Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate 206498 DVU1064 aconitate hydratase, putative
Query= curated2:O28084 (416 letters) >MicrobesOnline__882:206498 Length = 642 Score = 276 bits (706), Expect = 1e-78 Identities = 153/396 (38%), Positives = 224/396 (56%), Gaps = 1/396 (0%) Query: 17 DAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTHFFVDHAAPSPRRELSND 76 D G + IDQ QD T +A Q +G + D + +VDH ++D Sbjct: 18 DMAPGAPIALRIDQTLTQDATGTMAYLQFEAMGVDRVRTDLSVSYVDHNTLQMGFRNADD 77 Query: 77 QKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADSHTCTYGGIGAFSTGMGS 136 +F+ A + G F+ PG GI HQ+ +E + +PG VG+DSHT T GGIGA + G G Sbjct: 78 HRFLRTVAARHGIVFSAPGNGICHQLHLENFGRPGATLVGSDSHTPTAGGIGALAMGAGG 137 Query: 137 TDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIGDLGVDGATYKALEFHGE 196 VA+++A +P+ V+L+G L AKDVIL L+G L V G + E+ G Sbjct: 138 LSVALSMAGEPYTITMPKVVNVRLEGRLTGWAAAKDVILHLLGLLTVKGGVGRVFEYTGP 197 Query: 197 CAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGREGDFREVKADEDAEYEKE 256 ++V ER TI NM E GA IF SDE+TR FLA +GRE D++ + AD A Y++E Sbjct: 198 GVATLSVPERATITNMGAELGATTSIFPSDESTRAFLAAMGREADWQPLAADAGAVYDEE 257 Query: 257 IYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNGRLSDLEVAARILKGRKV 316 + +D+S L P+V+ PH D V ++ + G +V+QV IG+CTN +DL+ A+++ GR+V Sbjct: 258 VVIDLSQLEPLVATPHMPDRVVTVASLAGLKVDQVAIGSCTNSSYADLKSVAQVVAGRRV 317 Query: 317 KEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPCVGIHQGILADGEVCIST 376 ++ P S++V +GL+ ++AG +L CGPC+G+ G G V + T Sbjct: 318 DSTTDCMISPGSKQVLRMLATEGLLEPLLDAGIRMLECTCGPCIGM-GGSPVSGGVSVRT 376 Query: 377 QNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADP 412 NRNF+GR G +A ++LASP TAA A+ G DP Sbjct: 377 FNRNFEGRSGTKDAGVYLASPLTAAMVALHGGFTDP 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: 652 Number of extensions: 34 Number of successful extensions: 2 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: 642 Length adjustment: 35 Effective length of query: 381 Effective length of database: 607 Effective search space: 231267 Effective search space used: 231267 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