Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate 6936139 Sama_0336 3-isopropylmalate dehydrogenase (RefSeq)
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__SB2B:6936139 Length = 364 Score = 184 bits (466), Expect = 4e-51 Identities = 133/340 (39%), Positives = 187/340 (55%), Gaps = 29/340 (8%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETV 56 M+Y+I ++ GDGIG EV+ AR+VL L +E+ E + G + G +P+ T+ Sbjct: 1 MSYQIAVLAGDGIGPEVMAEARKVLAEVEARFDLNIEYSEYDVGGIAIDNHGCPLPDATL 60 Query: 57 EKILSCHATLFGAATSPT------RKVPGFFGAIRYLRRRLDLYANVRPAKSR------- 103 + + A LFG+ P + P GA+ LR +L+ N+RPA+ Sbjct: 61 KGCEAADAILFGSVGGPKWEHLPPNEQPER-GALLPLRGHFELFCNLRPARLHTGLEHMS 119 Query: 104 PVPG--SRPGVDLVIVRENTEGLYV-----EQERRYLDVAIADAVISKKASERIGRAALR 156 P+ S G D++ VRE T G+Y Q + A S++ RI + A Sbjct: 120 PLRADISAQGFDVLCVRELTGGIYFGKPKGRQGEGEEEEAFDTMRYSRREIRRIAKIAFE 179 Query: 157 IAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPER 216 A GR K + KANVL + L+ + V+EVAKDFP V ++ I +DN MQL+ RP Sbjct: 180 AARGRRGKVTSV-DKANVLACSV-LWREVVEEVAKDFPDVTLEHIYIDNATMQLLRRPFD 237 Query: 217 FDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNI-GDTTAVFEPVHGSAPDIAGKGIANPT 275 FDV++ +NL GDILSD A L G +GL S ++ G ++EP GSAPDIAGKGIANP Sbjct: 238 FDVMLCSNLFGDILSDEIAMLTGSMGLLSSASMNGSGFGLYEPAGGSAPDIAGKGIANPI 297 Query: 276 AAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDL 314 A ILSAA+ML + L ++EAA +E+AV LE G T +L Sbjct: 298 AQILSAALMLRHSLKQEEAAACIERAVGAALEAGFLTGEL 337 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: 298 Number of extensions: 18 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: 364 Length adjustment: 29 Effective length of query: 305 Effective length of database: 335 Effective search space: 102175 Effective search space used: 102175 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 Aug 03 2021. The underlying query database was built on Aug 03 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