Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_028486905.1 B076_RS0108370 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_000483485.1:WP_028486905.1 Length = 357 Score = 195 bits (496), Expect = 1e-54 Identities = 142/360 (39%), Positives = 200/360 (55%), Gaps = 32/360 (8%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETV 56 M + ++ GDGIG E+ A +VLEA GL + E G ++ G + +ET+ Sbjct: 1 MTQEVLVLPGDGIGPEITAEAIKVLEALKVSDGLDINMTEDLVGGAAYDVHGVPLADETM 60 Query: 57 EKILSCHATLFGAA-----TSPTRKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPGSRP- 110 + A L GA S V G +R LR ++L+AN+RPA P S Sbjct: 61 AAAKASDAVLLGAVGGYKWESLDISVRPEKGLLR-LRSEMELFANLRPAFLYPQLASAST 119 Query: 111 -------GVDLVIVRENTEGLYVEQER--RYLDVAIADA----VISKKASERIGRAALRI 157 G+D++IVRE T G+Y Q R R LD V S+ +RI A + Sbjct: 120 LKPEVVAGLDILIVRELTGGIYFGQPRGIRTLDNGERQGFNTYVYSESEIKRIAHVAFQA 179 Query: 158 AEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERF 217 A R +K + KANVL +T+ L+ + V +VAK++P V V+ + VDN AMQLV+ P++F Sbjct: 180 AMKRNKKLTSV-DKANVLEVTE-LWREIVDDVAKEYPEVEVKHMYVDNAAMQLVLNPKQF 237 Query: 218 DVIVTTNLLGDILSDLAAGLVGGLGLAPSGNI-GDTTAVFEPVHGSAPDIAGKGIANPTA 276 DV+VT N+ GDILSD A+ L G +G+ S ++ + ++EP HGSAPDIAG+ ANP A Sbjct: 238 DVMVTGNMFGDILSDEASMLTGSIGMLASASLDANNKGMYEPSHGSAPDIAGQNKANPLA 297 Query: 277 AILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGD----ATTEAFTEAVVEAL 331 ILSAAMML Y LG ++ A+++E AV VL++G RT D+ D T +AVV AL Sbjct: 298 TILSAAMMLRYSLGREDLAEKIETAVGKVLDQGLRTGDIHSDGSQLVTCSEMGDAVVAAL 357 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: 277 Number of extensions: 12 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: 357 Length adjustment: 29 Effective length of query: 305 Effective length of database: 328 Effective search space: 100040 Effective search space used: 100040 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 Jul 25 2024. The underlying query database was built on Jul 25 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