Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate HSERO_RS17185 HSERO_RS17185 2-isopropylmalate synthase
Query= SwissProt::P42455 (616 letters) >FitnessBrowser__HerbieS:HSERO_RS17185 Length = 567 Score = 618 bits (1593), Expect = 0.0 Identities = 318/581 (54%), Positives = 402/581 (69%), Gaps = 25/581 (4%) Query: 35 SMPVNRYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMF 94 S P +Y PF I LPDRTWP K I P W + DLRDGNQALI+PM+ ERK R F Sbjct: 4 SNPAAKYRPFPA----IDLPDRTWPSKVINTPPIWMSTDLRDGNQALIEPMNAERKLRFF 59 Query: 95 ELLVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACE 154 ELL++ G KEIEVGFPSASQTDFDFVR++I + IPDDVTI VL Q+RE LIRRT E+ E Sbjct: 60 ELLLKTGLKEIEVGFPSASQTDFDFVRKLIVENRIPDDVTIIVLTQSREELIRRTIESLE 119 Query: 155 GAKNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPES 214 GAK IVH YNS + R +VF M + ++K +A L+K + P T WR++YSPES Sbjct: 120 GAKKAIVHLYNSVAPAFRKIVFNMSREEIKNIAVTGTRLVKELTDARPGTEWRFEYSPES 179 Query: 215 FTGTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDS 274 F+ TE++++KE+ DAV E +PE +I+NLPSTVE TPNVYAD IEWM RNL R S Sbjct: 180 FSTTELDFSKEICDAVCETWGASPERKVILNLPSTVECATPNVYADQIEWMCRNLKDRAS 239 Query: 275 IILSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQ 334 I+S+HPHNDRGT V +AEL MAGADR+EGCLFGNGERTGNV LVTLALN+ TQGV+P Sbjct: 240 TIISVHPHNDRGTAVASAELAVMAGADRVEGCLFGNGERTGNVDLVTLALNLYTQGVNPG 299 Query: 335 LDFTDIRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGAS 394 LDF+DI +R VE CNQ+ V RHPY GDLVFTAFSGSHQDA+ KG AK QP Sbjct: 300 LDFSDIDVVRQVVEECNQIPVHPRHPYVGDLVFTAFSGSHQDAIKKGF----AKQQP--- 352 Query: 395 STEVSWEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRS 454 D WEVPYLPIDP D+GR Y+AVIRVNSQSGKGG+AY+++ ++GL +PR Sbjct: 353 ----------DAIWEVPYLPIDPADLGRSYDAVIRVNSQSGKGGMAYLLEQEYGLALPRR 402 Query: 455 MQVEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASIT 514 +Q+EFS +Q DA G E+ + + IF EYLER P A R+ ++ E +I Sbjct: 403 LQIEFSRAIQREADATGKEIAASDIHAIFQREYLERVEPYVYRAHRMSEDSSKAESINIE 462 Query: 515 AELIHNGKDVTVDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYVLAEV 574 +++ NG+ VTV G GNGP+ A+ +A LG+D+++ ++++HA +G DA+AA+Y+ + Sbjct: 463 VDIVRNGQPVTVRGSGNGPIDAFVHA---LGLDIKLMDFHEHAIGAGADAKAASYIELRL 519 Query: 575 NGRKV-WGVGIAGSITYASLKAVTSAVNRALDVNHEAVLAG 614 N +GVGI +I AS KAV SAVNR + ++ A AG Sbjct: 520 NEAPTGFGVGIDANIVTASFKAVLSAVNRQIAISESANQAG 560 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: 944 Number of extensions: 30 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: 567 Length adjustment: 37 Effective length of query: 579 Effective length of database: 530 Effective search space: 306870 Effective search space used: 306870 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 HSERO_RS17185 HSERO_RS17185 (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.27260.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-247 808.8 0.0 1.5e-247 808.6 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS17185 HSERO_RS17185 2-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS17185 HSERO_RS17185 2-isopropylmalate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 808.6 0.0 1.5e-247 1.5e-247 1 563 [. 6 550 .. 6 551 .. 0.96 Alignments for each domain: == domain 1 score: 808.6 bits; conditional E-value: 1.5e-247 TIGR00970 1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievg 68 p+ ky+pf ai l++r+wp kvi+ p w+s+dlrdGnqali+pm++erk r+f+ll++ G keievg lcl|FitnessBrowser__HerbieS:HSERO_RS17185 6 PAAKYRPFPAIDLPDRTWPSKVINTPPIWMSTDLRDGNQALIEPMNAERKLRFFELLLKTGLKEIEVG 73 889***************************************************************** PP TIGR00970 69 fpsasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvf 136 fpsasqtdfdfvr++i ++ ipddvti vltqsreeli+rt+e+l+Gakkaivhlyn++++ fr++vf lcl|FitnessBrowser__HerbieS:HSERO_RS17185 74 FPSASQTDFDFVRKLIVENRIPDDVTIIVLTQSREELIRRTIESLEGAKKAIVHLYNSVAPAFRKIVF 141 **************99999************************************************* PP TIGR00970 137 rasreevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerp 204 ++sree+ ++av g++lv++l++ +++t+w+feyspesfs tel+f++e+c+av e + ++er lcl|FitnessBrowser__HerbieS:HSERO_RS17185 142 NMSREEIKNIAVTGTRLVKELTDA---RPGTEWRFEYSPESFSTTELDFSKEICDAVCETWGASPERK 206 *******************99975...689************************************** PP TIGR00970 205 iifnlpatvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfG 272 +i+nlp+tve atpnvyad+ie++++n+ +r + i+s+hphndrGtava+ael ++aGadr+eGclfG lcl|FitnessBrowser__HerbieS:HSERO_RS17185 207 VILNLPSTVECATPNVYADQIEWMCRNLKDRASTIISVHPHNDRGTAVASAELAVMAGADRVEGCLFG 274 ******************************************************************** PP TIGR00970 273 nGertGnvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqda 340 nGertGnvdlvtlalnlytqGv+p ldfsd+d +++vve+cn+ipvh+rhpy Gdlv+tafsGshqda lcl|FitnessBrowser__HerbieS:HSERO_RS17185 275 NGERTGNVDLVTLALNLYTQGVNPGLDFSDIDVVRQVVEECNQIPVHPRHPYVGDLVFTAFSGSHQDA 342 ******************************************************************** PP TIGR00970 341 ikkGldaldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqi 408 ikkG+ ++ d++w+vpylp+dp d+gr y+avirvnsqsGkGG+ay+l +++Gl lprrlqi lcl|FitnessBrowser__HerbieS:HSERO_RS17185 343 IKKGFAK-----QQPDAIWEVPYLPIDPADLGRSYDAVIRVNSQSGKGGMAYLLEQEYGLALPRRLQI 405 ****964.....456889************************************************** PP TIGR00970 409 efssvvkdiadskGkelsskeisdlfkeeyllnveqlerislvdyaveddGteskvitavvki..kge 474 efs++++ ad+ Gke+ +++i +f+ eyl ve++ ++ + ++d +++++i+ v+i +g+ lcl|FitnessBrowser__HerbieS:HSERO_RS17185 406 EFSRAIQREADATGKEIAASDIHAIFQREYLERVEPYV-YRAHRM--SEDSSKAESINIEVDIvrNGQ 470 *******************************9888774.455544..445555666666666644899 PP TIGR00970 475 kkdieGsGnGplsalvdaladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvG 542 + + GsGnGp+ a+v+al +d++++d+ eha+g+G dakaasy+el +++a t +GvG lcl|FitnessBrowser__HerbieS:HSERO_RS17185 471 PVTVRGSGNGPIDAFVHALG----LDIKLMDFHEHAIGAGADAKAASYIELRLNEAP-----TGFGVG 529 99****************95....7889************************99887.....89**** PP TIGR00970 543 iaedvtsaslravlsavnraa 563 i++++ +as++avlsavnr + lcl|FitnessBrowser__HerbieS:HSERO_RS17185 530 IDANIVTASFKAVLSAVNRQI 550 ******************965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (564 nodes) Target sequences: 1 (567 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: 11.84 // [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