Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate Pf6N2E2_3170 2-isopropylmalate synthase (EC 2.3.3.13)
Query= SwissProt::P42455 (616 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 Length = 559 Score = 612 bits (1578), Expect = e-179 Identities = 317/572 (55%), Positives = 403/572 (70%), Gaps = 31/572 (5%) Query: 37 PVNRYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFEL 96 P ++Y F I+LPDRTWP K IT AP WC+ DLRDGNQ+LI+PM +K R ++ Sbjct: 7 PSSKYRAFPT----INLPDRTWPSKTITAAPIWCSSDLRDGNQSLIEPMDAVKKLRFWKT 62 Query: 97 LVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGA 156 LV +G KEIE FP+ASQTDFDFVR +IE+G IPDD TIQVL QARE LI RTFE+ GA Sbjct: 63 LVAVGVKEIEASFPAASQTDFDFVRTLIEEGHIPDDTTIQVLTQAREDLIARTFESLRGA 122 Query: 157 KNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFT 216 K IVH YN+T R +VF DK VK++A +AA+L A P+T W+++YSPE+F+ Sbjct: 123 KKAIVHLYNATCPSFRRIVFNQDKEGVKEIAVNAAKLFVKYAAQQPETQWQFEYSPETFS 182 Query: 217 GTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSII 276 TE+E+AKEV DAV+EV +PTPE +I+NLP+TVE+ TPN+YAD IEW HRN++RRDS++ Sbjct: 183 ATELEFAKEVCDAVIEVWNPTPERKVILNLPATVEVATPNIYADQIEWFHRNISRRDSVL 242 Query: 277 LSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLD 336 +SLH HNDRGTGV A ELG MAGADR+EGCLFGNGERTGNV LVT+ALN+ TQGV+P+LD Sbjct: 243 ISLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGERTGNVDLVTVALNLYTQGVNPELD 302 Query: 337 FTDIRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASST 396 F+DI +R VE CNQ+ V RHPY GDLV TAFSGSHQDA+ KG Sbjct: 303 FSDIDGVRKVVEECNQIPVHPRHPYVGDLVHTAFSGSHQDAIRKGFA------------- 349 Query: 397 EVSWEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQ 456 +Q D WEVPYLPIDP D+GR YEAVIRVNSQSGKGG+AY+++ ++G+ +PR MQ Sbjct: 350 ----QQKSDGLWEVPYLPIDPADIGRSYEAVIRVNSQSGKGGIAYLLEQEYGISLPRRMQ 405 Query: 457 VEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAE 516 +EFS VVQ TD G E+ ++ + + EYL+ P ++ R+ Q EN ++++ E Sbjct: 406 IEFSQVVQRETDRLGLEMTAQQIHALLQREYLQANTPYALVSHRL---QEENGNSAVEVE 462 Query: 517 LIHNGKDVT---VDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYVLAE 573 + G+ T G+GNG L A L I VEI +YN+HA +G +A+AAAY+ Sbjct: 463 VASKGQGETNLHWRGKGNGALEALVAGLP---IPVEIMDYNEHAIGAGTNAKAAAYIELR 519 Query: 574 VNG-RKVWGVGIAGSITYASLKAVTSAVNRAL 604 VNG R V GVGI +IT AS KA+ SA+NR+L Sbjct: 520 VNGERAVHGVGIDENITTASFKALFSALNRSL 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: 938 Number of extensions: 33 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 Pf6N2E2_3170 (2-isopropylmalate synthase (EC 2.3.3.13))
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.14071.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-245 800.0 0.0 6.8e-245 799.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 2-isopropylmalate synthase (EC 2 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 2-isopropylmalate synthase (EC 2.3.3.13) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 799.8 0.0 6.8e-245 6.8e-245 1 562 [. 7 550 .. 7 552 .. 0.95 Alignments for each domain: == domain 1 score: 799.8 bits; conditional E-value: 6.8e-245 TIGR00970 1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfke 64 ps+ky+ f +i+l++r+wp k it ap w+s dlrdGnq+li+pm++ +k r++k lv +G ke lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 7 PSSKYRAFPTINLPDRTWPSKTITAAPIWCSSDLRDGNQSLIEPMDAVKKLRFWKTLVAVGVKE 70 99************************************************************** PP TIGR00970 65 ievgfpsasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynats 128 ie +fp+asqtdfdfvr +ie+g ipdd tiqvltq+re+li rt+e+l+Gakkaivhlynat lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 71 IEASFPAASQTDFDFVRTLIEEGHIPDDTTIQVLTQAREDLIARTFESLRGAKKAIVHLYNATC 134 **************************************************************** PP TIGR00970 129 dlfrevvfrasreevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevcea 192 + fr++vf++++e v ++av+++kl vk aa+++et+w+feyspe+fs telefa+evc+a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 135 PSFRRIVFNQDKEGVKEIAVNAAKL---FVKYAAQQPETQWQFEYSPETFSATELEFAKEVCDA 195 **********************665...6889999***************************** PP TIGR00970 193 vkeviepteerpiifnlpatvevatpnvyadsieylstniaerekvilslhphndrGtavaaae 256 v ev++pt+er +i+nlpatvevatpn+yad+ie++ +ni+ r++v++slh+hndrGt+vaa+e lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 196 VIEVWNPTPERKVILNLPATVEVATPNIYADQIEWFHRNISRRDSVLISLHTHNDRGTGVAATE 259 **************************************************************** PP TIGR00970 257 lGllaGadrieGclfGnGertGnvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvhe 320 lGl+aGadr+eGclfGnGertGnvdlvt+alnlytqGv+p+ldfsd+d +++vve+cn+ipvh+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 260 LGLMAGADRVEGCLFGNGERTGNVDLVTVALNLYTQGVNPELDFSDIDGVRKVVEECNQIPVHP 323 **************************************************************** PP TIGR00970 321 rhpygGdlvvtafsGshqdaikkGldaldkkkaaadtlwkvpylpldpkdvgreyeavirvnsq 384 rhpy Gdlv+tafsGshqdai+kG+ ++ +d lw+vpylp+dp d+gr yeavirvnsq lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 324 RHPYVGDLVHTAFSGSHQDAIRKGFAQQK-----SDGLWEVPYLPIDPADIGRSYEAVIRVNSQ 382 *************************7654.....4789************************** PP TIGR00970 385 sGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdlfkeeyllnveqleri 448 sGkGG+ay+l +++G++lprr+qiefs+vv+ +d G e+++++i l++ eyl ++ ++ + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 383 SGKGGIAYLLEQEYGISLPRRMQIEFSQVVQRETDRLGLEMTAQQIHALLQREYLQANTPYALV 446 ********************************************************88888777 PP TIGR00970 449 slvdyaveddGteskvitavvkikge.kkdieGsGnGplsalvdaladllnvdvavadysehal 511 s + e++G+ + ++ k +ge + + G GnG l alv l + v+++dy+eha+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 447 SHRL--QEENGNSAVEVEVASKGQGEtNLHWRGKGNGALEALVAGLP----IPVEIMDYNEHAI 504 6554..46677444444444443333134589*********998874....788********** PP TIGR00970 512 gsGddakaasyvelsvrrasdaekatvwGvGiaedvtsaslravlsavnra 562 g+G +akaa+y+el v+ + v GvGi+e++t+as++a++sa+nr lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3170 505 GAGTNAKAAAYIELRVNGER-----AVHGVGIDENITTASFKALFSALNRS 550 **************998766.....799*********************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: 00:00:00.03 # Mc/sec: 10.07 // [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