Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate Echvi_2062 Echvi_2062 3-isopropylmalate dehydrogenase
Query= BRENDA::P54354 (353 letters) >FitnessBrowser__Cola:Echvi_2062 Length = 353 Score = 416 bits (1070), Expect = e-121 Identities = 210/352 (59%), Positives = 263/352 (74%), Gaps = 5/352 (1%) Query: 5 IAVLAGDGIGPEISVQGVEVMSAVCEKFGHKVNYEYAICGADAIDKVGDPFPEETYRVCK 64 IA+L GDGIGPE+ Q V+V+ AV +KFGH + ++ A+ GA AID G+P+P+ET+ +C Sbjct: 3 IALLPGDGIGPEVIEQTVKVVKAVGKKFGHTITFKEAVVGAAAIDATGNPYPDETHEICL 62 Query: 65 NADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCLVHKSPLRAE 124 ADAVLF A+GDPK+DNDP AKVRPEQGLLAMRKKLGLF+N+RP TF L+HKSPL+ E Sbjct: 63 QADAVLFGAIGDPKYDNDPKAKVRPEQGLLAMRKKLGLFSNVRPTFTFPSLIHKSPLKKE 122 Query: 125 LVEGADFLCIRELTGGMYFGEKYQDND---KAYDTNMYTRPEIERILKVGFEYAMKRRKH 181 +EG D + +RELTGG+YFGE N+ KA+DTN+YT+ EI R+ ++GFE+A KRRK Sbjct: 123 RIEGTDLVFLRELTGGIYFGEPRGRNEQGTKAFDTNVYTKEEITRLARMGFEFAQKRRKL 182 Query: 182 LTVVDKANVLASSRLWRQIAQEMAPQYPEVTTDYMFVDNAAMKMIQEPKFFDVMVTENTF 241 LT VDKANVLA+SRLWR+ QE+ P+YP+V +Y FVD AM++IQ PK +DV++TEN F Sbjct: 183 LTCVDKANVLATSRLWRETVQELEPEYPDVKVEYEFVDAVAMRLIQWPKAYDVLITENLF 242 Query: 242 GDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLFE 301 GDILTDE SVISGSMGL+PSAS G +FEPIHGS+PQA G +IANPLA +LS AM+FE Sbjct: 243 GDILTDEASVISGSMGLMPSASLGTDVKLFEPIHGSYPQAAGKDIANPLATVLSAAMMFE 302 Query: 302 Y-FDCKAEGALIRKAVDASLDANVRTPEIQVEGGEKFGTKEVGAWIVDYIRK 352 Y FD K E I V+ SL V T +I E + T EVG W+ I K Sbjct: 303 YAFDLKDEAKAISDVVNLSLAEGVVTEDI-AEESKPSKTSEVGDWLAAQILK 353 Lambda K H 0.319 0.136 0.403 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: 432 Number of extensions: 14 Number of successful extensions: 2 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: 353 Length of database: 353 Length adjustment: 29 Effective length of query: 324 Effective length of database: 324 Effective search space: 104976 Effective search space used: 104976 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate Echvi_2062 Echvi_2062 (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.7210.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-145 468.0 0.0 1e-144 467.8 0.0 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2062 Echvi_2062 3-isopropylmalate deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2062 Echvi_2062 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 467.8 0.0 1e-144 1e-144 1 347 [. 2 345 .. 2 347 .. 0.98 Alignments for each domain: == domain 1 score: 467.8 bits; conditional E-value: 1e-144 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGp 74 +ia+LpGDgiGpev+++ +kv+kav ++f++ ++f+ea +G aaidatg+P p+et + c +adavL+ga+G p lcl|FitnessBrowser__Cola:Echvi_2062 2 NIALLPGDGIGPEVIEQTVKVVKAVGKKFGHTITFKEAVVGAAAIDATGNPYPDETHEICLQADAVLFGAIGDP 75 69************************************************************************ PP TIGR00169 75 kWdnlpr.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkeree 147 k+dn p+ +vrPe+gLL++rk+l+lf+n+rP+ f+sL++ splk+e ++g+Dlv +reLtgGiYfGep++r+e lcl|FitnessBrowser__Cola:Echvi_2062 76 KYDNDPKaKVRPEQGLLAMRKKLGLFSNVRPTFTFPSLIHKSPLKKERIEGTDLVFLRELTGGIYFGEPRGRNE 149 ****986379**************************************************************99 PP TIGR00169 148 aeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDn 221 + +ka+dt +Ytkeei r+ar++fe a+krrk +t vDkanvL++srlWr+tv+e+ eyPdv++e ++D+ lcl|FitnessBrowser__Cola:Echvi_2062 150 --QGTKAFDTNVYTKEEITRLARMGFEFAQKRRKLLTCVDKANVLATSRLWRETVQELEPEYPDVKVEYEFVDA 221 ..6899******************************************************************** PP TIGR00169 222 aamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaai 295 +am+L++ P+ +dv++t+nlfGDil Deasvi+Gs+Gl+Psasl+ + ++lfep+hgs p+ agk+ianp+a++ lcl|FitnessBrowser__Cola:Echvi_2062 222 VAMRLIQWPKAYDVLITENLFGDILTDEASVISGSMGLMPSASLG-TDVKLFEPIHGSYPQAAGKDIANPLATV 294 *********************************************.6789************************ PP TIGR00169 296 lsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkevee 347 lsaa++ +y+++l+++a+ai ++v+ l+eg ted+a+e+ + + t+ev++ lcl|FitnessBrowser__Cola:Echvi_2062 295 LSAAMMFEYAFDLKDEAKAISDVVNLSLAEGVVTEDIAEES-KPSKTSEVGD 345 **************************************999.8888888776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (353 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: 11.85 // [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