Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 14219 b0073 3-isopropylmalate dehydrogenase (VIMSS)
Query= BRENDA::P30125 (363 letters) >FitnessBrowser__Keio:14219 Length = 363 Score = 726 bits (1874), Expect = 0.0 Identities = 363/363 (100%), Positives = 363/363 (100%) Query: 1 MSKNYHIAVLPGDGIGPEVMTQALKVLDAVRNRFAMRITTSHYDVGGAAIDNHGQPLPPA 60 MSKNYHIAVLPGDGIGPEVMTQALKVLDAVRNRFAMRITTSHYDVGGAAIDNHGQPLPPA Sbjct: 1 MSKNYHIAVLPGDGIGPEVMTQALKVLDAVRNRFAMRITTSHYDVGGAAIDNHGQPLPPA 60 Query: 61 TVEGCEQADAVLFGSVGGPKWEHLPPDQQPERGALLPLRKHFKLFSNLRPAKLYQGLEAF 120 TVEGCEQADAVLFGSVGGPKWEHLPPDQQPERGALLPLRKHFKLFSNLRPAKLYQGLEAF Sbjct: 61 TVEGCEQADAVLFGSVGGPKWEHLPPDQQPERGALLPLRKHFKLFSNLRPAKLYQGLEAF 120 Query: 121 CPLRADIAANGFDILCVRELTGGIYFGQPKGREGSGQYEKAFDTEVYHRFEIERIARIAF 180 CPLRADIAANGFDILCVRELTGGIYFGQPKGREGSGQYEKAFDTEVYHRFEIERIARIAF Sbjct: 121 CPLRADIAANGFDILCVRELTGGIYFGQPKGREGSGQYEKAFDTEVYHRFEIERIARIAF 180 Query: 181 ESARKRRHKVTSIDKANVLQSSILWREIVNEIATEYPDVELAHMYIDNATMQLIKDPSQF 240 ESARKRRHKVTSIDKANVLQSSILWREIVNEIATEYPDVELAHMYIDNATMQLIKDPSQF Sbjct: 181 ESARKRRHKVTSIDKANVLQSSILWREIVNEIATEYPDVELAHMYIDNATMQLIKDPSQF 240 Query: 241 DVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIA 300 DVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIA Sbjct: 241 DVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIA 300 Query: 301 QILSLALLLRYSLDADDAACAIERAINRALEEGIRTGDLARGAAAVSTDEMGDIIARYVA 360 QILSLALLLRYSLDADDAACAIERAINRALEEGIRTGDLARGAAAVSTDEMGDIIARYVA Sbjct: 301 QILSLALLLRYSLDADDAACAIERAINRALEEGIRTGDLARGAAAVSTDEMGDIIARYVA 360 Query: 361 EGV 363 EGV Sbjct: 361 EGV 363 Lambda K H 0.320 0.137 0.405 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: 598 Number of extensions: 12 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: 363 Length of database: 363 Length adjustment: 29 Effective length of query: 334 Effective length of database: 334 Effective search space: 111556 Effective search space used: 111556 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 14219 b0073 (3-isopropylmalate dehydrogenase (VIMSS))
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.2954614.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-176 572.4 0.0 1.8e-176 572.2 0.0 1.0 1 FitnessBrowser__Keio:14219 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Keio:14219 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 572.2 0.0 1.8e-176 1.8e-176 1 348 [. 6 354 .. 6 355 .. 0.99 Alignments for each domain: == domain 1 score: 572.2 bits; conditional E-value: 1.8e-176 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWdnlprdv 83 +iavLpGDgiGpev+++alkvL+av++rf+++++++++++GGaaid++g+Plp +t+++c++adavL+g+vGGpkW++lp+d+ FitnessBrowser__Keio:14219 6 HIAVLPGDGIGPEVMTQALKVLDAVRNRFAMRITTSHYDVGGAAIDNHGQPLPPATVEGCEQADAVLFGSVGGPKWEHLPPDQ 88 69********************************************************************************* PP TIGR00169 84 rPek.gLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGepkereeaeeekkaldtekYtkee 164 +Pe+ +LL+lrk+++lf+nLrPakl+++Le+++pl+++i+ +g+D+++vreLtgGiYfG+pk+re++++++ka+dte+Y++ e FitnessBrowser__Keio:14219 89 QPERgALLPLRKHFKLFSNLRPAKLYQGLEAFCPLRADIAaNGFDILCVRELTGGIYFGQPKGREGSGQYEKAFDTEVYHRFE 171 ****88*********************************989***************************************** PP TIGR00169 165 ieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDils 247 ieriar+afe+arkrr+kvts+DkanvL+ss+lWr++v+eia+eyPdvel+h+yiDna+mqL+k+P+q+dv+++snlfGDils FitnessBrowser__Keio:14219 172 IERIARIAFESARKRRHKVTSIDKANVLQSSILWREIVNEIATEYPDVELAHMYIDNATMQLIKDPSQFDVLLCSNLFGDILS 254 *********************************************************************************** PP TIGR00169 248 DeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrte 330 De+++itGs+G+LPsasl+++g++l+ep++gsapdiagk+ianpia+ils+alllrysl++++aa+aie+a++++leeg+rt FitnessBrowser__Keio:14219 255 DECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIAQILSLALLLRYSLDADDAACAIERAINRALEEGIRTG 337 *********************************************************************************** PP TIGR00169 331 dlaseattavstkeveee 348 dla+ a +avst+e+++ FitnessBrowser__Keio:14219 338 DLARGA-AAVSTDEMGDI 354 ****99.999***99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (363 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: 00:00:00.00 # Mc/sec: 19.56 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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