Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_015818168.1 TERTU_RS11085 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_000023025.1:WP_015818168.1 Length = 357 Score = 203 bits (517), Expect = 5e-57 Identities = 142/357 (39%), Positives = 201/357 (56%), Gaps = 30/357 (8%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAEAGWETFERRGTSVPEETV 56 M+ +I L+ GDGIG E++ A +VLE L L+F E G + G + T+ Sbjct: 1 MSKKIVLLPGDGIGPEIVAEAVKVLEVVDKKHKLGLKFEEELIGGSAIDVHGVPLASSTL 60 Query: 57 EKILSCHATLFGAATSPTRKVPGFFGAIR------YLRRRLDLYANVRPAKSRPV----- 105 EK + A L G+ P K +IR +R + L+ N+RPA P Sbjct: 61 EKCQAADAVLMGSVGGP--KWDTLDSSIRPEKGLLKIRYEMGLFGNLRPAILYPQLADAS 118 Query: 106 ---PGSRPGVDLVIVRENTEGLYVEQER--RYLDVAIADA----VISKKASERIGRAALR 156 P G+D++IVRE T G+Y + R R LD V ++ ERIGR A Sbjct: 119 SLKPELVAGLDILIVRELTGGIYFGEPRGIRLLDNGERQGYNTYVYAEHEIERIGRMAFE 178 Query: 157 IAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPER 216 +A R +K + KANVL T L+ + V+ +++++P V + + VDN AMQLV +P++ Sbjct: 179 MAMKRNKKVCSV-DKANVLEATV-LWREVVQSLSREYPEVELSHMYVDNAAMQLVRQPKQ 236 Query: 217 FDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIG-DTTAVFEPVHGSAPDIAGKGIANPT 275 FDVIVT N+ GDILSD AA L G +G+ PS ++ D ++EPVHGSAPDIAG+GIANP Sbjct: 237 FDVIVTGNMFGDILSDTAAMLTGSIGMLPSASLNKDKRGLYEPVHGSAPDIAGQGIANPL 296 Query: 276 AAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331 A ILSAAMML Y L + EAA +E AV VL+ G R+ D+ + T+ T+ + +A+ Sbjct: 297 ATILSAAMMLRYSLDQGEAADAIEAAVGKVLDDGYRSADIFSEGCTKVSTKEMGDAV 353 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: 303 Number of extensions: 13 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 Apr 10 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