Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; EC 1.1.1.85; Beta-IPM dehydrogenase (uncharacterized)
to candidate RR42_RS22955 RR42_RS22955 isocitrate dehydrogenase
Query= curated2:O29627 (326 letters) >FitnessBrowser__Cup4G11:RR42_RS22955 Length = 343 Score = 262 bits (669), Expect = 1e-74 Identities = 145/332 (43%), Positives = 211/332 (63%), Gaps = 14/332 (4%) Query: 6 VIPGDGIGKEVMEAAMLILEKLDLPFEYSYYDAGDEALEKYGKALPDETLEACRKSDAVL 65 +IPGDGIG EV++A + +L+ L PF + AG +E+ G LP TL++ R++ L Sbjct: 13 LIPGDGIGPEVVQATVKVLDALGAPFSWDVQQAGMAGIEQGGDPLPQATLDSIRRTGLAL 72 Query: 66 FGA----AGETAADVIVRLRRELGTFANVRPAKAIEGIECLYPGLDIVVVRENTECLYMG 121 G G V VRLR FANVRPA+ + + + +D+V+VREN Y+ Sbjct: 73 KGPLTTPVGGGFRSVNVRLREAFNLFANVRPARTL--VPGRFEDIDLVLVRENVGGFYVA 130 Query: 122 FEF--GFGDVTEAIRVIT----REASERIARYAFELAKREGRKKVTALHKANVMKKTCGL 175 ++ GD A+ V T R+A RIAR+AFE A + RKK+T +HKAN++K G+ Sbjct: 131 HDYYIAVGDDPHAVAVSTGTNTRDACRRIARFAFEYAVKNQRKKITVVHKANILKALTGI 190 Query: 176 FRDVCREVAKDYP-EIQYNDYYIDAACMYLVMDPFRFDVIVTTNMFGDIVSDLAAGLVGG 234 F + REVA+DY ++ +D +DA M LV++P++FD+++ TN+FGDI+SD AGLVGG Sbjct: 191 FLEAAREVAQDYVGRVEMDDRIVDACAMQLVLNPWQFDMLLCTNLFGDILSDQIAGLVGG 250 Query: 235 LGLAPSANVGERTAIFEPVHGAAFDIAGKGIANPTAMILTACMMLRHFGYVEEAKKVEEA 294 LG+AP AN+GE AIFE VHG+A DIAGKGIANP +++L A +ML H G + A ++ +A Sbjct: 251 LGMAPGANIGETAAIFEAVHGSAPDIAGKGIANPISLMLAAGLMLEHVGRQDLAVRLRQA 310 Query: 295 VEKTIKEGK-KTPDLGGNLKTMEFANEVASLL 325 ++ T+ + + KT DL G+ T++FA V L Sbjct: 311 IDLTLNQDQVKTGDLKGSASTLQFAEAVIKRL 342 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: 265 Number of extensions: 15 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: 343 Length adjustment: 28 Effective length of query: 298 Effective length of database: 315 Effective search space: 93870 Effective search space used: 93870 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 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