Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate HSERO_RS16500 HSERO_RS16500 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__HerbieS:HSERO_RS16500 Length = 356 Score = 194 bits (492), Expect = 4e-54 Identities = 142/367 (38%), Positives = 189/367 (51%), Gaps = 52/367 (14%) Query: 4 RICLIEGDGIGHEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVEKILSCH 63 +I ++ GDGIG E++ A RVL A E A G +E G +P+ T++ Sbjct: 2 KIAILPGDGIGPEIVNEAVRVLNALDEKFEMETAPVGGAGYEAHGHPLPDGTLKLAKEAD 61 Query: 64 ATLFGA-----------ATSPTRKVPGFFGAIRYLRRRLDLYANVRPAKSRPV------- 105 A LFGA A P + + G LR+ L L+AN RPA P Sbjct: 62 AILFGAVGDWKYDKLERALRPEQAILG-------LRKHLQLFANFRPAICYPELTGASSL 114 Query: 106 -PGSRPGVDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPRK 164 P +D++IVRE +Y Q R + +A R G +R +E R+ Sbjct: 115 KPELVANLDILIVRELNGDIYFGQPR-----GMREAPDGPFKGAREGFDTMRYSEPEIRR 169 Query: 165 TLHIAH--------------KANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQL 210 H+A KANVL Q + D V EV K++P V + + VDN AMQL Sbjct: 170 IAHVAFQAAAKRGKRLCSVDKANVLETFQ-FWKDIVTEVGKEYPDVELSHMYVDNAAMQL 228 Query: 211 VMRPERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNI-GDTTAVFEPVHGSAPDIAGK 269 V P+ FDVIVT N+ GDILSD AA L G +G+ PS ++ + ++EP HGSAPDIAG+ Sbjct: 229 VKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGR 288 Query: 270 GIANPTAAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFT---- 324 GIANP A ILSAAMML + L + E A R+E AV VL +G RT D+ + T+ T Sbjct: 289 GIANPLATILSAAMMLRFSLNKAEQADRIENAVKKVLAQGLRTADIYEEGCTKVNTQQMG 348 Query: 325 EAVVEAL 331 EAVV+AL Sbjct: 349 EAVVKAL 355 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: 310 Number of extensions: 27 Number of successful extensions: 4 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: 356 Length adjustment: 29 Effective length of query: 305 Effective length of database: 327 Effective search space: 99735 Effective search space used: 99735 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