Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate Ga0059261_3190 Ga0059261_3190 3-isopropylmalate dehydrogenase
Query= SwissProt::Q56268 (358 letters) >FitnessBrowser__Korea:Ga0059261_3190 Length = 348 Score = 397 bits (1019), Expect = e-115 Identities = 210/355 (59%), Positives = 260/355 (73%), Gaps = 9/355 (2%) Query: 1 MKKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQ 60 M IAI GDGIGPE+ A AR+VLDA+D LGL E VGGAA + PLPA +L Sbjct: 1 MPLIAILPGDGIGPEVTAQARRVLDALD----LGLSFEEAPVGGAAYFSDGHPLPARTLD 56 Query: 61 LAMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLR 120 LA ADA++ GAVG PR D RPEQ +L LRK L+L+ANLRPA++FP L DAS L+ Sbjct: 57 LAKRADALLFGAVGDPRCDGLDRHLRPEQAILGLRKELELFANLRPARLFPGLEDASALK 116 Query: 121 PELVRDVDILVVRELTGDIYFGQPRGLEVIDGKRRGFNTMVYDEDEIRRIAHVAFRAAQG 180 PE+ +D+++VREL GD+YFG+ G+R G++ M Y+EDE+ RIA V F AQ Sbjct: 117 PEVAGAIDMVIVRELNGDVYFGEKGMRTTASGRREGYDIMSYNEDEVARIARVGFETAQV 176 Query: 181 RRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLT 240 R ++LCSVDKANVLET++LWR+VV EV+ ++PDV L+HMYVDNAAMQL+R P QFDV++T Sbjct: 177 RNRKLCSVDKANVLETSQLWRDVVIEVSAEFPDVELTHMYVDNAAMQLVRNPGQFDVIVT 236 Query: 241 GNMFGDILSDEASQLTGSIGMLPSASL-GEGRAMYEPIHGSAPDIAGQDKANPLATILSV 299 GN+FGDILSD+AS GSIGMLPSA+L G G+ +YEPIHGSAPDIAGQ KANP ATILS Sbjct: 237 GNLFGDILSDQASMCAGSIGMLPSAALNGSGKGLYEPIHGSAPDIAGQGKANPCATILSA 296 Query: 300 AMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354 AM+LR+SL+ E A +VEAAV L G RTAD+ + T+AMG AV+ AL Sbjct: 297 AMLLRYSLDMEAAADKVEAAVTAALAGGARTADLGG----ALSTEAMGDAVLKAL 347 Lambda K H 0.320 0.137 0.396 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: 391 Number of extensions: 13 Number of successful extensions: 3 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: 358 Length of database: 348 Length adjustment: 29 Effective length of query: 329 Effective length of database: 319 Effective search space: 104951 Effective search space used: 104951 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate Ga0059261_3190 Ga0059261_3190 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00169.hmm # target sequence database: /tmp/gapView.24885.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00169 [M=349] Accession: TIGR00169 Description: leuB: 3-isopropylmalate dehydrogenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-142 459.5 0.0 4e-142 459.3 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_3190 Ga0059261_3190 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_3190 Ga0059261_3190 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.3 0.0 4e-142 4e-142 2 346 .. 4 344 .. 3 347 .. 0.98 Alignments for each domain: == domain 1 score: 459.3 bits; conditional E-value: 4e-142 TIGR00169 2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 ia+LpGDgiGpev+a+a +vL+a+ +l l feea +GGaa + g+Plp+ tl+ +k+ada+L+ga lcl|FitnessBrowser__Korea:Ga0059261_3190 4 IAILPGDGIGPEVTAQARRVLDAL----DLGLSFEEAPVGGAAYFSDGHPLPARTLDLAKRADALLFGA 68 89*******************987....699************************************** PP TIGR00169 71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYf 139 vG p+ d l r+ rPe+++L lrkel+lfanLrPa+lf++Le++s+lk+e++ +D+v+vreL g +Yf lcl|FitnessBrowser__Korea:Ga0059261_3190 69 VGDPRCDGLDRHLRPEQAILGLRKELELFANLRPARLFPGLEDASALKPEVAGAIDMVIVRELNGDVYF 137 ********************************************************************* PP TIGR00169 140 GepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiake 208 Ge+ r+ a+ +++++d ++Y+++e+ riarv+fe+a+ r++k++svDkanvLe+s+lWr++v e+ e lcl|FitnessBrowser__Korea:Ga0059261_3190 138 GEKGMRTTASGRREGYDIMSYNEDEVARIARVGFETAQVRNRKLCSVDKANVLETSQLWRDVVIEVSAE 206 **999999888********************************************************** PP TIGR00169 209 yPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvh 277 +Pdvel h+y+DnaamqLv++P q+dv+vt+nlfGDilsD+as+ +Gs+G+LPsa+l+++g++l+ep+h lcl|FitnessBrowser__Korea:Ga0059261_3190 207 FPDVELTHMYVDNAAMQLVRNPGQFDVIVTGNLFGDILSDQASMCAGSIGMLPSAALNGSGKGLYEPIH 275 ********************************************************************* PP TIGR00169 278 gsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeve 346 gsapdiag+g anp+a+ilsaa+llrysl++e aa+++eaav +l+ g rt+dl++ +t+++ ++v lcl|FitnessBrowser__Korea:Ga0059261_3190 276 GSAPDIAGQGKANPCATILSAAMLLRYSLDMEAAADKVEAAVTAALAGGARTADLGGALSTEAMGDAVL 344 ********************************************************9999888877765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (348 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.56 // [ok]
This GapMind analysis is from Apr 09 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