFGTGMGSTDVAIIFGLGQNW-FKVPETIKVVVNGKLQDGVYAKDI 173 G DSHT GLG G G+G + LGQ +PE I + GKL++G+ A D+ Sbjct: 210 -GTDSHTTMINGLGVLGWGVGGIEAEAAM-LGQPVSMLIPEVIGFKLTGKLREGITATDL 267 Query: 174 ILEIARILGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFL 233 +L + ++L G K +EF+G + + + DR TI+NMA E GA G P D+ T ++L Sbjct: 268 VLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRATIANMAPEYGATCGFFPVDQVTLDYL 327 Query: 234 KKMGREE 240 + GR E Sbjct: 328 RLSGRPE 334 Score = 35.4 bits (80), Expect = 7e-06 Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 13/116 (11%) Query: 308 IALKILEKH-GKHPDVRLIVGPASRKVYMDALEKGIIKKFVELGAAVIPPGCGPCVGIHM 366 +A K LEK + P V+ + P S+ V G+ +LG ++ GC C+G + Sbjct: 469 VAKKALEKGLQRKPWVKSSLAPGSKVVTDYFKAAGLTPYLDQLGFDLVGYGCTTCIG-NS 527 Query: 367 GVLGDG-ERVLSTQ----------NRNFKGRMGNPNAEIYLASPATAAATAVTGYI 411 G L + E+ + + NRNF+GR+ +LASP A A+ G + Sbjct: 528 GPLDEAIEKAIGSADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSV 583 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: 820 Number of extensions: 44 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 418 Length of database: 913 Length adjustment: 37 Effective length of query: 381 Effective length of database: 876 Effective search space: 333756 Effective search space used: 333756 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: 53 (25.0 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