Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate GFF4515 PS417_23110 2-isopropylmalate synthase
Query= SwissProt::P42455 (616 letters) >FitnessBrowser__WCS417:GFF4515 Length = 559 Score = 603 bits (1556), Expect = e-177 Identities = 315/572 (55%), Positives = 396/572 (69%), Gaps = 31/572 (5%) Query: 37 PVNRYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFEL 96 P ++Y F I +PDRTWP K IT AP WC+ DLRDGNQ+LI+PM +K R ++ Sbjct: 7 PSSKYRAFPT----IDIPDRTWPSKTITEAPIWCSSDLRDGNQSLIEPMDAVKKLRFWKT 62 Query: 97 LVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGA 156 LV +G KEIE FP+ASQTDFDFVR +IE IP+D TIQVL Q RE LI RTFE+ GA Sbjct: 63 LVAVGVKEIEASFPAASQTDFDFVRTLIEDNHIPEDTTIQVLTQGREDLIARTFESLRGA 122 Query: 157 KNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFT 216 K IVH YN+TS R +VF DK +K +A +AA+L A P+T W ++YSPE+F+ Sbjct: 123 KKAIVHLYNATSPSFRRIVFNQDKEGIKAIAVNAAKLFVKYAAQQPETQWTFEYSPETFS 182 Query: 217 GTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSII 276 TE+E+AKEV DAV+EV +PTPE+ MI+NLP+TVE TPN+YAD IEW R++NRRDS+I Sbjct: 183 ATELEFAKEVCDAVIEVWNPTPEHKMILNLPATVECATPNIYADQIEWFGRHINRRDSVI 242 Query: 277 LSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLD 336 +SLH HNDRGTGV A ELG MAGADR+EGCLFGNGERTGNV LVT+ALNM TQG+DPQLD Sbjct: 243 ISLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGERTGNVDLVTVALNMYTQGLDPQLD 302 Query: 337 FTDIRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASST 396 F+DI +R VE CNQ++V RHPY GDLV TAFSGSHQDA+ KG Sbjct: 303 FSDIDGVRKVVEECNQIQVHPRHPYVGDLVHTAFSGSHQDAIRKGFS------------- 349 Query: 397 EVSWEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQ 456 +Q D WEVPYLPIDP D+GR YEAVIRVNSQSGKGG+AY+++ ++ + +PR MQ Sbjct: 350 ----QQKDDALWEVPYLPIDPADIGRSYEAVIRVNSQSGKGGIAYLLEQEYDISLPRRMQ 405 Query: 457 VEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAE 516 +EFS VVQ TD G E+ + ++ + EYL+ P ++ R+ Q EN ++ + E Sbjct: 406 IEFSQVVQAETDRVGLEMTAPQIYALLQREYLQANTPYALVSHRL---QEENGNSFVEVE 462 Query: 517 LIHNGKDVT---VDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYVLAE 573 + G+ T G+GNG L A L I VEI +YN+HA +G +A+AAAY+ Sbjct: 463 VSGKGQGETNLHWKGKGNGALEALVAGLP---IGVEIMDYNEHAIGAGTNAKAAAYIELR 519 Query: 574 VNG-RKVWGVGIAGSITYASLKAVTSAVNRAL 604 VNG R V GVGI +IT AS KA+ SA+NR+L Sbjct: 520 VNGERPVHGVGIDENITTASFKALFSALNRSL 551 Lambda K H 0.316 0.133 0.390 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: 945 Number of extensions: 39 Number of successful extensions: 4 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: 616 Length of database: 559 Length adjustment: 37 Effective length of query: 579 Effective length of database: 522 Effective search space: 302238 Effective search space used: 302238 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 53 (25.0 bits)
Align candidate GFF4515 PS417_23110 (2-isopropylmalate synthase)
to HMM TIGR00970 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))
# 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/TIGR00970.hmm # target sequence database: /tmp/gapView.16124.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00970 [M=564] Accession: TIGR00970 Description: leuA_yeast: 2-isopropylmalate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-240 784.6 0.0 3.2e-240 784.4 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF4515 PS417_23110 2-isopropylmalate sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF4515 PS417_23110 2-isopropylmalate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 784.4 0.0 3.2e-240 3.2e-240 1 562 [. 7 550 .. 7 552 .. 0.95 Alignments for each domain: == domain 1 score: 784.4 bits; conditional E-value: 3.2e-240 TIGR00970 1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfpsasqt 75 ps+ky+ f +i +++r+wp k it ap w+s dlrdGnq+li+pm++ +k r++k lv +G keie +fp+asqt lcl|FitnessBrowser__WCS417:GFF4515 7 PSSKYRAFPTIDIPDRTWPSKTITEAPIWCSSDLRDGNQSLIEPMDAVKKLRFWKTLVAVGVKEIEASFPAASQT 81 99************************************************************************* PP TIGR00970 76 dfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasreevlalaveg 150 dfdfvr +ie++ ip+d tiqvltq re+li rt+e+l+Gakkaivhlynats+ fr++vf++++e + a+av++ lcl|FitnessBrowser__WCS417:GFF4515 82 DFDFVRTLIEDNHIPEDTTIQVLTQGREDLIARTFESLRGAKKAIVHLYNATSPSFRRIVFNQDKEGIKAIAVNA 156 *************************************************************************** PP TIGR00970 151 sklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatvevatpnvyadsi 225 +kl vk aa+++et+w+feyspe+fs telefa+evc+av ev++pt+e+ +i+nlpatve atpn+yad+i lcl|FitnessBrowser__WCS417:GFF4515 157 AKL---FVKYAAQQPETQWTFEYSPETFSATELEFAKEVCDAVIEVWNPTPEHKMILNLPATVECATPNIYADQI 228 665...6889999************************************************************** PP TIGR00970 226 eylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnvdlvtlalnlytqGvspnldf 300 e++ ++i r++vi+slh+hndrGt+vaa+elGl+aGadr+eGclfGnGertGnvdlvt+aln+ytqG++p+ldf lcl|FitnessBrowser__WCS417:GFF4515 229 EWFGRHINRRDSVIISLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGERTGNVDLVTVALNMYTQGLDPQLDF 303 *************************************************************************** PP TIGR00970 301 sdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldkkkaaadtlwkvpylpldpkdvgrey 375 sd+d +++vve+cn+i+vh+rhpy Gdlv+tafsGshqdai+kG+ ++ d+lw+vpylp+dp d+gr y lcl|FitnessBrowser__WCS417:GFF4515 304 SDIDGVRKVVEECNQIQVHPRHPYVGDLVHTAFSGSHQDAIRKGFSQQKD-----DALWEVPYLPIDPADIGRSY 373 *********************************************86643.....579***************** PP TIGR00970 376 eavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdlfkeeyllnveqlerisl 450 eavirvnsqsGkGG+ay+l +++ ++lprr+qiefs+vv+ +d G e+++ +i+ l++ eyl ++ ++ +s lcl|FitnessBrowser__WCS417:GFF4515 374 EAVIRVNSQSGKGGIAYLLEQEYDISLPRRMQIEFSQVVQAETDRVGLEMTAPQIYALLQREYLQANTPYALVSH 448 *****************************************************************8888877765 PP TIGR00970 451 vdyaveddGteskvitavvkikgekkd...ieGsGnGplsalvdaladllnvdvavadysehalgsGddakaasy 522 + e++G+ ++ v kg+ +G GnG l alv l + v+++dy+eha+g+G +akaa+y lcl|FitnessBrowser__WCS417:GFF4515 449 RL--QEENGN--SFVEVEVSGKGQGETnlhWKGKGNGALEALVAGLP----IGVEIMDYNEHAIGAGTNAKAAAY 515 54..466773..44455555444422223489*********998874....779********************* PP TIGR00970 523 velsvrrasdaekatvwGvGiaedvtsaslravlsavnra 562 +el v+ + v GvGi+e++t+as++a++sa+nr lcl|FitnessBrowser__WCS417:GFF4515 516 IELRVNGER-----PVHGVGIDENITTASFKALFSALNRS 550 ***998877.....589*********************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (564 nodes) Target sequences: 1 (559 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 12.72 // [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