Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 351385 BT1857 3-isopropylmalate dehydrogenase (NCBI ptt file)
Query= BRENDA::P54354 (353 letters) >FitnessBrowser__Btheta:351385 Length = 353 Score = 679 bits (1751), Expect = 0.0 Identities = 335/353 (94%), Positives = 341/353 (96%) Query: 1 MDFKIAVLAGDGIGPEISVQGVEVMSAVCEKFGHKVNYEYAICGADAIDKVGDPFPEETY 60 MDFKIAVLAGDGIGPEISVQGV+VMSAVCEKFGHKV+YEYAICGADAIDKVGDPFPEETY Sbjct: 1 MDFKIAVLAGDGIGPEISVQGVDVMSAVCEKFGHKVSYEYAICGADAIDKVGDPFPEETY 60 Query: 61 RVCKNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCLVHKSP 120 VCKNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCL+HKSP Sbjct: 61 EVCKNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCLIHKSP 120 Query: 121 LRAELVEGADFLCIRELTGGMYFGEKYQDNDKAYDTNMYTRPEIERILKVGFEYAMKRRK 180 LRAELVE ADF+CIRELTGGMYFGEKYQDNDKAYDTN YTRPEIERILKV FEYAMKRRK Sbjct: 121 LRAELVENADFICIRELTGGMYFGEKYQDNDKAYDTNYYTRPEIERILKVAFEYAMKRRK 180 Query: 181 HLTVVDKANVLASSRLWRQIAQEMAPQYPEVTTDYMFVDNAAMKMIQEPKFFDVMVTENT 240 HLTVVDKANVLASSRLWRQIAQEMAP YPEVTTDYMFVDNAAMKMIQEP FFDVMVTENT Sbjct: 181 HLTVVDKANVLASSRLWRQIAQEMAPNYPEVTTDYMFVDNAAMKMIQEPAFFDVMVTENT 240 Query: 241 FGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLF 300 FGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLF Sbjct: 241 FGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLF 300 Query: 301 EYFDCKAEGALIRKAVDASLDANVRTPEIQVEGGEKFGTKEVGAWIVDYIRKA 353 EYFDCK EGALIRKAVDASLD NVRTPEIQV G K+GTKEVG WIVDYI+KA Sbjct: 301 EYFDCKEEGALIRKAVDASLDENVRTPEIQVADGAKYGTKEVGQWIVDYIKKA 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: 626 Number of extensions: 20 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: 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 351385 BT1857 (3-isopropylmalate dehydrogenase (NCBI ptt file))
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.7397.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-132 427.6 0.0 1.9e-132 427.5 0.0 1.0 1 lcl|FitnessBrowser__Btheta:351385 BT1857 3-isopropylmalate dehydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:351385 BT1857 3-isopropylmalate dehydrogenase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 427.5 0.0 1.9e-132 1.9e-132 1 347 [. 4 344 .. 4 346 .. 0.98 Alignments for each domain: == domain 1 score: 427.5 bits; conditional E-value: 1.9e-132 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkW 76 kiavL+GDgiGpe+ + ++v+ av e+f++k+ +e+a G aid++g+P+peet + ck+adavL++avG pk+ lcl|FitnessBrowser__Btheta:351385 4 KIAVLAGDGIGPEISVQGVDVMSAVCEKFGHKVSYEYAICGADAIDKVGDPFPEETYEVCKNADAVLFSAVGDPKF 79 79************************************************************************** PP TIGR00169 77 dnlpr.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereeaeee 151 dn p+ +vrPe+gLL++rk+l+lfan+rP++ fk L++ spl++e+v++ D++++reLtgG+YfGe+ ++++ lcl|FitnessBrowser__Btheta:351385 80 DNDPTaKVRPEQGLLAMRKKLGLFANIRPVQTFKCLIHKSPLRAELVENADFICIRELTGGMYFGEKYQDND---- 151 **986379**********************************************************999888.... PP TIGR00169 152 kkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLv 227 ka+dt Yt++eieri +vafe a+krrk++t vDkanvL+ssrlWr++++e+a +yP+v+ + +++Dnaam+++ lcl|FitnessBrowser__Btheta:351385 152 -KAYDTNYYTRPEIERILKVAFEYAMKRRKHLTVVDKANVLASSRLWRQIAQEMAPNYPEVTTDYMFVDNAAMKMI 226 .8************************************************************************** PP TIGR00169 228 ksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllr 303 ++P+ +dv+vt+n fGDil De svi+Gs+GlLPsas + + + +fep+hgs p+ g +ianp+a+ils+a+l + lcl|FitnessBrowser__Btheta:351385 227 QEPAFFDVMVTENTFGDILTDEGSVISGSMGLLPSASTG-ESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLFE 301 **************************************9.8899******************************99 PP TIGR00169 304 yslnleeaaeaieaavkkvleegkrtedlaseattavstkevee 347 y ++ +e+ + i +av+ l+e rt++++ ++++ +tkev++ lcl|FitnessBrowser__Btheta:351385 302 Y-FDCKEEGALIRKAVDASLDENVRTPEIQVADGAKYGTKEVGQ 344 8.89999999***********************9******9986 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: 6.83 // [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