Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; EC 1.1.1.85; Beta-IPM dehydrogenase (uncharacterized)
to candidate WP_015739105.1 ADEG_RS05580 isocitrate/isopropylmalate dehydrogenase family protein
Query= curated2:O29627 (326 letters) >NCBI__GCF_000024605.1:WP_015739105.1 Length = 334 Score = 303 bits (775), Expect = 5e-87 Identities = 157/327 (48%), Positives = 220/327 (67%), Gaps = 6/327 (1%) Query: 3 KIVVIPGDGIGKEVMEAAMLILEKLDLPFEYSYYDAGDEALEKYGKALPDETLEACRKSD 62 ++ +IPGDGIG E+ AA +L+ E+ +AG++ + +YG LP+ L++ R++ Sbjct: 4 RVTLIPGDGIGPEITAAARQVLDASGAEIEWEVVEAGEKVIPEYGTPLPEHVLDSIRRNR 63 Query: 63 AVLFGAA----GETAADVIVRLRRELGTFANVRPAKAIEGIECLYPGLDIVVVRENTECL 118 L G G V V LR+EL +A VRPAK + GI+ + +D++VVRENTE L Sbjct: 64 VALKGPLTTPIGHGFRSVNVTLRQELDLYACVRPAKTLPGIKTRFDHVDLIVVRENTEDL 123 Query: 119 YMGFEFGFG-DVTEAIRVITREASERIARYAFELAKREGRKKVTALHKANVMKKTCGLFR 177 Y G E G + E+I+++TREAS RI R+AFELA+REGR+KVTA+HKAN+MK T GLF Sbjct: 124 YAGIEHRVGKNAAESIKIVTREASTRIVRFAFELARREGRRKVTAVHKANIMKLTDGLFL 183 Query: 178 DVCREVAKDYPEIQYNDYYIDAACMYLVMDPFRFDVIVTTNMFGDIVSDLAAGLVGGLGL 237 + REVA +YP+I + + +DA CM LV P +DVIVT N++GDI+SDLAAGLVGGLG+ Sbjct: 184 ECAREVAAEYPDIAFEEMIVDAMCMKLVQSPENYDVIVTLNLYGDIISDLAAGLVGGLGV 243 Query: 238 APSANVGERTAIFEPVHGAAFDIAGKGIANPTAMILTACMMLRHFGYVEEAKKVEEAVEK 297 AP AN+G+ A+FEPVHG+A AG+ NP A IL+ MML+H G +E A++V + Sbjct: 244 APGANIGDEAAVFEPVHGSAPKHAGQDKVNPLATILSGVMMLKHLGEMEAAERVMRGIIG 303 Query: 298 TIKEGKK-TPDLGGNLKTMEFANEVAS 323 ++EGK T DLGG+ +T E A + + Sbjct: 304 VLQEGKALTYDLGGSARTSEMAAAIVA 330 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: 299 Number of extensions: 9 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: 334 Length adjustment: 28 Effective length of query: 298 Effective length of database: 306 Effective search space: 91188 Effective search space used: 91188 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