Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate Pf6N2E2_66 3-isopropylmalate dehydrogenase (EC 1.1.1.85)
Query= BRENDA::P96197 (360 letters) >lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_66 3-isopropylmalate dehydrogenase (EC 1.1.1.85) Length = 360 Score = 521 bits (1342), Expect = e-152 Identities = 280/372 (75%), Positives = 308/372 (82%), Gaps = 24/372 (6%) Query: 1 MSKQILVLPGDGIGPEIMAEAVKVLQLANEKYQLGFVLGYDELGGAAVDKYGVPLADETL 60 MSKQIL+LPGDGIGPEIMAEAVKVL+LAN+KY LGF L +D +GGAA+DK+GVPLADETL Sbjct: 1 MSKQILILPGDGIGPEIMAEAVKVLELANDKYGLGFELSHDVIGGAAIDKHGVPLADETL 60 Query: 61 ERARR------------RCHPARRRRRSEMGRHRPGHPPGARPAENPFATGPVRQPAPGV 108 +RAR + R R E G + G G +R P + Sbjct: 61 DRARAADAVLLGAVGGPKWDKIERDIRPERGLLKIRAQLGL--------FGNLR---PAI 109 Query: 109 LYPQLAEASTLRPEVVAGLDILIVRELTGGIYFGAPRESRLLANGERMAYDTLPYSESEI 168 LYPQLA+AS+L+PE+V+GLDILIVRELTGGIYFGAPR +R L NGER AYDTLPYSESEI Sbjct: 110 LYPQLADASSLKPEIVSGLDILIVRELTGGIYFGAPRGTRELENGERQAYDTLPYSESEI 169 Query: 169 RRIAKVGFDMARVRGKKLCSVDKANVLASSQLWRAVVEEVAKDYPDVVLSHMYVDNAAMQ 228 RRIA+VGFDMARVRGKKLCSVDKANVLASSQLWR VVE+VAKDYPD+ LSHMYVDNAAMQ Sbjct: 170 RRIARVGFDMARVRGKKLCSVDKANVLASSQLWREVVEQVAKDYPDIELSHMYVDNAAMQ 229 Query: 229 LVRAPKQFDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGSRRPDIA 288 LVRAPKQFDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDA+NKGMYEPCHGS PDIA Sbjct: 230 LVRAPKQFDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDANNKGMYEPCHGS-APDIA 288 Query: 289 GKGIANPLATILSVSMMLRYSFGQVEAANAIEQAVSKVLDQGLRTGDIWSEGCRKVGTAE 348 G+GIANPLATILSVSMMLRYSF +AA+AIE+AVS VLDQGLRTGDIWS+GC KVGT + Sbjct: 289 GQGIANPLATILSVSMMLRYSFNLNDAADAIEKAVSVVLDQGLRTGDIWSQGCTKVGTQQ 348 Query: 349 MGDAVVAALATL 360 MGDAVVAAL L Sbjct: 349 MGDAVVAALRNL 360 Lambda K H 0.318 0.135 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: 476 Number of extensions: 6 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 360 Length of database: 360 Length adjustment: 29 Effective length of query: 331 Effective length of database: 331 Effective search space: 109561 Effective search space used: 109561 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 Pf6N2E2_66 (3-isopropylmalate dehydrogenase (EC 1.1.1.85))
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.16099.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-166 539.5 0.0 1.9e-166 539.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_66 3-isopropylmalate dehydrogenase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_66 3-isopropylmalate dehydrogenase (EC 1.1.1.85) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 539.3 0.0 1.9e-166 1.9e-166 1 348 [. 4 352 .. 4 353 .. 0.99 Alignments for each domain: == domain 1 score: 539.3 bits; conditional E-value: 1.9e-166 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadav 66 +i +LpGDgiGpe++aea+kvL+ +++++l +e ++ iGGaaid++g Pl++etl+ +++adav lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_66 4 QILILPGDGIGPEIMAEAVKVLELANDKYGLGFELSHDVIGGAAIDKHGVPLADETLDRARAADAV 69 589*************************************************************** PP TIGR00169 67 LlgavGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvre 132 LlgavGGpkWd+ rd+rPe+gLLk+r +l+lf nLrPa l+++L ++s+lk+eiv+g+D+++vre lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_66 70 LLGAVGGPKWDKIERDIRPERGLLKIRAQLGLFGNLRPAILYPQLADASSLKPEIVSGLDILIVRE 135 ****************************************************************** PP TIGR00169 133 LtgGiYfGepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrl 197 LtgGiYfG p++++e e+ e++a+dt Y+++ei+riarv+f +ar r kk++svDkanvL+ss+l lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_66 136 LTGGIYFGAPRGTRELENgERQAYDTLPYSESEIRRIARVGFDMARVRGKKLCSVDKANVLASSQL 201 ***************9999*********************************************** PP TIGR00169 198 WrktveeiakeyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsa 263 Wr++ve++ak+yPd+el+h+y+DnaamqLv++P+q+dv+vt+n+fGDilsDeas++tGs+G+LPsa lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_66 202 WREVVEQVAKDYPDIELSHMYVDNAAMQLVRAPKQFDVIVTDNMFGDILSDEASMLTGSIGMLPSA 267 ****************************************************************** PP TIGR00169 264 slsskglalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrt 329 sl + ++++ep hgsapdiag+gianp+a+ils++++lrys+nl++aa+aie+av+ vl++g rt lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_66 268 SLDANNKGMYEPCHGSAPDIAGQGIANPLATILSVSMMLRYSFNLNDAADAIEKAVSVVLDQGLRT 333 ****************************************************************** PP TIGR00169 330 edlaseattavstkeveee 348 d+ s+++t+v+t+++++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_66 334 GDIWSQGCTKVGTQQMGDA 352 ****************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (360 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: 8.23 // [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