Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate AO356_21415 AO356_21415 3-isopropylmalate dehydrogenase
Query= BRENDA::P96197 (360 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_21415 Length = 360 Score = 521 bits (1341), 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 LYPQLADASSLKPEIVSGLDILIVRELTGGIYFGAPRGTRELDNGERQAYDTLPYSESEI 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: 480 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 AO356_21415 AO356_21415 (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.2540.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-166 538.9 0.0 2.8e-166 538.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21415 AO356_21415 3-isopropylmalate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21415 AO356_21415 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 538.7 0.0 2.8e-166 2.8e-166 1 348 [. 4 352 .. 4 353 .. 0.99 Alignments for each domain: == domain 1 score: 538.7 bits; conditional E-value: 2.8e-166 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackea 63 +i +LpGDgiGpe++aea+kvL+ +++++l +e ++ iGGaaid++g Pl++etl+ +++a lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21415 4 QILILPGDGIGPEIMAEAVKVLELANDKYGLGFELSHDVIGGAAIDKHGVPLADETLDRARAA 66 589************************************************************ PP TIGR00169 64 davLlgavGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvD 126 davLlgavGGpkWd+ rd+rPe+gLLk+r +l+lf nLrPa l+++L ++s+lk+eiv+g+D lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21415 67 DAVLLGAVGGPKWDKIERDIRPERGLLKIRAQLGLFGNLRPAILYPQLADASSLKPEIVSGLD 129 *************************************************************** PP TIGR00169 127 lvvvreLtgGiYfGepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDk 188 +++vreLtgGiYfG p++++e ++ e++a+dt Y+++ei+riarv+f +ar r kk++svDk lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21415 130 ILIVRELTGGIYFGAPRGTRELDNgERQAYDTLPYSESEIRRIARVGFDMARVRGKKLCSVDK 192 *******************999988************************************** PP TIGR00169 189 anvLessrlWrktveeiakeyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeas 251 anvL+ss+lWr++ve++ak+yPd+el+h+y+DnaamqLv++P+q+dv+vt+n+fGDilsDeas lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21415 193 ANVLASSQLWREVVEQVAKDYPDIELSHMYVDNAAMQLVRAPKQFDVIVTDNMFGDILSDEAS 255 *************************************************************** PP TIGR00169 252 vitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllryslnleeaaea 314 ++tGs+G+LPsasl + ++++ep hgsapdiag+gianp+a+ils++++lrys+nl++aa+a lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21415 256 MLTGSIGMLPSASLDANNKGMYEPCHGSAPDIAGQGIANPLATILSVSMMLRYSFNLNDAADA 318 *************************************************************** PP TIGR00169 315 ieaavkkvleegkrtedlaseattavstkeveee 348 ie+av+ vl++g rt d+ s+++t+v+t+++++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21415 319 IEKAVSVVLDQGLRTGDIWSQGCTKVGTQQMGDA 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.79 // [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