Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate GFF2539 Psest_2589 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__psRCH2:GFF2539 Length = 360 Score = 190 bits (482), Expect = 5e-53 Identities = 137/357 (38%), Positives = 198/357 (55%), Gaps = 30/357 (8%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAEAGWETFERRGTSVPEETV 56 M+ +I ++ GDGIG E++ A +VL+ L E E G ++ G + +ET+ Sbjct: 1 MSKQILVLPGDGIGPEIMAEAVKVLQLANDKFQLDFELSYDELGGAAVDKYGVPLADETL 60 Query: 57 EKILSCHATLFGAATSPTRKVPGFFGAIR------YLRRRLDLYANVRPAKSRPV----- 105 E+ + A L GA P K AIR +R +L L+ N+RPA P Sbjct: 61 ERARAADAILLGAVGGP--KWDTIDPAIRPERGLLKIRSQLGLFGNLRPALLYPQLAEAS 118 Query: 106 ---PGSRPGVDLVIVRENTEGLYVEQER--RYLD----VAIADAVISKKASERIGRAALR 156 P G+D++IVRE T G+Y Q R + L+ +A S+ RI + Sbjct: 119 SLKPEIVAGLDILIVRELTGGIYFGQPRESKVLESGERMAYDTLPYSESEIRRIAKVGFD 178 Query: 157 IAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPER 216 +A R +K + KANVL +Q L+ V+EVAK +P V + + VDN AMQLV P++ Sbjct: 179 MAMVRNKKLCSV-DKANVLASSQ-LWRAVVEEVAKYYPDVELSHMYVDNAAMQLVRAPKQ 236 Query: 217 FDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNI-GDTTAVFEPVHGSAPDIAGKGIANPT 275 FDVIVT N+ GDILSD A+ L G +G+ PS ++ ++EP HGSAPDIAG+GIANP Sbjct: 237 FDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDAGNKGMYEPCHGSAPDIAGQGIANPL 296 Query: 276 AAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331 A ILS +MML Y + AA +E+AV VL++G RT D+ + T+ T+A+ +A+ Sbjct: 297 ATILSVSMMLRYSFNQVAAADAIEQAVSDVLDQGLRTGDIWSEGCTKVGTQAMGDAV 353 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: 4 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: 360 Length adjustment: 29 Effective length of query: 305 Effective length of database: 331 Effective search space: 100955 Effective search space used: 100955 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