Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 203316 SO4235 3-isopropylmalate dehydrogenase (NCBI ptt file)
Query= BRENDA::Q8E9N3 (364 letters) >FitnessBrowser__MR1:203316 Length = 364 Score = 719 bits (1857), Expect = 0.0 Identities = 364/364 (100%), Positives = 364/364 (100%) Query: 1 MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYTEYDVGGIAIDNHGCPLPEATL 60 MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYTEYDVGGIAIDNHGCPLPEATL Sbjct: 1 MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYTEYDVGGIAIDNHGCPLPEATL 60 Query: 61 KGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSP 120 KGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSP Sbjct: 61 KGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSP 120 Query: 121 LRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREISRIARIAFEA 180 LRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREISRIARIAFEA Sbjct: 121 LRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREISRIARIAFEA 180 Query: 181 ARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV 240 ARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV Sbjct: 181 ARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV 240 Query: 241 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQI 300 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQI Sbjct: 241 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQI 300 Query: 301 LSAALMLRHSLKQEEAASAIERAVTKALNSGYLTGELLSSDQRHKAKTTVQMGDFIADAV 360 LSAALMLRHSLKQEEAASAIERAVTKALNSGYLTGELLSSDQRHKAKTTVQMGDFIADAV Sbjct: 301 LSAALMLRHSLKQEEAASAIERAVTKALNSGYLTGELLSSDQRHKAKTTVQMGDFIADAV 360 Query: 361 KAGV 364 KAGV Sbjct: 361 KAGV 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: 579 Number of extensions: 15 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 203316 SO4235 (3-isopropylmalate dehydrogenase (NCBI ptt file))
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.15150.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-162 526.2 0.0 2e-162 526.0 0.0 1.0 1 lcl|FitnessBrowser__MR1:203316 SO4235 3-isopropylmalate dehydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:203316 SO4235 3-isopropylmalate dehydrogenase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 526.0 0.0 2e-162 2e-162 1 342 [. 4 347 .. 4 356 .. 0.97 Alignments for each domain: == domain 1 score: 526.0 bits; conditional E-value: 2e-162 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWdnl 79 +iavL+GDgiGpev+aea kvLkave rf+l++e+ e+++GG aid++g Plpe+tlk+c++ada+L+g+vGGpkW++l lcl|FitnessBrowser__MR1:203316 4 QIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYTEYDVGGIAIDNHGCPLPEATLKGCEAADAILFGSVGGPKWEKL 82 69***************************************************************************** PP TIGR00169 80 prdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGepkereeaeeekkald 156 p++ +Pe+ +LL+lr +++lf+nLrPakl+++Le++spl+++i +g+D+++vreLtgGiYfG+pk+r++++e+++a+d lcl|FitnessBrowser__MR1:203316 83 PPNEQPERgALLPLRGHFELFCNLRPAKLHDGLEHMSPLRSDISaRGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFD 161 ********88*********************************77********************************** PP TIGR00169 157 tekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvksPeqldv 235 t++Y+++ei+riar+afe+ar rrkkvtsvDkanvL+ s lWr++vee+a ++Pdveleh+yiDna+mqL+++P+++dv lcl|FitnessBrowser__MR1:203316 162 TMRYSRREISRIARIAFEAARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV 240 ******************************************************************************* PP TIGR00169 236 vvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllryslnleeaaea 314 +++snlfGDilsDe +++tGs+GlL sas++s+g++lfep++gsapdiagkgianpia+ilsaal+lr+sl++eeaa+a lcl|FitnessBrowser__MR1:203316 241 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQILSAALMLRHSLKQEEAASA 319 ******************************************************************************* PP TIGR00169 315 ieaavkkvleegkrtedlaseattavst 342 ie+av k+l++g+ t +l s++ + ++ lcl|FitnessBrowser__MR1:203316 320 IERAVTKALNSGYLTGELLSSDQRHKAK 347 ***************9999887544433 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: 8.58 // [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