Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; EC 1.1.1.85; Beta-IPM dehydrogenase (uncharacterized)
to candidate WP_019868382.1 METMI_RS0121605 isocitrate/isopropylmalate dehydrogenase family protein
Query= curated2:O29627 (326 letters) >NCBI__GCF_000384075.1:WP_019868382.1 Length = 336 Score = 298 bits (762), Expect = 2e-85 Identities = 162/336 (48%), Positives = 219/336 (65%), Gaps = 10/336 (2%) Query: 1 MKKIVVIPGDGIGKEVMEAAMLILEKLDLPFEYSYYDAGDEALEKYGKALPDETLEACRK 60 M I +I GDGIG +M+ A+ +++ + + AG A EK+G LPDET+ + K Sbjct: 1 MHTITLIKGDGIGPSIMDEAVKVIDATGVKITWEETYAGMSAFEKFGTPLPDETMASFDK 60 Query: 61 SDAVLFG----AAGETAADVIVRLRRELGTFANVRPAKAIEGIECLYPGLDIVVVRENTE 116 + G G + V LR++ +ANVRPAK+ GI+ + +DIV+VRENTE Sbjct: 61 TRVAFKGPLTTVVGTGFRSINVALRQKYDLYANVRPAKSWAGIKTRFEDVDIVIVRENTE 120 Query: 117 CLYMGFEFGFG---DVTEAIRVITREASERIARYAFELAKREGRKKVTALHKANVMKKTC 173 LY G E D+ E++ V+TR ASERI YAF+ A+ R+KVT HKAN++K T Sbjct: 121 GLYAGLEHYLTPKKDIAESLAVVTRAASERIIDYAFQYARDNHRQKVTVCHKANILKYTQ 180 Query: 174 GLFRDVCREVAKDYPEIQYNDYYIDAACMYLVMDPFRFDVIVTTNMFGDIVSDLAAGLVG 233 GLF DV RE+A YP+IQ+++ IDAACM++VM+P +FDV+VTTNMFGDI+SDL AGLVG Sbjct: 181 GLFLDVAREIAPRYPDIQFDEKIIDAACMHMVMNPKQFDVVVTTNMFGDILSDLTAGLVG 240 Query: 234 GLGLAPSANVGERTAIFEPVHGAAFDIAGKGIANPTAMILTACMMLRHFGYVEEAKKVEE 293 GLGL P AN+G A+FE VHG+A DIAGK +ANP A+I+ MML H G VE A++V + Sbjct: 241 GLGLIPGANIGSDAALFEAVHGSAPDIAGKNLANPIAVIMAGAMMLSHIGEVEAAERVVK 300 Query: 294 AVEKTIKEG-KKTPDLGGNLK--TMEFANEVASLLD 326 AVEK + EG TPDL N K T E + + + ++ Sbjct: 301 AVEKVVNEGVYVTPDLNPNSKVGTTEMGSAIVAAME 336 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: 307 Number of extensions: 10 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: 326 Length of database: 336 Length adjustment: 28 Effective length of query: 298 Effective length of database: 308 Effective search space: 91784 Effective search space used: 91784 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