Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate Pf1N1B4_3888 Aconitate hydratase (EC 4.2.1.3)
Query= curated2:Q9WYC7 (418 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 Length = 913 Score = 96.3 bits (238), Expect = 3e-24 Identities = 119/493 (24%), Positives = 198/493 (40%), Gaps = 115/493 (23%) Query: 25 LARVDIAMAQDGTGPLMINEFRELGFKEVKVPKAFLFIDHASPSP-------RKELSNSQ 77 LA + AMA+ G P IN + ++ + + + +AS S + ++ + Sbjct: 100 LAAMRAAMAKAGGDPQRINPLSPV---DLVIDHSVMVDKYASASAFGQNVDIEMQRNHER 156 Query: 78 KMMREFGKEM--GVKVFDAGDGISHQILAE--------------KYVKPGDLVAGADSHT 121 +G+ V G GI HQ+ E Y P LV G DSHT Sbjct: 157 YAFLRWGQSAFNNFSVVPPGTGICHQVNLEYLGRTVWTKDEDGRTYAFPDTLV-GTDSHT 215 Query: 122 CTAGGLGAFGTGMGSTDVAIIFGLGQNW-FKVPETIKVVVNGKLQDGVYAKDIILEIARI 180 GLG G G+G + LGQ +PE I + GKL++G+ A D++L + ++ Sbjct: 216 TMINGLGVLGWGVGGIEAEAAM-LGQPVSMLIPEVIGFKLTGKLKEGITATDLVLTVTQM 274 Query: 181 LGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFLKKMGREE 240 L G K +EF+G + ++ + DR TI+NMA E GA G P DE T E+L+ GR Sbjct: 275 LRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYGATCGFFPVDEVTLEYLRLSGRTP 334 Query: 241 DFREL------------KADPDAVYETEIEIDATTLE----------PLVSLPH------ 272 +L + V+ + +D ++E VSLP+ Sbjct: 335 QTVKLVEAYSKTQGLWRLPGKEPVFTDSLALDMGSVEASLAGPKRPQDRVSLPNVAQAFT 394 Query: 273 -YVDNVRKVSEVEKEKIKID---QVFIGTC------------TNGRLQDLEIALKILEK- 315 ++ K S E+ +++ + V +G + RL++ + + + Sbjct: 395 DFLGLQFKPSSKEEGRLESEGGGGVAVGNADLIGEADYHHEGSTYRLKNGAVVIAAITSC 454 Query: 316 -HGKHPDVRLIVGPASRKVYMDALEKGIIKK--------------------------FVE 348 + +P V + G ++K A+EKG+ +K E Sbjct: 455 TNTSNPSVMMAAGLVAKK----AVEKGLKRKPWVKSSLAPGSKVVTDYYKAAGLTQYLDE 510 Query: 349 LGAAVIPPGCGPCVGIHMGVLGDGERVLS----------TQNRNFKGRMGNPNAEIYLAS 398 LG A++ GC C+G + E+ + + NRNF+GR+ +LAS Sbjct: 511 LGFALVGYGCTTCIGNSGPLPEPIEKAIQKADLTVASVLSGNRNFEGRVHPLVKTNWLAS 570 Query: 399 PATAAATAVTGYI 411 P A A+ G + Sbjct: 571 PPLVVAYALAGTV 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: 790 Number of extensions: 42 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