Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_090219233.1 CV091_RS13570 isocitrate/isopropylmalate dehydrogenase family protein
Query= BRENDA::Q4JB37 (337 letters) >NCBI__GCF_002796795.1:WP_090219233.1 Length = 357 Score = 203 bits (516), Expect = 6e-57 Identities = 123/337 (36%), Positives = 196/337 (58%), Gaps = 20/337 (5%) Query: 11 DGIGPEVVSKSKTILARLNEKFSLPIEYIEVEAGDTTKNKFGDALPKDSL-RVIEKADMI 69 DGIGPE+++++ ++ N KF L + + E E+G + K+G L ++ L R + D + Sbjct: 9 DGIGPEIMAETLRVVEAANHKFDLGLTFHEEESGFKSLEKYGITLREEVLDRARTEFDGV 68 Query: 70 LKG--------PVGETAADVVVKLRLMYDLYANLRPAKSLPGLENKFGDVDILVVRENTE 121 + G P+ E +V R+ DLYAN+RPA++ + NK D+D++++RE TE Sbjct: 69 ILGTQSHMDYPPLVEGGRNVSAGFRIGLDLYANVRPARTRDFIPNKAPDMDLVIMREATE 128 Query: 122 ------DLYKGLEHVISD-GVTVGIKVITRAASTRIAQVALNQALRRKKKVVCVHKSNVM 174 ++Y+G+ ++ D + + ++ ITR S RI + A++RKKK+ +HK+N Sbjct: 129 GFYPDRNMYQGVGEMMPDPNMALSVRKITREGSLRICREGFKLAMQRKKKIAAIHKANSF 188 Query: 175 RITDGLFAESCRNVLKG--KVEYSEMYVDAAAANLVRNPQAFDVIVTENTYGDILSDEAG 232 +TDGLF E R V K +V+ E+ VDA AA LVR P+A+DV+V N YGDILSD A Sbjct: 189 LMTDGLFLECFREVAKDFPEVQTEELIVDAFAALLVRKPEAYDVVVATNFYGDILSDLAS 248 Query: 233 QIAGSLGISPSANIGDRKSL--FEPVHGAAFDIAGKNIANPTAFLLSVGMMLDRMQELSG 290 +++GSLG++ S N L + HG+A DI G N+ANPT+ +LS MML + E G Sbjct: 249 ELSGSLGLAGSINANAETGLCCAQAQHGSAPDIQGLNVANPTSLILSAAMMLTWLGEQRG 308 Query: 291 DIRYNNAAKSLRDAIYSVYSEGKYLTPDVGGSSTTDE 327 + +A ++ A+ +V + T D+GG+ D+ Sbjct: 309 IQKLQDAGHAIAAAVDAVIDDPAKRTRDLGGTVNCDD 345 Lambda K H 0.316 0.135 0.369 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: 266 Number of extensions: 16 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: 337 Length of database: 357 Length adjustment: 29 Effective length of query: 308 Effective length of database: 328 Effective search space: 101024 Effective search space used: 101024 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 26 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