Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate SMc04405 SMc04405 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Smeli:SMc04405 Length = 370 Score = 165 bits (417), Expect = 2e-45 Identities = 129/364 (35%), Positives = 188/364 (51%), Gaps = 39/364 (10%) Query: 7 LIEGDGIGHEVIPAARRVLEATGLPLE--FVEAEA--GWETFERRGTSVPEETVEKILSC 62 L+ GDGIG E + R+++ + FV E G ++ G ++ E + K L+ Sbjct: 8 LLPGDGIGPEAMAEVRKIIAYMNAERDAGFVTDEGLVGGSAYDAHGAAISEGDMAKALAA 67 Query: 63 HATLFGAATSPT-----RKVPGFFGAIRYLRRRLDLYANVRPAKSRPV--------PGSR 109 A LFGA P +V G +R LR+ L+L+AN+RPA P P Sbjct: 68 DAVLFGAVGGPKWDAVPYEVRPEAGLLR-LRKDLELFANLRPAICYPALANASSLKPELV 126 Query: 110 PGVDLVIVRENTEGLYVEQERRYLDVA------IADAVISKKASERIGRAALRIAEGRPR 163 G+D++IVRE T G+Y + + +D+ I V ERI A +A R Sbjct: 127 EGLDILIVRELTGGVYFGEPKEIVDLGNGQKRGIDTQVYDTYEIERIAGVAFELARTRNN 186 Query: 164 KTLHIAHKANVLPLTQGLFLDTVKEVAK-DFPLVNVQDIIVDNCAMQLVMRPERFDVIVT 222 + + K NV+ + L+ V E K + V ++ ++ D MQLV +P++FDVIVT Sbjct: 187 RVCSM-EKRNVMK-SGVLWNQVVTETHKAKYSDVQLEHMLADAGGMQLVRQPKQFDVIVT 244 Query: 223 TNLLGDILSDLAAGLVGGLGLAPSGNI-------GDTTAVFEPVHGSAPDIAGKGIANPT 275 NL GD+LSD+AA L G LG+ PS ++ G A++EPVHGSAPDIAG G+ANP Sbjct: 245 DNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKALYEPVHGSAPDIAGTGVANPI 304 Query: 276 AAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFT----EAVVEA 330 A I S AM L Y + A +EKA+ VL++G RT D+ + + T +A++ Sbjct: 305 AMIASFAMCLRYSFNLVKEADDLEKAIANVLDQGIRTGDIMAEGCRKVGTAEMGDAILAE 364 Query: 331 LKSL 334 KSL Sbjct: 365 FKSL 368 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: 292 Number of extensions: 16 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: 334 Length of database: 370 Length adjustment: 29 Effective length of query: 305 Effective length of database: 341 Effective search space: 104005 Effective search space used: 104005 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 Aug 03 2021. The underlying query database was built on Aug 03 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