Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate BWI76_RS04675 BWI76_RS04675 3-isopropylmalate dehydrogenase
Query= BRENDA::P30125 (363 letters) >FitnessBrowser__Koxy:BWI76_RS04675 Length = 363 Score = 673 bits (1736), Expect = 0.0 Identities = 336/363 (92%), Positives = 348/363 (95%) Query: 1 MSKNYHIAVLPGDGIGPEVMTQALKVLDAVRNRFAMRITTSHYDVGGAAIDNHGQPLPPA 60 MSKNYHIAVLPGDGIGPEVM QALKVL+AVR+RF MRITTS +DVGG AID G PLP + Sbjct: 1 MSKNYHIAVLPGDGIGPEVMNQALKVLEAVRHRFDMRITTSQHDVGGIAIDRQGTPLPQS 60 Query: 61 TVEGCEQADAVLFGSVGGPKWEHLPPDQQPERGALLPLRKHFKLFSNLRPAKLYQGLEAF 120 TVEGCEQADA+LFGSVGGPKWEHLPP +QPERGALLPLRKHFKLFSNLRPAKLYQGLE F Sbjct: 61 TVEGCEQADAILFGSVGGPKWEHLPPAEQPERGALLPLRKHFKLFSNLRPAKLYQGLEEF 120 Query: 121 CPLRADIAANGFDILCVRELTGGIYFGQPKGREGSGQYEKAFDTEVYHRFEIERIARIAF 180 CPLRADIAANGFDILCVRELTGGIYFGQPKGREGSGQ+EKAFDTEVYHRFEIERIA IAF Sbjct: 121 CPLRADIAANGFDILCVRELTGGIYFGQPKGREGSGQHEKAFDTEVYHRFEIERIAHIAF 180 Query: 181 ESARKRRHKVTSIDKANVLQSSILWREIVNEIATEYPDVELAHMYIDNATMQLIKDPSQF 240 ESARKRRHKVTSIDKANVLQSSILWREIV+EI+ +YPDVEL+HMYIDNATMQLIKDPSQF Sbjct: 181 ESARKRRHKVTSIDKANVLQSSILWREIVSEISKQYPDVELSHMYIDNATMQLIKDPSQF 240 Query: 241 DVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIA 300 DVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIA Sbjct: 241 DVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIA 300 Query: 301 QILSLALLLRYSLDADDAACAIERAINRALEEGIRTGDLARGAAAVSTDEMGDIIARYVA 360 QILSLALLLRYSLDAD AA AIE AINRALEEG+RTGDLARGAAAVSTDEMGDIIARYVA Sbjct: 301 QILSLALLLRYSLDADSAATAIENAINRALEEGVRTGDLARGAAAVSTDEMGDIIARYVA 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: 559 Number of extensions: 10 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 BWI76_RS04675 BWI76_RS04675 (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.10519.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-172 558.7 0.0 2.6e-172 558.6 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS04675 BWI76_RS04675 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS04675 BWI76_RS04675 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 558.6 0.0 2.6e-172 2.6e-172 1 348 [. 6 354 .. 6 355 .. 0.99 Alignments for each domain: == domain 1 score: 558.6 bits; conditional E-value: 2.6e-172 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgav 71 +iavLpGDgiGpev+++alkvL+av++rf+++++++++++GG aid++g+Plp+ t+++c++ada+L+g+v lcl|FitnessBrowser__Koxy:BWI76_RS04675 6 HIAVLPGDGIGPEVMNQALKVLEAVRHRFDMRITTSQHDVGGIAIDRQGTPLPQSTVEGCEQADAILFGSV 76 69********************************************************************* PP TIGR00169 72 GGpkWdnlprdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfG 140 GGpkW++lp+ +Pe+ +LL+lrk+++lf+nLrPakl+++Le+++pl+++i+ +g+D+++vreLtgGiYfG lcl|FitnessBrowser__Koxy:BWI76_RS04675 77 GGPKWEHLPPAEQPERgALLPLRKHFKLFSNLRPAKLYQGLEEFCPLRADIAaNGFDILCVRELTGGIYFG 147 ****************88*********************************989***************** PP TIGR00169 141 epkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPd 211 +pk+re++++++ka+dte+Y++ eieria++afe+arkrr+kvts+DkanvL+ss+lWr++v+ei k+yPd lcl|FitnessBrowser__Koxy:BWI76_RS04675 148 QPKGREGSGQHEKAFDTEVYHRFEIERIAHIAFESARKRRHKVTSIDKANVLQSSILWREIVSEISKQYPD 218 *********************************************************************** PP TIGR00169 212 velehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapd 282 vel+h+yiDna+mqL+k+P+q+dv+++snlfGDilsDe+++itGs+G+LPsasl+++g++l+ep++gsapd lcl|FitnessBrowser__Koxy:BWI76_RS04675 219 VELSHMYIDNATMQLIKDPSQFDVLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPD 289 *********************************************************************** PP TIGR00169 283 iagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348 iagk+ianpia+ils+alllrysl+++ aa+aie+a++++leeg rt dla+ a +avst+e+++ lcl|FitnessBrowser__Koxy:BWI76_RS04675 290 IAGKNIANPIAQILSLALLLRYSLDADSAATAIENAINRALEEGVRTGDLARGA-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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 8.30 // [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