Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate PP_1988 PP_1988 3-isopropylmalate dehydrogenase
Query= BRENDA::P96197 (360 letters) >FitnessBrowser__Putida:PP_1988 Length = 360 Score = 524 bits (1350), Expect = e-153 Identities = 284/376 (75%), Positives = 307/376 (81%), Gaps = 32/376 (8%) Query: 1 MSKQILVLPGDGIGPEIMAEAVKVLQLANEKYQLGFVLGYDELGGAAVDKYGVPLADETL 60 MSKQIL+LPGDGIGPEIMAEAVKVL+LAN+K+QLGF L +D +GGAA+DK+GVPLADETL Sbjct: 1 MSKQILILPGDGIGPEIMAEAVKVLELANDKFQLGFSLAHDVIGGAAIDKHGVPLADETL 60 Query: 61 ERARR------------RCHPARRRRRSEMG----RHRPGHPPGARPAENPFATGPVRQP 104 ERAR+ + R R E G R + G RPA Sbjct: 61 ERARKADAVLLGAVGGPKWDKIERDIRPERGLLKIRSQLGLFANLRPA------------ 108 Query: 105 APGVLYPQLAEASTLRPEVVAGLDILIVRELTGGIYFGAPRESRLLANGERMAYDTLPYS 164 +LYPQLA+AS+L+PE+V+GLDILIVRELTGGIYFGAPR R L GER AYDTLPYS Sbjct: 109 ---ILYPQLADASSLKPEIVSGLDILIVRELTGGIYFGAPRGQRELEGGERQAYDTLPYS 165 Query: 165 ESEIRRIAKVGFDMARVRGKKLCSVDKANVLASSQLWRAVVEEVAKDYPDVVLSHMYVDN 224 ESE+RRIA+VGFDMARVRGKKLCSVDKANVLASSQLWR VVE+VAKDYPDV LSHMYVDN Sbjct: 166 ESEVRRIARVGFDMARVRGKKLCSVDKANVLASSQLWREVVEDVAKDYPDVELSHMYVDN 225 Query: 225 AAMQLVRAPKQFDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGSRR 284 AAMQLVRAPKQFDV+VTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGS Sbjct: 226 AAMQLVRAPKQFDVMVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGS-A 284 Query: 285 PDIAGKGIANPLATILSVSMMLRYSFGQVEAANAIEQAVSKVLDQGLRTGDIWSEGCRKV 344 PDIAG GIANPLATILSVSMMLRYSF Q AA AIE+AVS VLDQGLRTGDI+SEGCRKV Sbjct: 285 PDIAGLGIANPLATILSVSMMLRYSFNQSAAAEAIEKAVSLVLDQGLRTGDIFSEGCRKV 344 Query: 345 GTAEMGDAVVAALATL 360 GT EMGDAVVAAL L Sbjct: 345 GTQEMGDAVVAALRNL 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: 473 Number of extensions: 11 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: 1 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 PP_1988 PP_1988 (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.22704.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-165 535.2 0.0 3.9e-165 535.0 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_1988 PP_1988 3-isopropylmalate dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1988 PP_1988 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 535.0 0.0 3.9e-165 3.9e-165 1 348 [. 4 352 .. 4 353 .. 0.99 Alignments for each domain: == domain 1 score: 535.0 bits; conditional E-value: 3.9e-165 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpk 75 +i +LpGDgiGpe++aea+kvL+ +++f+l + + iGGaaid++g Pl++etl+ +++adavLlgavGGpk lcl|FitnessBrowser__Putida:PP_1988 4 QILILPGDGIGPEIMAEAVKVLELANDKFQLGFSLAHDVIGGAAIDKHGVPLADETLERARKADAVLLGAVGGPK 78 589************************************************************************ PP TIGR00169 76 WdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereeaee 150 Wd+ rd+rPe+gLLk+r +l+lfanLrPa l+++L ++s+lk+eiv+g+D+++vreLtgGiYfG p++++e e lcl|FitnessBrowser__Putida:PP_1988 79 WDKIERDIRPERGLLKIRSQLGLFANLRPAILYPQLADASSLKPEIVSGLDILIVRELTGGIYFGAPRGQRELEG 153 *********************************************************************999887 PP TIGR00169 151 .ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaam 224 e++a+dt Y+++e++riarv+f +ar r kk++svDkanvL+ss+lWr++ve++ak+yPdvel+h+y+Dnaam lcl|FitnessBrowser__Putida:PP_1988 154 gERQAYDTLPYSESEVRRIARVGFDMARVRGKKLCSVDKANVLASSQLWREVVEDVAKDYPDVELSHMYVDNAAM 228 8************************************************************************** PP TIGR00169 225 qLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaa 299 qLv++P+q+dv+vt+n+fGDilsDeas++tGs+G+LPsasl + ++++ep hgsapdiag gianp+a+ils++ lcl|FitnessBrowser__Putida:PP_1988 229 QLVRAPKQFDVMVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGSAPDIAGLGIANPLATILSVS 303 *************************************************************************** PP TIGR00169 300 lllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348 ++lrys+n++ aaeaie+av+ vl++g rt d+ se++ +v+t+e+++ lcl|FitnessBrowser__Putida:PP_1988 304 MMLRYSFNQSAAAEAIEKAVSLVLDQGLRTGDIFSEGCRKVGTQEMGDA 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: 8.77 // [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