Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate GFF3631 PS417_18585 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__WCS417:GFF3631 Length = 360 Score = 200 bits (509), Expect = 4e-56 Identities = 140/363 (38%), Positives = 201/363 (55%), Gaps = 32/363 (8%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAEAGWETFERRGTSVPEETV 56 M+ +I ++ GDGIG E++ A +VLE L E G ++ G + +ET+ Sbjct: 1 MSKQILILPGDGIGPEIMAEAVKVLELANSKYSLGFEMSHDVIGGAAIDKHGVPLADETL 60 Query: 57 EKILSCHATLFGAATSPT-----RKVPGFFGAIRYLRRRLDLYANVRPAKSRPV------ 105 ++ + A L GA P R + G ++ +R +L L+ N+RPA P Sbjct: 61 DRARAADAVLLGAVGGPKWDKIERDIRPERGLLK-IRAQLGLFGNLRPAILYPQLADASS 119 Query: 106 --PGSRPGVDLVIVRENTEGLYVEQERRYLDV------AIADAVISKKASERIGRAALRI 157 P G+D++IVRE T G+Y R ++ A S+ RI R + Sbjct: 120 LKPEVVAGLDILIVRELTGGIYFGSPRGVRELENGERQAYDTLPYSESEIRRIARVGFDM 179 Query: 158 AEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERF 217 A R +K + KANVL +Q L+ + V+EVA+D+P V + + VDN AMQLV P++F Sbjct: 180 ARVRGKKVCSV-DKANVLASSQ-LWREIVEEVARDYPDVELSHMYVDNAAMQLVRAPKQF 237 Query: 218 DVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIG-DTTAVFEPVHGSAPDIAGKGIANPTA 276 DVIVT NL GDILSD A+ L G +G+ PS ++ + ++EP HGSAPDIAG+GIANP A Sbjct: 238 DVIVTDNLFGDILSDQASMLTGSIGMLPSASLDTNNKGMYEPCHGSAPDIAGQGIANPLA 297 Query: 277 AILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFT----EAVVEAL 331 ILS +MML Y +AA +EKAV LVL++G RT D+ T+ T +AVV AL Sbjct: 298 TILSVSMMLRYSFNLSDAADAIEKAVSLVLDQGLRTGDIWSQGCTKVGTQEMGDAVVAAL 357 Query: 332 KSL 334 ++L Sbjct: 358 RNL 360 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: 13 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: 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 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