Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_011386420.1 AMB_RS20570 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_000009985.1:WP_011386420.1 Length = 369 Score = 186 bits (473), Expect = 6e-52 Identities = 137/370 (37%), Positives = 189/370 (51%), Gaps = 42/370 (11%) Query: 2 AYRICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAEAGWETFERRGTSVPEETVE 57 A ++ ++ GDGIG EV+ RR+++ G + E E G ++ GT P ET+E Sbjct: 3 AKKLLILPGDGIGVEVMAQVRRIIDWMGRKRKIEFEITEGLLGGAAYDVHGTPYPAETLE 62 Query: 58 KILSCHATLFGAATSPT--------RKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPGSR 109 L+ A L GA P + G G +R+ + L+AN+RPA Sbjct: 63 AALAADAVLLGAVGGPKWDDLPFDKKPERGLLG----IRKDMGLFANLRPATVLEALADA 118 Query: 110 P--------GVDLVIVRENTEGLYVEQERRYLDV------AIADAVISKKASERIGRAAL 155 G+D++I+RE T GLY Q R + V + +RIGR A Sbjct: 119 STLKAEVVSGLDIMILRELTGGLYFGQPRGIDTLPDGTRKGYNTLVYTTPEIQRIGRVAF 178 Query: 156 RIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPE 215 +A R +K + KANVL T + +K ++FP V + + VDN AMQLV P+ Sbjct: 179 DLARKRNKKLCSV-DKANVLECTVLWREEMIKLQKEEFPDVELTHMYVDNAAMQLVRNPK 237 Query: 216 RFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIGDT------TAVFEPVHGSAPDIAGK 269 +FDV+VT N+ GDILSD AA L G LG+ PS ++G+ A++EPVHGSAPDIAGK Sbjct: 238 QFDVMVTENMFGDILSDCAAMLTGSLGMLPSASLGEADAQGKRKALYEPVHGSAPDIAGK 297 Query: 270 GIANPTAAILSAAMMLDYLGEKEA-AKRVEKAVDLVLERGPRTPDL----GGDATTEAFT 324 +ANP A I+S AM L Y + A A +E AV VL+ G RT D+ +T Sbjct: 298 DMANPLATIMSFAMCLRYSFDMAAEADLIETAVKNVLKGGLRTADIMQPGKAKVSTTVMG 357 Query: 325 EAVVEALKSL 334 EAVV L L Sbjct: 358 EAVVRELDKL 367 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: 300 Number of extensions: 21 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: 369 Length adjustment: 29 Effective length of query: 305 Effective length of database: 340 Effective search space: 103700 Effective search space used: 103700 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