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 YP_002825162.1 NGR_c06160 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000018545.1:YP_002825162.1 Length = 371 Score = 249 bits (637), Expect = 6e-71 Identities = 147/351 (41%), Positives = 212/351 (60%), Gaps = 29/351 (8%) Query: 4 ICVIEGDGIGKEVVPATIQVLEAT----GLP-FEFVYAEAGDEVYKRTGKALPEETIETA 58 I V+ GDGIG+EV+PA ++++ A G P F AG + Y +G ALP T++ Sbjct: 10 IAVLPGDGIGREVMPACLELVNAATTMAGAPALAFQTHNAGAQYYAESGDALPASTLDAC 69 Query: 59 LDCDAVLFGAAG------ETAADVI--VKLRHILDTYANIRPVKAYKGVKCLRPD----- 105 DA+LFGA G ++I + LR L +A +RP++ + G+ + D Sbjct: 70 RKSDAILFGAMGWPDIRFPDGTEIIPQLDLRMELGLFAGVRPIRWFPGLPRVLTDPRAEQ 129 Query: 106 IDYVIVRENTEGLY--KGIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGKEG 163 ID+V+VRE TEGL+ +G ++ T IT +R+ FAF++AR+RK+ GK G Sbjct: 130 IDFVLVREQTEGLFYARGRGEIRNDEEAYDTMQITRSGTQRVTEFAFDIARQRKRRGKPG 189 Query: 164 KVTCAHKANVLKLTDGLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSN 223 VTC KANV + + F+K+F +VA+ + D+ + Y+DA+ + ++ KP FDV+VT N Sbjct: 190 NVTCVDKANVFQ-SMAFFRKVFDEVADRHSDLTKDHAYVDALALNMVKKPWTFDVLVTEN 248 Query: 224 LFGDILSDGAAGTVGGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLM 283 +FGDILSD AAG +GG+G+APSA+IGD+HGLF+P HG+APDIAGK ANP+A LSA +M Sbjct: 249 MFGDILSDLAAGLIGGMGMAPSADIGDKHGLFQPAHGTAPDIAGKGCANPSAMFLSAAMM 308 Query: 284 LRYLGE-------YEAADKVEKALEEVLALGLTTP-DLGGNLNTFEMAEEV 326 L +L +AA +E A+E L+ L P + GGN N EM V Sbjct: 309 LDWLAAKFGQPTLADAARLMEGAVEHTLSTKLAIPMEYGGNANCAEMTRSV 359 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: 312 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: 333 Length of database: 371 Length adjustment: 29 Effective length of query: 304 Effective length of database: 342 Effective search space: 103968 Effective search space used: 103968 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