Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_011386420.1 AMB_RS20570 3-isopropylmalate dehydrogenase
Query= BRENDA::P24404 (370 letters) >NCBI__GCF_000009985.1:WP_011386420.1 Length = 369 Score = 429 bits (1103), Expect = e-125 Identities = 214/370 (57%), Positives = 277/370 (74%), Gaps = 1/370 (0%) Query: 1 MTVRSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDAD 60 M + L +LPGDGIG E M +VR++I++M F ++EGL+GG+AYD HG Sbjct: 1 MAAKKLLILPGDGIGVEVMAQVRRIIDWMGRKRKIEFEITEGLLGGAAYDVHGTPYPAET 60 Query: 61 MEKALAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASS 120 +E ALAADA+L GAVGGPKWD +P++ +PE GLL +RKD+ LFANLRPA ALA AS+ Sbjct: 61 LEAALAADAVLLGAVGGPKWDDLPFDKKPERGLLGIRKDMGLFANLRPATVLEALADAST 120 Query: 121 LKPELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFEL 180 LK E+V GLDI+I+RELTGG+YFG+P+ I L +G ++G +T +Y T EI+RI VAF+L Sbjct: 121 LKAEVVSGLDIMILRELTGGLYFGQPRGIDTLPDGTRKGYNTLVYTTPEIQRIGRVAFDL 180 Query: 181 ARSRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFD 240 AR R+ ++CS++K NV++ VLW + + + ++ DV+L HM D MQLVR PKQFD Sbjct: 181 ARKRNKKLCSVDKANVLECTVLWREEMIKLQKEEFPDVELTHMYVDNAAMQLVRNPKQFD 240 Query: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSI 300 V+VT+N+FGD+LSD AAMLTGSLGMLPSASLG DA+ GKRKA+YEPVHGSAPDIAGK + Sbjct: 241 VMVTENMFGDILSDCAAMLTGSLGMLPSASLGEADAQ-GKRKALYEPVHGSAPDIAGKDM 299 Query: 301 ANPIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDA 360 ANP+A I SFAMCLRYSF+M EA +E A+ NVL G+RTADIM G +V T+ MG+A Sbjct: 300 ANPLATIMSFAMCLRYSFDMAAEADLIETAVKNVLKGGLRTADIMQPGKAKVSTTVMGEA 359 Query: 361 VLAEFKALSA 370 V+ E L+A Sbjct: 360 VVRELDKLNA 369 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: 434 Number of extensions: 8 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: 370 Length of database: 369 Length adjustment: 30 Effective length of query: 340 Effective length of database: 339 Effective search space: 115260 Effective search space used: 115260 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_011386420.1 AMB_RS20570 (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.9834.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-150 486.3 0.0 2.8e-150 486.1 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386420.1 AMB_RS20570 3-isopropylmalate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386420.1 AMB_RS20570 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 486.1 0.0 2.8e-150 2.8e-150 2 348 .. 6 359 .. 5 360 .. 0.98 Alignments for each domain: == domain 1 score: 486.1 bits; conditional E-value: 2.8e-150 TIGR00169 2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 + +LpGDgiG ev+a+ ++++ + + ++++e e l+GGaa d +g+P p+etl+a+ +adavLlga lcl|NCBI__GCF_000009985.1:WP_011386420.1 6 LLILPGDGIGVEVMAQVRRIIDWMGRKRKIEFEITEGLLGGAAYDVHGTPYPAETLEAALAADAVLLGA 74 679****************************************************************** PP TIGR00169 71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYf 139 vGGpkWd+lp d++Pe+gLL +rk+++lfanLrPa++ ++L ++s+lk+e+v+g+D++++reLtgG+Yf lcl|NCBI__GCF_000009985.1:WP_011386420.1 75 VGGPKWDDLPFDKKPERGLLGIRKDMGLFANLRPATVLEALADASTLKAEVVSGLDIMILRELTGGLYF 143 ********************************************************************* PP TIGR00169 140 Gepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak 207 G+p++++ + ++k+++t +Yt++ei+ri rvaf larkr+kk++svDkanvLe + lWr+ + +++k lcl|NCBI__GCF_000009985.1:WP_011386420.1 144 GQPRGIDTLPDgTRKGYNTLVYTTPEIQRIGRVAFDLARKRNKKLCSVDKANVLECTVLWREEMIKLQK 212 ******9987779*************************************************9999988 PP TIGR00169 208 .eyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss.....kgl 270 e+Pdvel h+y+DnaamqLv++P+q+dv+vt+n+fGDilsD a+++tGslG+LPsasl++ k++ lcl|NCBI__GCF_000009985.1:WP_011386420.1 213 eEFPDVELTHMYVDNAAMQLVRNPKQFDVMVTENMFGDILSDCAAMLTGSLGMLPSASLGEadaqgKRK 281 8************************************************************99999999 PP TIGR00169 271 alfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseatta 339 al+epvhgsapdiagk++anp+a+i+s a+ lrys+++ +a+ ie+avk+vl+ g rt+d+++ + ++ lcl|NCBI__GCF_000009985.1:WP_011386420.1 282 ALYEPVHGSAPDIAGKDMANPLATIMSFAMCLRYSFDMAAEADLIETAVKNVLKGGLRTADIMQPGKAK 350 ********************************************************************* PP TIGR00169 340 vstkeveee 348 vst+ ++e lcl|NCBI__GCF_000009985.1:WP_011386420.1 351 VSTTVMGEA 359 ****99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (369 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: 9.30 // [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