Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_077277800.1 B1C78_RS03700 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_002000365.1:WP_077277800.1 Length = 359 Score = 208 bits (529), Expect = 2e-58 Identities = 141/359 (39%), Positives = 202/359 (56%), Gaps = 34/359 (9%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETV 56 M +I ++ GDGIG E++ A ++LE GL EF EA G ++ G +PE+T+ Sbjct: 1 MTKKILVLPGDGIGPEIVAEATKLLEVLRREHGLVAEFEEAPVGGAGYDAAGHPLPEDTL 60 Query: 57 EKILSCHATLFGAATSPT--------RKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPGS 108 + A L GA P R G G LR L+L+AN+RPA P S Sbjct: 61 RLAKAADAVLLGAVGGPRYDTLDWELRPERGLLG----LRSELNLFANLRPAILYPQLAS 116 Query: 109 RP--------GVDLVIVRENTEGLYVEQER--RYLDVAIADA----VISKKASERIGRAA 154 G+D++I+RE T G Y + R R D + + + + ERI R+ Sbjct: 117 ASALKPEIVGGLDIMILRELTGGAYFGKPRGIRTRDDGVREGFNTIIYDEGEIERIVRSG 176 Query: 155 LRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRP 214 IA R R+ + KANVL ++Q L+ + V++DFP V + + VDN AMQLV P Sbjct: 177 FEIAMKRGRRLCSV-DKANVLEVSQ-LWREVAIRVSEDFPDVELSHMYVDNAAMQLVRAP 234 Query: 215 ERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNI-GDTTAVFEPVHGSAPDIAGKGIAN 273 ++FDVIVT N+ GDILSD AA L G +G+ PS ++ D ++EP+HGSAPDIAG+G+AN Sbjct: 235 KQFDVIVTENMFGDILSDAAAMLTGSIGMLPSASLDADGKGMYEPIHGSAPDIAGQGVAN 294 Query: 274 PTAAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331 P A +LS +MML Y L E A RV+ AV VL++G RTPD+ + +++ T A+ +A+ Sbjct: 295 PLATLLSVSMMLRYSLDEGALADRVDAAVSRVLDQGLRTPDIWTEGSSKVGTTAMGDAV 353 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: 290 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: 359 Length adjustment: 29 Effective length of query: 305 Effective length of database: 330 Effective search space: 100650 Effective search space used: 100650 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 10 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