Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 7026627 Shewana3_3760 3-isopropylmalate dehydrogenase (RefSeq)
Query= BRENDA::Q8E9N3 (364 letters) >lcl|FitnessBrowser__ANA3:7026627 Shewana3_3760 3-isopropylmalate dehydrogenase (RefSeq) Length = 364 Score = 711 bits (1834), Expect = 0.0 Identities = 358/364 (98%), Positives = 364/364 (100%) Query: 1 MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYTEYDVGGIAIDNHGCPLPEATL 60 MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEY+EYDVGGIAIDNHGCPLPEATL Sbjct: 1 MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYSEYDVGGIAIDNHGCPLPEATL 60 Query: 61 KGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSP 120 KGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSP Sbjct: 61 KGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSP 120 Query: 121 LRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREISRIARIAFEA 180 LRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREI+RIARIAFEA Sbjct: 121 LRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREIARIARIAFEA 180 Query: 181 ARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV 240 ARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV Sbjct: 181 ARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV 240 Query: 241 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQI 300 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQI Sbjct: 241 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQI 300 Query: 301 LSAALMLRHSLKQEEAASAIERAVTKALNSGYLTGELLSSDQRHKAKTTVQMGDFIADAV 360 LSAALMLRHSLKQEEAASAIERAV+KALNSGYLTGELLSSDQRHKAK+TV+MG+FIADAV Sbjct: 301 LSAALMLRHSLKQEEAASAIERAVSKALNSGYLTGELLSSDQRHKAKSTVEMGNFIADAV 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: 572 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 7026627 Shewana3_3760 (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.1281.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-162 526.0 0.0 2.4e-162 525.8 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7026627 Shewana3_3760 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7026627 Shewana3_3760 3-isopropylmalate dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 525.8 0.0 2.4e-162 2.4e-162 1 342 [. 4 347 .. 4 356 .. 0.97 Alignments for each domain: == domain 1 score: 525.8 bits; conditional E-value: 2.4e-162 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWd 77 +iavL+GDgiGpev+aea kvLkave rf+l++e++e+++GG aid++g Plpe+tlk+c++ada+L+g+vGGpkW+ lcl|FitnessBrowser__ANA3:7026627 4 QIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYSEYDVGGIAIDNHGCPLPEATLKGCEAADAILFGSVGGPKWE 80 69*************************************************************************** PP TIGR00169 78 nlprdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGepkereeaeeek 152 +lp++ +Pe+ +LL+lr +++lf+nLrPakl+++Le++spl+++i +g+D+++vreLtgGiYfG+pk+r++++e++ lcl|FitnessBrowser__ANA3:7026627 81 KLPPNEQPERgALLPLRGHFELFCNLRPAKLHDGLEHMSPLRSDISaRGFDVLCVRELTGGIYFGKPKGRQGEGESE 157 **********88*********************************77****************************** PP TIGR00169 153 kaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvks 229 +a+dt++Y+++ei riar+afe+ar rrkkvtsvDkanvL+ s lWr++vee+a ++Pdveleh+yiDna+mqL+++ lcl|FitnessBrowser__ANA3:7026627 158 EAFDTMRYSRREIARIARIAFEAARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRR 234 ***************************************************************************** PP TIGR00169 230 PeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllrysl 306 P+++dv+++snlfGDilsDe +++tGs+GlL sas++s+g++lfep++gsapdiagkgianpia+ilsaal+lr+sl lcl|FitnessBrowser__ANA3:7026627 235 PDEFDVMLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQILSAALMLRHSL 311 ***************************************************************************** PP TIGR00169 307 nleeaaeaieaavkkvleegkrtedlaseattavst 342 ++eeaa+aie+av+k+l++g+ t +l s++ + ++ lcl|FitnessBrowser__ANA3:7026627 312 KQEEAASAIERAVSKALNSGYLTGELLSSDQRHKAK 347 ************************999887544433 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 9.02 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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