Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_012040686.1 BBTA_RS01645 3-isopropylmalate dehydrogenase
Query= BRENDA::P24404 (370 letters) >NCBI__GCF_000015165.1:WP_012040686.1 Length = 370 Score = 541 bits (1394), Expect = e-158 Identities = 271/370 (73%), Positives = 308/370 (83%) Query: 1 MTVRSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDAD 60 M L LLPGDGIGPE M EV++LI ++N A F EGLVGG+AYDAHG +IS+AD Sbjct: 1 MATHKLLLLPGDGIGPEVMAEVKRLIGWLNGKGLASFETEEGLVGGAAYDAHGASISEAD 60 Query: 61 MEKALAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASS 120 M+KA AADAI+FGAVGGPKWDGVPYE RPEAGLLRLRKDL LFANLRPA+CYPALA ASS Sbjct: 61 MDKAKAADAIIFGAVGGPKWDGVPYEVRPEAGLLRLRKDLGLFANLRPAVCYPALADASS 120 Query: 121 LKPELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFEL 180 LK E+VEGLDI+IVRELTGGVYFGEPK I DLGNGQKR +DTQ+YDT+EIERIA VAF+L Sbjct: 121 LKREIVEGLDIMIVRELTGGVYFGEPKTITDLGNGQKRAVDTQVYDTYEIERIARVAFDL 180 Query: 181 ARSRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFD 240 AR R N+V SMEKRNVMKSGVLWN+VVT H +YKDV LEH LAD+GGM LV+ PK FD Sbjct: 181 ARKRRNKVTSMEKRNVMKSGVLWNEVVTAVHNREYKDVTLEHQLADSGGMNLVKYPKMFD 240 Query: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSI 300 VIVTDNLFGDMLSD+AAMLTGSLGMLPSASLG DAKT KR+A+YEPVHGSAPDIAGK + Sbjct: 241 VIVTDNLFGDMLSDIAAMLTGSLGMLPSASLGEVDAKTHKRRALYEPVHGSAPDIAGKGL 300 Query: 301 ANPIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDA 360 ANPIAM+ SF M LRYSF++ A KL+AAIA VL G+RTADI A+G T+ MG+A Sbjct: 301 ANPIAMLTSFGMALRYSFDLGALADKLDAAIAAVLASGLRTADIKAEGSTPASTAQMGEA 360 Query: 361 VLAEFKALSA 370 ++ E + L+A Sbjct: 361 IIKELEKLTA 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: 503 Number of extensions: 11 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 WP_012040686.1 BBTA_RS01645 (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.19441.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-138 447.2 0.0 2.2e-138 447.0 0.0 1.0 1 lcl|NCBI__GCF_000015165.1:WP_012040686.1 BBTA_RS01645 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015165.1:WP_012040686.1 BBTA_RS01645 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 447.0 0.0 2.2e-138 2.2e-138 2 349 .] 6 361 .. 5 361 .. 0.99 Alignments for each domain: == domain 1 score: 447.0 bits; conditional E-value: 2.2e-138 TIGR00169 2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 + +LpGDgiGpev+ae + + ++ + ++e+ee l+GGaa da+g ++e+ ++++k+ada+++ga lcl|NCBI__GCF_000015165.1:WP_012040686.1 6 LLLLPGDGIGPEVMAEVKRLIGWLNGKGLASFETEEGLVGGAAYDAHGASISEADMDKAKAADAIIFGA 74 679****************************************************************** PP TIGR00169 71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYf 139 vGGpkWd p +vrPe gLL+lrk+l+lfanLrPa +++L ++s+lk+eiv+g+D+++vreLtgG+Yf lcl|NCBI__GCF_000015165.1:WP_012040686.1 75 VGGPKWDGVPYEVRPEAGLLRLRKDLGLFANLRPAVCYPALADASSLKREIVEGLDIMIVRELTGGVYF 143 ********************************************************************* PP TIGR00169 140 Gepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak 207 Gepk +++ ++ +k+a+dt++Y ++eieriarvaf larkrr+kvts++k nv++s+ lW ++v+++++ lcl|NCBI__GCF_000015165.1:WP_012040686.1 144 GEPKTITDLGNgQKRAVDTQVYDTYEIERIARVAFDLARKRRNKVTSMEKRNVMKSGVLWNEVVTAVHN 212 *******99999*******************************************************99 PP TIGR00169 208 .eyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss......kg 269 ey dv+leh++ D+ m+Lvk P+ +dv+vt+nlfGD+lsD+a+++tGslG+LPsasl++ k+ lcl|NCBI__GCF_000015165.1:WP_012040686.1 213 rEYKDVTLEHQLADSGGMNLVKYPKMFDVIVTDNLFGDMLSDIAAMLTGSLGMLPSASLGEvdakthKR 281 9***************************************************************99999 PP TIGR00169 270 lalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseatt 338 al+epvhgsapdiagkg+anpia++ s + lrys++l a++++aa++ vl++g rt+d++ e++t lcl|NCBI__GCF_000015165.1:WP_012040686.1 282 RALYEPVHGSAPDIAGKGLANPIAMLTSFGMALRYSFDLGALADKLDAAIAAVLASGLRTADIKAEGST 350 9******************************************************************** PP TIGR00169 339 avstkeveeel 349 +st++++e + lcl|NCBI__GCF_000015165.1:WP_012040686.1 351 PASTAQMGEAI 361 *******9975 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.35 // [ok]
This GapMind analysis is from Apr 10 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