Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; EC 1.1.1.85; Beta-IPM dehydrogenase (uncharacterized)
to candidate WP_038210839.1 Q392_RS18435 isocitrate dehydrogenase
Query= curated2:O29627 (326 letters) >NCBI__GCF_000745855.1:WP_038210839.1 Length = 345 Score = 241 bits (616), Expect = 1e-68 Identities = 143/331 (43%), Positives = 200/331 (60%), Gaps = 14/331 (4%) Query: 6 VIPGDGIGKEVMEAAMLILEKLDLPFEYSYYDAGDEALEKYGKALPDETLEACRKSDAVL 65 +I GDGIG E+MEA + L+ L PFE+ AG ++ G LP TL++ RK+ L Sbjct: 10 LISGDGIGPEIMEATLAALDALGSPFEWDAQIAGLGGVKAAGDPLPQATLDSIRKTRLAL 69 Query: 66 FGA----AGETAADVIVRLRRELGTFANVRPAKAIEGIECLYPGLDIVVVRENTECLYMG 121 G +G VRLR E FANVRPA+ I + +D++VVREN E LY+G Sbjct: 70 KGPLETPSGGGYRSSNVRLREEFQLFANVRPARTIVP-GGRFDNIDLLVVRENLEGLYIG 128 Query: 122 FEFGFG------DVTEAIRVITREASERIARYAFELAKREGRKKVTALHKANVMKKTCGL 175 E V A + TR+ I RYAF+ A +GR+KVT +HKAN+MK G+ Sbjct: 129 HEHYIRIDDDPHAVAMATGINTRQGCLHILRYAFDTAIAQGRRKVTVVHKANIMKALTGI 188 Query: 176 FRDVCREV-AKDYP-EIQYNDYYIDAACMYLVMDPFRFDVIVTTNMFGDIVSDLAAGLVG 233 F + + A +Y + ++ +DA M LV+DP++FD++VTTN+FGDI+SDL AGLVG Sbjct: 189 FLETAERLYAAEYQGKFEFQTMIVDACAMKLVLDPWQFDMLVTTNLFGDILSDLVAGLVG 248 Query: 234 GLGLAPSANVGERTAIFEPVHGAAFDIAGKGIANPTAMILTACMMLRHFGYVEEAKKVEE 293 GLG+AP AN+G AIFE VHG+A DIAGKGIANP A++L A ML H + A ++ Sbjct: 249 GLGMAPGANIGNDAAIFEAVHGSAPDIAGKGIANPIALMLAAAQMLDHVKRADLAGRLRT 308 Query: 294 AVEKTIK-EGKKTPDLGGNLKTMEFANEVAS 323 A+++T+ + +T DLGG+ T+ F + + Sbjct: 309 AIDETLNVDQVRTGDLGGSAGTLAFTKALVA 339 Lambda K H 0.321 0.139 0.399 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: 272 Number of extensions: 11 Number of successful extensions: 5 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: 326 Length of database: 345 Length adjustment: 28 Effective length of query: 298 Effective length of database: 317 Effective search space: 94466 Effective search space used: 94466 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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