Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate 208498 DVU2985 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >MicrobesOnline__882:208498 Length = 357 Score = 186 bits (471), Expect = 1e-51 Identities = 134/342 (39%), Positives = 176/342 (51%), Gaps = 34/342 (9%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETV 56 M ICL+ GDGIG E++ +VL+A G + A G + G+ +P+ TV Sbjct: 1 MHMNICLLPGDGIGPEIVAQGTKVLDAVARRFGHTVSTSSALIGGAAIDATGSPLPDATV 60 Query: 57 EKILSCHATLFGAATSPT--------RKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPG- 107 E + A L GA P R G G +R+ L L+AN+RPA P Sbjct: 61 EACRTSDAVLLGAVGGPKWDDLPSEKRPEKGLLG----IRKALGLFANLRPAALFPELAG 116 Query: 108 --------SRPGVDLVIVRENTEGLYVEQE-----RRYLDVAIADAVISKKASERIGRAA 154 + G+DLV+VRE T +Y Q R L + + RI R A Sbjct: 117 ACLLRADIAAAGLDLVVVRELTGDVYFGQPAGIETRDGLRTGFNTMIYDEDEVRRIARVA 176 Query: 155 LRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRP 214 A R R+ + KANVL T L+ + V+EVA+D+P V + + VDN AMQLV P Sbjct: 177 FDTARARKRRVCSV-DKANVLA-TSRLWREVVEEVARDYPDVELSHMYVDNAAMQLVRWP 234 Query: 215 ERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIGD-TTAVFEPVHGSAPDIAGKGIAN 273 +FDVIVT NL GDILSD AA + G +G+ PS ++G A+FEP+HGSAPDIAG+ AN Sbjct: 235 AQFDVIVTGNLFGDILSDEAAVITGSIGMLPSASMGSGGPALFEPIHGSAPDIAGQDKAN 294 Query: 274 PTAAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDL 314 P A ILS MML G A ++ AV VL G RT D+ Sbjct: 295 PIATILSVGMMLRLGFGLAAEADAIDAAVRRVLAEGYRTGDI 336 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: 330 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: 357 Length adjustment: 29 Effective length of query: 305 Effective length of database: 328 Effective search space: 100040 Effective search space used: 100040 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