Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate BPHYT_RS33900 BPHYT_RS33900 3-isopropylmalate dehydrogenase
Query= SwissProt::Q56268 (358 letters) >FitnessBrowser__BFirm:BPHYT_RS33900 Length = 355 Score = 400 bits (1029), Expect = e-116 Identities = 213/358 (59%), Positives = 266/358 (74%), Gaps = 10/358 (2%) Query: 3 KIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLA 62 KIA+ GDGIGPEIV A +VL+ + + L E VGGA +A PLP ++L LA Sbjct: 2 KIAVLPGDGIGPEIVKEAVKVLNVLGEKFEL----EEAPVGGAGYEAKGHPLPDSTLALA 57 Query: 63 MAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPE 122 ADA++ GAVG ++D+ A RPEQ +L LRK L L+AN RPA +PQL AS L+ E Sbjct: 58 KEADAILFGAVGDWKYDSLERALRPEQAILGLRKHLQLFANFRPAICYPQLTGASSLKEE 117 Query: 123 LVRDVDILVVRELTGDIYFGQPRGLE-----VIDGKRRGFNTMVYDEDEIRRIAHVAFRA 177 +V +DIL+VREL GDIYFG PRG+ + +G + GF+TM Y E E+RRIAHVAF+A Sbjct: 118 IVSGLDILIVRELNGDIYFGAPRGVRSSPDGLFEGAKEGFDTMRYSEPEVRRIAHVAFQA 177 Query: 178 AQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDV 237 AQ R+K+L SVDKANVLET++ WR+V+ +V+++Y DV LSHMYVDNAAMQL++AP FDV Sbjct: 178 AQKRQKKLTSVDKANVLETSQFWRDVMIDVSKEYADVELSHMYVDNAAMQLVKAPKAFDV 237 Query: 238 LLTGNMFGDILSDEASQLTGSIGMLPSASLGE-GRAMYEPIHGSAPDIAGQDKANPLATI 296 ++TGNMFGDILSDEA+ LTGSIGMLPSASL + + +YEP HGSAPDIAG+ ANPLATI Sbjct: 238 VVTGNMFGDILSDEAAMLTGSIGMLPSASLDKNNKGLYEPSHGSAPDIAGKGVANPLATI 297 Query: 297 LSVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354 LS AMMLR+SLN A R+E+AV++VL+QG RT DI PG +GT AMG AVV AL Sbjct: 298 LSAAMMLRYSLNKAEQADRIESAVKKVLEQGYRTGDILTPGCKQVGTVAMGDAVVAAL 355 Lambda K H 0.320 0.137 0.396 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: 391 Number of extensions: 10 Number of successful extensions: 4 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: 358 Length of database: 355 Length adjustment: 29 Effective length of query: 329 Effective length of database: 326 Effective search space: 107254 Effective search space used: 107254 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 BPHYT_RS33900 BPHYT_RS33900 (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.23412.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-150 487.6 0.0 1.1e-150 487.4 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS33900 BPHYT_RS33900 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS33900 BPHYT_RS33900 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 487.4 0.0 1.1e-150 1.1e-150 1 348 [. 2 350 .. 2 351 .. 0.97 Alignments for each domain: == domain 1 score: 487.4 bits; conditional E-value: 1.1e-150 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 kiavLpGDgiGpe+v+ea+kvL+++ e+ +e eea +GGa +a+g+Plp+ tl+ +keada+L+ga lcl|FitnessBrowser__BFirm:BPHYT_RS33900 2 KIAVLPGDGIGPEIVKEAVKVLNVLGEK----FELEEAPVGGAGYEAKGHPLPDSTLALAKEADAILFGA 67 79*********************99885....6789********************************** PP TIGR00169 71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfG 140 vG k+d+l r rPe+++L lrk+l+lfan+rPa +++L+ +s+lkeeiv+g+D+++vreL g iYfG lcl|FitnessBrowser__BFirm:BPHYT_RS33900 68 VGDWKYDSLERALRPEQAILGLRKHLQLFANFRPAICYPQLTGASSLKEEIVSGLDILIVRELNGDIYFG 137 ********************************************************************** PP TIGR00169 141 epkereea....ee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveei 205 p++ + + e k+++dt++Y+++e++ria+vaf++a+kr+kk+tsvDkanvLe+s++Wr+++ ++ lcl|FitnessBrowser__BFirm:BPHYT_RS33900 138 APRGVRSSpdglFEgAKEGFDTMRYSEPEVRRIAHVAFQAAQKRQKKLTSVDKANVLETSQFWRDVMIDV 207 ***988752222124899**************************************************** PP TIGR00169 206 akeyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfep 275 key dvel+h+y+DnaamqLvk+P+ +dvvvt+n+fGDilsDea+++tGs+G+LPsasl ++ ++l+ep lcl|FitnessBrowser__BFirm:BPHYT_RS33900 208 SKEYADVELSHMYVDNAAMQLVKAPKAFDVVVTGNMFGDILSDEAAMLTGSIGMLPSASLDKNNKGLYEP 277 ********************************************************************** PP TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkev 345 hgsapdiagkg+anp+a+ilsaa++lrysln+ e+a++ie+avkkvle+g+rt d+ + ++++v+t ++ lcl|FitnessBrowser__BFirm:BPHYT_RS33900 278 SHGSAPDIAGKGVANPLATILSAAMMLRYSLNKAEQADRIESAVKKVLEQGYRTGDILTPGCKQVGTVAM 347 *******************************************************************999 PP TIGR00169 346 eee 348 ++ lcl|FitnessBrowser__BFirm:BPHYT_RS33900 348 GDA 350 876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (355 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.48 // [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