Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_106714781.1 CU100_RS01435 3-isopropylmalate dehydrogenase
Query= BRENDA::P24404 (370 letters) >NCBI__GCF_003010935.1:WP_106714781.1 Length = 370 Score = 604 bits (1557), Expect = e-177 Identities = 300/370 (81%), Positives = 334/370 (90%) Query: 1 MTVRSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDAD 60 M + L LLPGDGIGPEAM EVRK+I YMNS + F + EGLVGGSAYDAHG AIS+AD Sbjct: 1 MASKKLLLLPGDGIGPEAMAEVRKIIGYMNSELKSEFVLDEGLVGGSAYDAHGAAISEAD 60 Query: 61 MEKALAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASS 120 M KALAADA+LFGAVGGPKWD VPY+ RPEAGLLRLRKD+ELFANLRPAICYPALA +SS Sbjct: 61 MAKALAADAVLFGAVGGPKWDSVPYDVRPEAGLLRLRKDMELFANLRPAICYPALADSSS 120 Query: 121 LKPELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFEL 180 LK E+VEGLDILIVRELTGGVYFGEPK+I DLGNGQKRGIDTQ+YDT+EIERI+ VAFEL Sbjct: 121 LKKEIVEGLDILIVRELTGGVYFGEPKEIRDLGNGQKRGIDTQVYDTYEIERISGVAFEL 180 Query: 181 ARSRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFD 240 AR+R N+V SMEKRNVMKSGVLWN+VVT TH KY DV+LEHMLADAGGMQLVR PKQFD Sbjct: 181 ARTRGNKVTSMEKRNVMKSGVLWNEVVTATHKTKYSDVKLEHMLADAGGMQLVRWPKQFD 240 Query: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSI 300 VIVTDNLFGDMLSD+AAMLTGSLGMLPSASLGAPDAKTGKRKA+YEPVHGSAPDIAG Sbjct: 241 VIVTDNLFGDMLSDIAAMLTGSLGMLPSASLGAPDAKTGKRKALYEPVHGSAPDIAGTGT 300 Query: 301 ANPIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDA 360 ANPIAMIASFAMCLRYSFNM+ EA +LE+A+A VLD G+RTADIMA+G ++GT++MGDA Sbjct: 301 ANPIAMIASFAMCLRYSFNMIAEADRLESAVAGVLDDGLRTADIMAEGKTRIGTAEMGDA 360 Query: 361 VLAEFKALSA 370 +LA+F+AL+A Sbjct: 361 ILAKFRALAA 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: 572 Number of extensions: 12 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_106714781.1 CU100_RS01435 (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.2880579.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-136 438.9 0.0 7.3e-136 438.7 0.0 1.0 1 NCBI__GCF_003010935.1:WP_106714781.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106714781.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.7 0.0 7.3e-136 7.3e-136 2 348 .. 6 360 .. 5 361 .. 0.99 Alignments for each domain: == domain 1 score: 438.7 bits; conditional E-value: 7.3e-136 TIGR00169 2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGp 74 + +LpGDgiGpe +ae k++ ++ + + ++ +e l+GG a da+g ++e+ ++++ +adavL+gavGGp NCBI__GCF_003010935.1:WP_106714781.1 6 LLLLPGDGIGPEAMAEVRKIIGYMNSELKSEFVLDEGLVGGSAYDAHGAAISEADMAKALAADAVLFGAVGGP 78 679********************************************************************** PP TIGR00169 75 kWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkeree 147 kWd+ p dvrPe gLL+lrk+++lfanLrPa +++L ++s+lk+eiv+g+D+++vreLtgG+YfGepke+++ NCBI__GCF_003010935.1:WP_106714781.1 79 KWDSVPYDVRPEAGLLRLRKDMELFANLRPAICYPALADSSSLKKEIVEGLDILIVRELTGGVYFGEPKEIRD 151 ************************************************************************9 PP TIGR00169 148 aee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak.eyPdvelehly 218 ++ +k+++dt++Y ++eieri vafelar+r +kvts++k nv++s+ lW ++v++++k +y dv+leh++ NCBI__GCF_003010935.1:WP_106714781.1 152 LGNgQKRGIDTQVYDTYEIERISGVAFELARTRGNKVTSMEKRNVMKSGVLWNEVVTATHKtKYSDVKLEHML 224 9999********************************************************99*********** PP TIGR00169 219 iDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss......kglalfepvhgsapdiag 285 D+ mqLv+ P+q+dv+vt+nlfGD+lsD+a+++tGslG+LPsasl+ k++al+epvhgsapdiag NCBI__GCF_003010935.1:WP_106714781.1 225 ADAGGMQLVRWPKQFDVIVTDNLFGDMLSDIAAMLTGSLGMLPSASLGApdaktgKRKALYEPVHGSAPDIAG 297 ************************************************999999999**************** PP TIGR00169 286 kgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348 g anpia+i s a+ lrys+n+ +a+++e+av+ vl++g rt+d++ e+ t+ +t+e+++ NCBI__GCF_003010935.1:WP_106714781.1 298 TGTANPIAMIASFAMCLRYSFNMIAEADRLESAVAGVLDDGLRTADIMAEGKTRIGTAEMGDA 360 ************************************************************987 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 25.26 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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