Align 3-isopropylmalate/3-methylmalate dehydrogenase; 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; IPMDH; Beta-IPM dehydrogenase; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.85; EC 1.1.1.n5; EC 1.1.1.83 (characterized)
to candidate WP_011868824.1 MMARC5_RS05395 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000016125.1:WP_011868824.1 Length = 330 Score = 518 bits (1333), Expect = e-151 Identities = 252/330 (76%), Positives = 295/330 (89%) Query: 1 MHKICVIEGDGIGKEVVPATIQVLEATGLPFEFVYAEAGDEVYKRTGKALPEETIETALD 60 MHKICVIEGDGIGKEVVPA ++VL+ATG+ FEF YA AGDEV+++TG ALPEETI A Sbjct: 1 MHKICVIEGDGIGKEVVPAAVEVLKATGIEFEFNYALAGDEVFEKTGVALPEETINAAKT 60 Query: 61 CDAVLFGAAGETAADVIVKLRHILDTYANIRPVKAYKGVKCLRPDIDYVIVRENTEGLYK 120 DAVLFGAAGETAADVIVKLR ILDTYANIRPVK+Y G+ CL+ IDY+IVRENTEGLYK Sbjct: 61 ADAVLFGAAGETAADVIVKLRKILDTYANIRPVKSYNGINCLKTGIDYIIVRENTEGLYK 120 Query: 121 GIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGKEGKVTCAHKANVLKLTDGL 180 GIE+EI EG+T+ATRVIT++A ERIF+ AF +A++RK GKE KVTCAHKANVLK+TDGL Sbjct: 121 GIESEITEGVTVATRVITKEASERIFKHAFEMAKDRKSTGKEVKVTCAHKANVLKITDGL 180 Query: 181 FKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGL 240 FKK FY+V+++Y+DIK ED+Y+DAMNMYII++P+ FD+VVTSNLFGDILSDGA G VGGL Sbjct: 181 FKKTFYEVSKDYEDIKTEDFYVDAMNMYIISRPETFDIVVTSNLFGDILSDGAVGMVGGL 240 Query: 241 GLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKAL 300 G+APS N+GD++GLFEP+HGSAPDIAGK +ANPTATIL+AV+MLRYL E AADKVEKAL Sbjct: 241 GMAPSGNVGDDYGLFEPIHGSAPDIAGKGLANPTATILTAVMMLRYLKENGAADKVEKAL 300 Query: 301 EEVLALGLTTPDLGGNLNTFEMAEEVAKRV 330 EEVL+LGLTTPDLGG L+T EM +EVAKRV Sbjct: 301 EEVLSLGLTTPDLGGTLSTSEMGQEVAKRV 330 Lambda K H 0.318 0.138 0.390 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: 425 Number of extensions: 9 Number of successful extensions: 1 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: 333 Length of database: 330 Length adjustment: 28 Effective length of query: 305 Effective length of database: 302 Effective search space: 92110 Effective search space used: 92110 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 (21.7 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