Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 3606650 Dshi_0081 3-isopropylmalate dehydrogenase (RefSeq)
Query= BRENDA::P24404 (370 letters) >FitnessBrowser__Dino:3606650 Length = 368 Score = 446 bits (1147), Expect = e-130 Identities = 235/368 (63%), Positives = 279/368 (75%), Gaps = 3/368 (0%) Query: 1 MTVRSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDAD 60 M+ SL +L GDGIGPE M EVRK+I++ + + F VSE LVGG+AYD HGV ++D Sbjct: 1 MSTASLLILAGDGIGPEVMAEVRKIIDWYGAKRDLAFDVSEDLVGGAAYDVHGVPLADET 60 Query: 61 MEKALAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASS 120 M KA A DA+L GAVGGPK+D + + +PE GLLRLRK+++LFANLRPA C+ ALA SS Sbjct: 61 MAKAQAVDAVLLGAVGGPKYDTLDFSLKPERGLLRLRKEMDLFANLRPAQCFDALADFSS 120 Query: 121 LKPELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFEL 180 LK ++V GLDI+IVRELT GVYFGEP+ I GN ++ GI+TQ Y EI R+A AFEL Sbjct: 121 LKKDIVAGLDIMIVRELTSGVYFGEPRGIHKEGN-ERVGINTQRYTESEIARVARSAFEL 179 Query: 181 ARSRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFD 240 A+ R N+VCSMEK NVM+SG+LW VVTE HAA+Y DV+L HM ADAG MQLVR PKQFD Sbjct: 180 AKKRGNKVCSMEKANVMESGILWRDVVTEIHAAEYADVELSHMYADAGAMQLVRAPKQFD 239 Query: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSI 300 VIVTDNLFGD+LSD AAMLTGSLGMLPSASLG P + G+ KA+YEPVHGSAPDIAG+ Sbjct: 240 VIVTDNLFGDLLSDAAAMLTGSLGMLPSASLGLP-MENGRPKALYEPVHGSAPDIAGQGK 298 Query: 301 ANPIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADG-CRQVGTSDMGD 359 ANP A I SFAM LRYSF+ EA +LEAA+ VL +GIRTAD+M G TS MGD Sbjct: 299 ANPCACILSFAMALRYSFDQGAEADRLEAAVNQVLAQGIRTADLMQAGDTAPASTSQMGD 358 Query: 360 AVLAEFKA 367 AV+A A Sbjct: 359 AVIAALDA 366 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: 448 Number of extensions: 14 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: 370 Length of database: 368 Length adjustment: 30 Effective length of query: 340 Effective length of database: 338 Effective search space: 114920 Effective search space used: 114920 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 3606650 Dshi_0081 (3-isopropylmalate dehydrogenase (RefSeq))
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.29293.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-144 467.4 0.0 1.6e-144 467.2 0.0 1.0 1 lcl|FitnessBrowser__Dino:3606650 Dshi_0081 3-isopropylmalate dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3606650 Dshi_0081 3-isopropylmalate dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 467.2 0.0 1.6e-144 1.6e-144 3 348 .. 7 359 .. 5 360 .. 0.97 Alignments for each domain: == domain 1 score: 467.2 bits; conditional E-value: 1.6e-144 TIGR00169 3 avLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWdnl 79 +L+GDgiGpev+ae k+++ + +l+++ +e l+GGaa d +g Pl++et+++++++davLlgavGGpk+d+l lcl|FitnessBrowser__Dino:3606650 7 LILAGDGIGPEVMAEVRKIIDWYGAKRDLAFDVSEDLVGGAAYDVHGVPLADETMAKAQAVDAVLLGAVGGPKYDTL 83 68*************************************************************************** PP TIGR00169 80 prdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereeaeeekkald 156 + +Pe+gLL+lrke+dlfanLrPa+ f++L ++s+lk++iv g+D+++vreLt+G+YfGep++++++++e+ +++ lcl|FitnessBrowser__Dino:3606650 84 DFSLKPERGLLRLRKEMDLFANLRPAQCFDALADFSSLKKDIVAGLDIMIVRELTSGVYFGEPRGIHKEGNERVGIN 160 ***************************************************************************** PP TIGR00169 157 tekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak.eyPdvelehlyiDnaamqLvksPeq 232 t++Yt++ei r+ar afela+kr +kv+s++kanv+es++lWr++v+ei+ ey dvel+h+y D+ amqLv++P+q lcl|FitnessBrowser__Dino:3606650 161 TQRYTESEIARVARSAFELAKKRGNKVCSMEKANVMESGILWRDVVTEIHAaEYADVELSHMYADAGAMQLVRAPKQ 237 *************************************************999************************* PP TIGR00169 233 ldvvvtsnlfGDilsDeasvitGslGlLPsaslss.....kglalfepvhgsapdiagkgianpiaailsaalllry 304 +dv+vt+nlfGD+lsD a+++tGslG+LPsasl+ + +al+epvhgsapdiag+g anp+a ils a+ lry lcl|FitnessBrowser__Dino:3606650 238 FDVIVTDNLFGDLLSDAAAMLTGSLGMLPSASLGLpmengRPKALYEPVHGSAPDIAGQGKANPCACILSFAMALRY 314 *********************************98777778899********************************* PP TIGR00169 305 slnleeaaeaieaavkkvleegkrtedlasea.ttavstkeveee 348 s+++ +a+++eaav++vl++g+rt+dl++ + t+ +st+++++ lcl|FitnessBrowser__Dino:3606650 315 SFDQGAEADRLEAAVNQVLAQGIRTADLMQAGdTAPASTSQMGDA 359 ***************************988652667888888775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (368 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.68 // [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