Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate N515DRAFT_0570 N515DRAFT_0570 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Dyella79:N515DRAFT_0570 Length = 365 Score = 217 bits (552), Expect = 4e-61 Identities = 144/353 (40%), Positives = 194/353 (54%), Gaps = 28/353 (7%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVLEATGL----PLEFVEAEAGWETFERRGTSVPEETV 56 M RI + GDG+G EV AA VL+A ++ + G + G +P + + Sbjct: 1 MKARIVTLPGDGVGPEVTAAAVAVLDAVAAHYDHTFDYEQHLIGGCAIDATGEPLPADAL 60 Query: 57 EKILSCHATLFGAA--------TSPTRKVPGFFGAIRYLRRRLDLYANVRPAKSRPV--- 105 S A L GA ++P R G LR L +YAN+RP + P Sbjct: 61 AACKSADAVLLGAVGGPKWSDPSAPVRPEQGLLA----LRAALGVYANLRPLQVHPALTA 116 Query: 106 -----PGSRPGVDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIGRAALRIAEG 160 VD++ VRE T G Y + R +D A + + ER+ R A +A G Sbjct: 117 LSPLKDDKLRNVDVLFVRELTGGAYFGAKTRTVDTATDECKYTVVEVERVVRRAFELARG 176 Query: 161 RPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVI 220 R K + KANVL T L+ TV+ +A D+P V ++ +VD+ AM L+ +P +DV+ Sbjct: 177 RRHKVTSV-DKANVLE-TSRLWRSTVQRIAADYPDVKLEHQLVDSMAMLLLTQPASYDVV 234 Query: 221 VTTNLLGDILSDLAAGLVGGLGLAPSGNIGD-TTAVFEPVHGSAPDIAGKGIANPTAAIL 279 VT NL GDIL+D AA L G LGL PS ++G+ ++EP+HGSAPDIAGKG+ANP AIL Sbjct: 235 VTENLFGDILTDEAAALAGSLGLLPSASLGEGARGLYEPIHGSAPDIAGKGVANPVGAIL 294 Query: 280 SAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331 SAAM+L + LG +E A VE AV+ VLE GPR+ D+GGDA T A EAVV AL Sbjct: 295 SAAMLLRHSLGLEEEAGAVEAAVEHVLEHGPRSRDIGGDAGTAAIREAVVAAL 347 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: 289 Number of extensions: 14 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: 365 Length adjustment: 29 Effective length of query: 305 Effective length of database: 336 Effective search space: 102480 Effective search space used: 102480 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 09 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