Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate 8502313 DvMF_3021 aconitate hydratase (RefSeq)
Query= curated2:O28084 (416 letters) >FitnessBrowser__Miya:8502313 Length = 641 Score = 298 bits (764), Expect = 2e-85 Identities = 166/413 (40%), Positives = 235/413 (56%), Gaps = 2/413 (0%) Query: 1 MGKTIAEKILSEKSKSDAYA-GDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTH 59 M + +KI++ S A G + IDQ QD T +A Q +G + D + Sbjct: 1 MSMNLTQKIIAAHLVSGEMAPGAEIGLRIDQTLTQDATGTMAYLQFEAMGVDRVRTDLSV 60 Query: 60 FFVDHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADS 119 +VDH +D +F+ A K G F+PPG GI HQ+ +E + PG VG+DS Sbjct: 61 SYVDHNTLQMGFRNPDDHRFLRTVAAKHGVIFSPPGTGICHQLHLENFALPGATLVGSDS 120 Query: 120 HTCTYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIG 179 HT T GGIG+ + G G VA+A+A + +P RV+L+G L AKDVIL L+G Sbjct: 121 HTPTAGGIGSLAMGAGGLSVALAMAGEPYFISMPRVVRVRLEGRLTGWASAKDVILHLLG 180 Query: 180 DLGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGRE 239 L V G K EF G ++V ER I NM E GA A +F SDE TR FLA + RE Sbjct: 181 LLTVKGGVGKVFEFAGPGVATLSVPERAVITNMGAELGATASLFPSDERTRAFLASMDRE 240 Query: 240 GDFREVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNG 299 GD++ + AD DA Y+ EI +D+S+LVP+V++PH D V ++E+ G V+QV IG+CTN Sbjct: 241 GDWKPLAADADATYDDEIVIDLSALVPLVAQPHMPDRVVPVAELAGLSVDQVAIGSCTNS 300 Query: 300 RLSDLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPC 359 +D+ + A +L+GR V G +V P S++V +GL+ ++AG +L CGPC Sbjct: 301 SYADMRMVAEVLRGRMVHVGTDTMVSPGSKQVLKMLAAEGLVEPLLDAGVRILECSCGPC 360 Query: 360 VGIHQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADP 412 +G+ G G V + T NRNF+GR G +A+++L SP TAA +A+ G DP Sbjct: 361 IGM-GGSPVSGGVSVRTFNRNFEGRSGTKDAKVYLVSPLTAAMAALHGQFTDP 412 Lambda K H 0.318 0.136 0.391 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: 658 Number of extensions: 29 Number of successful extensions: 3 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: 416 Length of database: 641 Length adjustment: 35 Effective length of query: 381 Effective length of database: 606 Effective search space: 230886 Effective search space used: 230886 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 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