Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate PP_1988 PP_1988 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Putida:PP_1988 Length = 360 Score = 200 bits (509), Expect = 4e-56 Identities = 139/363 (38%), Positives = 200/363 (55%), Gaps = 32/363 (8%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAEAGWETFERRGTSVPEETV 56 M+ +I ++ GDGIG E++ A +VLE L G ++ G + +ET+ Sbjct: 1 MSKQILILPGDGIGPEIMAEAVKVLELANDKFQLGFSLAHDVIGGAAIDKHGVPLADETL 60 Query: 57 EKILSCHATLFGAATSPT-----RKVPGFFGAIRYLRRRLDLYANVRPAKSRPV------ 105 E+ A L GA P R + G ++ +R +L L+AN+RPA P Sbjct: 61 ERARKADAVLLGAVGGPKWDKIERDIRPERGLLK-IRSQLGLFANLRPAILYPQLADASS 119 Query: 106 --PGSRPGVDLVIVRENTEGLYVEQERRYLDV------AIADAVISKKASERIGRAALRI 157 P G+D++IVRE T G+Y R ++ A S+ RI R + Sbjct: 120 LKPEIVSGLDILIVRELTGGIYFGAPRGQRELEGGERQAYDTLPYSESEVRRIARVGFDM 179 Query: 158 AEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERF 217 A R +K + KANVL +Q L+ + V++VAKD+P V + + VDN AMQLV P++F Sbjct: 180 ARVRGKKLCSV-DKANVLASSQ-LWREVVEDVAKDYPDVELSHMYVDNAAMQLVRAPKQF 237 Query: 218 DVIVTTNLLGDILSDLAAGLVGGLGLAPSGNI-GDTTAVFEPVHGSAPDIAGKGIANPTA 276 DV+VT N+ GDILSD A+ L G +G+ PS ++ D ++EP HGSAPDIAG GIANP A Sbjct: 238 DVMVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGSAPDIAGLGIANPLA 297 Query: 277 AILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDAT----TEAFTEAVVEAL 331 ILS +MML Y + AA+ +EKAV LVL++G RT D+ + T+ +AVV AL Sbjct: 298 TILSVSMMLRYSFNQSAAAEAIEKAVSLVLDQGLRTGDIFSEGCRKVGTQEMGDAVVAAL 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: 294 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: 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 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