Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_013402600.1 CALHY_RS03340 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_000166355.1:WP_013402600.1 Length = 355 Score = 208 bits (529), Expect = 2e-58 Identities = 138/337 (40%), Positives = 197/337 (58%), Gaps = 29/337 (8%) Query: 3 YRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETVEK 58 +RI +I GDGIG EVI A VL+ G+ E++ +AG ++ G + EE +E Sbjct: 2 HRIAVIPGDGIGPEVIEQALIVLDKISSKFGVKFEYIFIDAGGCAIDKYGVPIREEDLEL 61 Query: 59 ILSCHATLFGAATSPTRKVPGFFGAIR------YLRRRLDLYANVRPA-------KSRPV 105 + C ATL GA P K G G +R LR L +YAN+RPA S P+ Sbjct: 62 VKKCEATLLGAVGGP--KWDGLPGNLRPEQALLKLRGGLKVYANLRPAVLYDELKDSSPL 119 Query: 106 PGS--RPGVDLVIVRENTEGLYVEQERRYL----DVAIADAVISKKASERIGRAALRIAE 159 G+D+++VRE G+Y + R + +VA V SK RI + A A Sbjct: 120 KKEIVDKGIDILVVRELIGGMYFGPKGREVKDGDEVAYDTEVYSKSEVRRIAKVAFEAAR 179 Query: 160 GRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDV 219 R +K + KAN+L ++ L+ +TV+EVAKD+P V + + VDN +MQLV P +FDV Sbjct: 180 KRKKKVTSV-DKANILESSR-LWRETVEEVAKDYPDVELSHMYVDNASMQLVKDPSQFDV 237 Query: 220 IVTTNLLGDILSDLAAGLVGGLGLAPSGNIGD-TTAVFEPVHGSAPDIAGKGIANPTAAI 278 I+T+N+ GDILSD A+ +VG +G+ S ++G+ ++EP+HG+APDIAG+ +ANP A I Sbjct: 238 ILTSNMFGDILSDEASMIVGSIGMLASASLGEGRVGLYEPIHGTAPDIAGQDLANPIATI 297 Query: 279 LSAAMMLDYLGEKE-AAKRVEKAVDLVLERGPRTPDL 314 LSAAMML Y + E AAK +E AV + L+ G RT D+ Sbjct: 298 LSAAMMLRYSFDMEDAAKAIENAVKIALKEGYRTRDI 334 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: 278 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: 355 Length adjustment: 29 Effective length of query: 305 Effective length of database: 326 Effective search space: 99430 Effective search space used: 99430 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 24 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