Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate 3606650 Dshi_0081 3-isopropylmalate dehydrogenase (RefSeq)
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Dino:3606650 Length = 368 Score = 177 bits (449), Expect = 4e-49 Identities = 137/362 (37%), Positives = 195/362 (53%), Gaps = 38/362 (10%) Query: 5 ICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAEAGWETFERRGTSVPEETVEKIL 60 + ++ GDGIG EV+ R++++ G L + E G ++ G + +ET+ K Sbjct: 6 LLILAGDGIGPEVMAEVRKIIDWYGAKRDLAFDVSEDLVGGAAYDVHGVPLADETMAKAQ 65 Query: 61 SCHATLFGAATSPTRKVPGFF-----GAIRYLRRRLDLYANVRPAK--------SRPVPG 107 + A L GA P F G +R LR+ +DL+AN+RPA+ S Sbjct: 66 AVDAVLLGAVGGPKYDTLDFSLKPERGLLR-LRKEMDLFANLRPAQCFDALADFSSLKKD 124 Query: 108 SRPGVDLVIVRENTEGLYVEQERRYLD-----VAIADAVISKKASERIGRAALRIAEGRP 162 G+D++IVRE T G+Y + R V I ++ R+ R+A +A+ R Sbjct: 125 IVAGLDIMIVRELTSGVYFGEPRGIHKEGNERVGINTQRYTESEIARVARSAFELAKKRG 184 Query: 163 RKTLHIAHKANVLPLTQGLFLDTVKEV-AKDFPLVNVQDIIVDNCAMQLVMRPERFDVIV 221 K + KANV+ + L+ D V E+ A ++ V + + D AMQLV P++FDVIV Sbjct: 185 NKVCSM-EKANVME-SGILWRDVVTEIHAAEYADVELSHMYADAGAMQLVRAPKQFDVIV 242 Query: 222 TTNLLGDILSDLAAGLVGGLGLAPSGNI------GDTTAVFEPVHGSAPDIAGKGIANPT 275 T NL GD+LSD AA L G LG+ PS ++ G A++EPVHGSAPDIAG+G ANP Sbjct: 243 TDNLFGDLLSDAAAMLTGSLGMLPSASLGLPMENGRPKALYEPVHGSAPDIAGQGKANPC 302 Query: 276 AAILSAAMMLDYLGEKEA-AKRVEKAVDLVLERGPRTPDL--GGD---ATTEAFTEAVVE 329 A ILS AM L Y ++ A A R+E AV+ VL +G RT DL GD A+T +AV+ Sbjct: 303 ACILSFAMALRYSFDQGAEADRLEAAVNQVLAQGIRTADLMQAGDTAPASTSQMGDAVIA 362 Query: 330 AL 331 AL Sbjct: 363 AL 364 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: 315 Number of extensions: 18 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: 368 Length adjustment: 29 Effective length of query: 305 Effective length of database: 339 Effective search space: 103395 Effective search space used: 103395 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