Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate SMc04405 SMc04405 3-isopropylmalate dehydrogenase
Query= BRENDA::P24404 (370 letters) >FitnessBrowser__Smeli:SMc04405 Length = 370 Score = 652 bits (1681), Expect = 0.0 Identities = 324/370 (87%), Positives = 347/370 (93%) Query: 1 MTVRSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDAD 60 MTVR+LFLLPGDGIGPEAM EVRK+I YMN+ +AGF EGLVGGSAYDAHG AIS+ D Sbjct: 1 MTVRNLFLLPGDGIGPEAMAEVRKIIAYMNAERDAGFVTDEGLVGGSAYDAHGAAISEGD 60 Query: 61 MEKALAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASS 120 M KALAADA+LFGAVGGPKWD VPYE RPEAGLLRLRKDLELFANLRPAICYPALA ASS Sbjct: 61 MAKALAADAVLFGAVGGPKWDAVPYEVRPEAGLLRLRKDLELFANLRPAICYPALANASS 120 Query: 121 LKPELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFEL 180 LKPELVEGLDILIVRELTGGVYFGEPK+I+DLGNGQKRGIDTQ+YDT+EIERIA VAFEL Sbjct: 121 LKPELVEGLDILIVRELTGGVYFGEPKEIVDLGNGQKRGIDTQVYDTYEIERIAGVAFEL 180 Query: 181 ARSRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFD 240 AR+R+NRVCSMEKRNVMKSGVLWNQVVTETH AKY DVQLEHMLADAGGMQLVR+PKQFD Sbjct: 181 ARTRNNRVCSMEKRNVMKSGVLWNQVVTETHKAKYSDVQLEHMLADAGGMQLVRQPKQFD 240 Query: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSI 300 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKA+YEPVHGSAPDIAG + Sbjct: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKALYEPVHGSAPDIAGTGV 300 Query: 301 ANPIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDA 360 ANPIAMIASFAMCLRYSFN+V EA LE AIANVLD+GIRT DIMA+GCR+VGT++MGDA Sbjct: 301 ANPIAMIASFAMCLRYSFNLVKEADDLEKAIANVLDQGIRTGDIMAEGCRKVGTAEMGDA 360 Query: 361 VLAEFKALSA 370 +LAEFK+LSA Sbjct: 361 ILAEFKSLSA 370 Lambda K H 0.319 0.135 0.387 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: 615 Number of extensions: 15 Number of successful extensions: 1 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: 370 Length of database: 370 Length adjustment: 30 Effective length of query: 340 Effective length of database: 340 Effective search space: 115600 Effective search space used: 115600 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 SMc04405 SMc04405 (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.29101.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-137 444.6 0.0 1.3e-137 444.4 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc04405 SMc04405 3-isopropylmalate dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc04405 SMc04405 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 444.4 0.0 1.3e-137 1.3e-137 3 349 .] 7 361 .. 5 361 .. 0.99 Alignments for each domain: == domain 1 score: 444.4 bits; conditional E-value: 1.3e-137 TIGR00169 3 avLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWd 77 +LpGDgiGpe +ae k++ ++ + + + ++e l+GG a da+g ++e ++++ +adavL+gavGGpkWd lcl|FitnessBrowser__Smeli:SMc04405 7 FLLPGDGIGPEAMAEVRKIIAYMNAERDAGFVTDEGLVGGSAYDAHGAAISEGDMAKALAADAVLFGAVGGPKWD 81 68************************************************************************* PP TIGR00169 78 nlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereeaee.e 151 + p +vrPe gLL+lrk+l+lfanLrPa +++L ++s+lk+e+v+g+D+++vreLtgG+YfGepke+ + ++ + lcl|FitnessBrowser__Smeli:SMc04405 82 AVPYEVRPEAGLLRLRKDLELFANLRPAICYPALANASSLKPELVEGLDILIVRELTGGVYFGEPKEIVDLGNgQ 156 *********************************************************************99999* PP TIGR00169 152 kkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak.eyPdvelehlyiDnaamq 225 k+++dt++Y ++eieria vafelar+r+++v+s++k nv++s+ lW ++v+e++k +y dv+leh++ D+ mq lcl|FitnessBrowser__Smeli:SMc04405 157 KRGIDTQVYDTYEIERIAGVAFELARTRNNRVCSMEKRNVMKSGVLWNQVVTETHKaKYSDVQLEHMLADAGGMQ 231 ********************************************************9****************** PP TIGR00169 226 LvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss......kglalfepvhgsapdiagkgianpiaa 294 Lv++P+q+dv+vt+nlfGD+lsD a+++tGslG+LPsasl+ k++al+epvhgsapdiag g+anpia+ lcl|FitnessBrowser__Smeli:SMc04405 232 LVRQPKQFDVIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGApdaktgKRKALYEPVHGSAPDIAGTGVANPIAM 306 *****************************************999999999************************* PP TIGR00169 295 ilsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveeel 349 i s a+ lrys+nl ++a+ +e+a+++vl++g+rt d++ e++ +v+t+e+++ + lcl|FitnessBrowser__Smeli:SMc04405 307 IASFAMCLRYSFNLVKEADDLEKAIANVLDQGIRTGDIMAEGCRKVGTAEMGDAI 361 ***************************************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (370 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 9.06 // [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