Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate HSERO_RS16500 HSERO_RS16500 3-isopropylmalate dehydrogenase
Query= SwissProt::Q56268 (358 letters) >FitnessBrowser__HerbieS:HSERO_RS16500 Length = 356 Score = 403 bits (1036), Expect = e-117 Identities = 218/358 (60%), Positives = 261/358 (72%), Gaps = 10/358 (2%) Query: 3 KIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLA 62 KIAI GDGIGPEIV A +VL+A+D+ + VGGA +A PLP +L+LA Sbjct: 2 KIAILPGDGIGPEIVNEAVRVLNALDEKFEM----ETAPVGGAGYEAHGHPLPDGTLKLA 57 Query: 63 MAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPE 122 ADA++ GAVG ++D A RPEQ +L LRK L L+AN RPA +P+L AS L+PE Sbjct: 58 KEADAILFGAVGDWKYDKLERALRPEQAILGLRKHLQLFANFRPAICYPELTGASSLKPE 117 Query: 123 LVRDVDILVVRELTGDIYFGQPRGLEV-----IDGKRRGFNTMVYDEDEIRRIAHVAFRA 177 LV ++DIL+VREL GDIYFGQPRG+ G R GF+TM Y E EIRRIAHVAF+A Sbjct: 118 LVANLDILIVRELNGDIYFGQPRGMREAPDGPFKGAREGFDTMRYSEPEIRRIAHVAFQA 177 Query: 178 AQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDV 237 A R K+LCSVDKANVLET + W+++VTEV ++YPDV LSHMYVDNAAMQL++AP FDV Sbjct: 178 AAKRGKRLCSVDKANVLETFQFWKDIVTEVGKEYPDVELSHMYVDNAAMQLVKAPKNFDV 237 Query: 238 LLTGNMFGDILSDEASQLTGSIGMLPSASL-GEGRAMYEPIHGSAPDIAGQDKANPLATI 296 ++TGNMFGDILSD A+ LTGSIGMLPSASL + +YEP HGSAPDIAG+ ANPLATI Sbjct: 238 IVTGNMFGDILSDAAAMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGRGIANPLATI 297 Query: 297 LSVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354 LS AMMLR SLN A R+E AV++VL QGLRTADI G + T+ MG AVV AL Sbjct: 298 LSAAMMLRFSLNKAEQADRIENAVKKVLAQGLRTADIYEEGCTKVNTQQMGEAVVKAL 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: 407 Number of extensions: 16 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: 356 Length adjustment: 29 Effective length of query: 329 Effective length of database: 327 Effective search space: 107583 Effective search space used: 107583 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 HSERO_RS16500 HSERO_RS16500 (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.696364.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-150 485.8 0.0 3.9e-150 485.7 0.0 1.0 1 FitnessBrowser__HerbieS:HSERO_RS16500 Domain annotation for each sequence (and alignments): >> FitnessBrowser__HerbieS:HSERO_RS16500 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.7 0.0 3.9e-150 3.9e-150 1 348 [. 2 350 .. 2 351 .. 0.97 Alignments for each domain: == domain 1 score: 485.7 bits; conditional E-value: 3.9e-150 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavG 72 kia+LpGDgiGpe+v+ea++vL+a++e+ +e+e+a +GGa +a+g+Plp+ tlk +keada+L+gavG FitnessBrowser__HerbieS:HSERO_RS16500 2 KIAILPGDGIGPEIVNEAVRVLNALDEK----FEMETAPVGGAGYEAHGHPLPDGTLKLAKEADAILFGAVG 69 79***********************996....567899********************************** PP TIGR00169 73 GpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepke 144 k+d+l r rPe+++L lrk+l+lfan+rPa +++L+ +s+lk+e+v ++D+++vreL g iYfG+p++ FitnessBrowser__HerbieS:HSERO_RS16500 70 DWKYDKLERALRPEQAILGLRKHLQLFANFRPAICYPELTGASSLKPELVANLDILIVRELNGDIYFGQPRG 141 ************************************************************************ PP TIGR00169 145 reeaee.....ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPd 211 ++ea + ++++dt++Y+++ei+ria+vaf++a+kr k+++svDkanvLe+ ++W+++v+e+ keyPd FitnessBrowser__HerbieS:HSERO_RS16500 142 MREAPDgpfkgAREGFDTMRYSEPEIRRIAHVAFQAAAKRGKRLCSVDKANVLETFQFWKDIVTEVGKEYPD 213 99974322324789********************************************************** PP TIGR00169 212 velehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdi 283 vel+h+y+DnaamqLvk+P+++dv+vt+n+fGDilsD a+++tGs+G+LPsasl + ++l+ep hgsapdi FitnessBrowser__HerbieS:HSERO_RS16500 214 VELSHMYVDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGMLPSASLDANNKGLYEPSHGSAPDI 285 ************************************************************************ PP TIGR00169 284 agkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348 ag+gianp+a+ilsaa++lr sln+ e+a++ie+avkkvl++g rt+d+++e++t+v t++++e FitnessBrowser__HerbieS:HSERO_RS16500 286 AGRGIANPLATILSAAMMLRFSLNKAEQADRIENAVKKVLAQGLRTADIYEEGCTKVNTQQMGEA 350 **************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (356 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: 10.80 // [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