Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate GFF2936 PGA1_c29830 3-isopropylmalate dehydrogenase LeuB
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Phaeo:GFF2936 Length = 367 Score = 186 bits (472), Expect = 8e-52 Identities = 138/361 (38%), Positives = 191/361 (52%), Gaps = 37/361 (10%) Query: 5 ICLIEGDGIGHEVIPAARRVL----EATGLPLEFVEAEAGWETFERRGTSVPEETVEKIL 60 I ++ GDGIG EV+ R+V+ E L + E G ++ G + +ET+EK Sbjct: 6 ILILPGDGIGPEVMAEVRKVISWYGEKRDLQFDVSEDLVGGAAYDVHGKPLADETMEKAQ 65 Query: 61 SCHATLFGAATSPTRKVPGFF-----GAIRYLRRRLDLYANVRPAK--------SRPVPG 107 A L GA P F G +R LR+ +DLY+N+RPA+ S Sbjct: 66 EVDAVLLGAVGGPKYDDLDFSVKPERGLLR-LRKEMDLYSNLRPAQCFDALADFSSLKKD 124 Query: 108 SRPGVDLVIVRENTEGLYVEQERRYLD-----VAIADAVISKKASERIGRAALRIAEGRP 162 G+D++IVRE T G+Y + R + V I ++ ER R+A +A R Sbjct: 125 IVAGLDIMIVRELTSGVYFGEPRGIFEEGNERVGINTQRYTESEIERAARSAFELAMRRN 184 Query: 163 RKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVT 222 +K + KANV+ + L+ + V VA D+P V + + DN AMQLV P++FDVI+T Sbjct: 185 KKLCSM-EKANVME-SGILWREVVTRVAADYPEVELSHMYADNGAMQLVRAPKQFDVILT 242 Query: 223 TNLLGDILSDLAAGLVGGLGLAPSGNI------GDTTAVFEPVHGSAPDIAGKGIANPTA 276 NL GDILSD AA L G LG+ PS ++ G A++EPVHGSAPDIAG+G ANP A Sbjct: 243 DNLFGDILSDCAAMLTGSLGMLPSASLGAPMANGRPKALYEPVHGSAPDIAGQGKANPIA 302 Query: 277 AILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGD-----ATTEAFTEAVVEA 330 ILS AM L Y + A R+E AV+ VL G RT DL G+ +T + ++ A Sbjct: 303 CILSFAMALRYSFDQGSEADRLETAVEKVLADGHRTGDLLGEEGVSPISTSEMGDVIIAA 362 Query: 331 L 331 L Sbjct: 363 L 363 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: 321 Number of extensions: 20 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: 367 Length adjustment: 29 Effective length of query: 305 Effective length of database: 338 Effective search space: 103090 Effective search space used: 103090 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