Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate 5211055 Shew_3471 3-isopropylmalate dehydrogenase (RefSeq)
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__PV4:5211055 Length = 364 Score = 183 bits (465), Expect = 5e-51 Identities = 131/339 (38%), Positives = 187/339 (55%), Gaps = 27/339 (7%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETV 56 M+Y++ ++ GDGIG EV+ AR+VL+A L +E+ E + G + G +PE T+ Sbjct: 1 MSYQVAVLAGDGIGPEVMAEARKVLKAVEERFSLDIEYSEYDVGGAAIDHHGCPLPESTL 60 Query: 57 EKILSCHATLFGAATSPT-RKVPGFF----GAIRYLRRRLDLYANVRPAKSR-------P 104 + A LFG+ P +P GA+ LR +L+ N+RPAK P Sbjct: 61 KGCEEADAILFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHVGLEHMSP 120 Query: 105 VPG--SRPGVDLVIVRENTEGLYV-----EQERRYLDVAIADAVISKKASERIGRAALRI 157 + S G D++ VRE T G+Y Q + A S++ RI + A Sbjct: 121 LRSDISAQGFDVLCVRELTGGIYFGKPKGRQGEGEQEEAFDTMRYSRREVRRIAKIAFEA 180 Query: 158 AEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERF 217 A GR +K + KANVL + L+ + V+EVAK+FP V ++ I +DN MQL+ RP F Sbjct: 181 ARGRRKKVTSV-DKANVLACSV-LWREVVEEVAKEFPDVALEHIYIDNATMQLLRRPFDF 238 Query: 218 DVIVTTNLLGDILSDLAAGLVGGLGLAPSGNI-GDTTAVFEPVHGSAPDIAGKGIANPTA 276 DV++ +NL GDI+SD A L G +GL S ++ D ++EP GSAPDIAG+GIANP A Sbjct: 239 DVMLCSNLFGDIISDEIAMLTGSMGLLSSVSLNSDGFGLYEPAGGSAPDIAGQGIANPIA 298 Query: 277 AILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDL 314 ILSAA++L + L E+ AAK +E AV L G T +L Sbjct: 299 QILSAALLLRHSLKEEAAAKAIEDAVAKALSDGYLTGEL 337 Lambda K H 0.319 0.137 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: 291 Number of extensions: 15 Number of successful extensions: 6 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: 334 Length of database: 364 Length adjustment: 29 Effective length of query: 305 Effective length of database: 335 Effective search space: 102175 Effective search space used: 102175 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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