Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 6936139 Sama_0336 3-isopropylmalate dehydrogenase (RefSeq)
Query= BRENDA::Q8E9N3 (364 letters) >FitnessBrowser__SB2B:6936139 Length = 364 Score = 653 bits (1684), Expect = 0.0 Identities = 326/364 (89%), Positives = 345/364 (94%) Query: 1 MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYTEYDVGGIAIDNHGCPLPEATL 60 MSYQIAVLAGDGIGPEVMAEARKVL VEARF LNIEY+EYDVGGIAIDNHGCPLP+ATL Sbjct: 1 MSYQIAVLAGDGIGPEVMAEARKVLAEVEARFDLNIEYSEYDVGGIAIDNHGCPLPDATL 60 Query: 61 KGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSP 120 KGCEAADAILFGSVGGPKWE LPPNEQPERGALLPLRGHFELFCNLRPA+LH GLEHMSP Sbjct: 61 KGCEAADAILFGSVGGPKWEHLPPNEQPERGALLPLRGHFELFCNLRPARLHTGLEHMSP 120 Query: 121 LRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREISRIARIAFEA 180 LR+DISA+GFDVLCVRELTGGIYFGKPKGRQGEGE EEAFDTMRYSRREI RIA+IAFEA Sbjct: 121 LRADISAQGFDVLCVRELTGGIYFGKPKGRQGEGEEEEAFDTMRYSRREIRRIAKIAFEA 180 Query: 181 ARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV 240 ARGRR KVTSVDKANVLACSVLWR+VVEEVA DFPDV LEHIYIDNATMQLLRRP +FDV Sbjct: 181 ARGRRGKVTSVDKANVLACSVLWREVVEEVAKDFPDVTLEHIYIDNATMQLLRRPFDFDV 240 Query: 241 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQI 300 MLCSNLFGDILSDEIAMLTGSMGLLSSASMN +GFGL+EPAGGSAPDIAGKGIANPIAQI Sbjct: 241 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNGSGFGLYEPAGGSAPDIAGKGIANPIAQI 300 Query: 301 LSAALMLRHSLKQEEAASAIERAVTKALNSGYLTGELLSSDQRHKAKTTVQMGDFIADAV 360 LSAALMLRHSLKQEEAA+ IERAV AL +G+LTGELLS+DQRH AK+T +MGDFIA+A+ Sbjct: 301 LSAALMLRHSLKQEEAAACIERAVGAALEAGFLTGELLSADQRHNAKSTKEMGDFIANAI 360 Query: 361 KAGV 364 + GV Sbjct: 361 REGV 364 Lambda K H 0.318 0.136 0.393 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: 559 Number of extensions: 16 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: 364 Length of database: 364 Length adjustment: 29 Effective length of query: 335 Effective length of database: 335 Effective search space: 112225 Effective search space used: 112225 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)
Align candidate 6936139 Sama_0336 (3-isopropylmalate dehydrogenase (RefSeq))
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.21741.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-159 514.1 0.0 9.8e-159 513.9 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6936139 Sama_0336 3-isopropylmalate dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936139 Sama_0336 3-isopropylmalate dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 513.9 0.0 9.8e-159 9.8e-159 1 347 [. 4 354 .. 4 356 .. 0.97 Alignments for each domain: == domain 1 score: 513.9 bits; conditional E-value: 9.8e-159 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWd 77 +iavL+GDgiGpev+aea kvL +ve rf+l++e++e+++GG aid++g Plp++tlk+c++ada+L+g+vGGpkW+ lcl|FitnessBrowser__SB2B:6936139 4 QIAVLAGDGIGPEVMAEARKVLAEVEARFDLNIEYSEYDVGGIAIDNHGCPLPDATLKGCEAADAILFGSVGGPKWE 80 69*************************************************************************** PP TIGR00169 78 nlprdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGepkereeaeeek 152 +lp++ +Pe+ +LL+lr +++lf+nLrPa+l+ +Le++spl+++i +g+D+++vreLtgGiYfG+pk+r++++ee+ lcl|FitnessBrowser__SB2B:6936139 81 HLPPNEQPERgALLPLRGHFELFCNLRPARLHTGLEHMSPLRADISaQGFDVLCVRELTGGIYFGKPKGRQGEGEEE 157 **********88*********************************77****************************** PP TIGR00169 153 kaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvks 229 +a+dt++Y+++ei+ria++afe+ar rr kvtsvDkanvL+ s lWr++vee+ak++Pdv+leh+yiDna+mqL+++ lcl|FitnessBrowser__SB2B:6936139 158 EAFDTMRYSRREIRRIAKIAFEAARGRRGKVTSVDKANVLACSVLWREVVEEVAKDFPDVTLEHIYIDNATMQLLRR 234 ***************************************************************************** PP TIGR00169 230 PeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllrysl 306 P +dv+++snlfGDilsDe +++tGs+GlL sas++++g++l+ep++gsapdiagkgianpia+ilsaal+lr+sl lcl|FitnessBrowser__SB2B:6936139 235 PFDFDVMLCSNLFGDILSDEIAMLTGSMGLLSSASMNGSGFGLYEPAGGSAPDIAGKGIANPIAQILSAALMLRHSL 311 ***************************************************************************** PP TIGR00169 307 nleeaaeaieaavkkvleegkrtedlasea..ttavstkevee 347 ++eeaa+ ie+av +le g t +l s + +a stke+++ lcl|FitnessBrowser__SB2B:6936139 312 KQEEAAACIERAVGAALEAGFLTGELLSADqrHNAKSTKEMGD 354 *********************9999876551145667777766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (364 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.70 // [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