Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate WP_013461086.1 SULKU_RS11215 2-isopropylmalate synthase
Query= SwissProt::P42455 (616 letters) >NCBI__GCF_000183725.1:WP_013461086.1 Length = 555 Score = 553 bits (1424), Expect = e-162 Identities = 282/566 (49%), Positives = 375/566 (66%), Gaps = 22/566 (3%) Query: 40 RYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFELLVQ 99 +Y P+ + LP+R WP K IT AP WC+VDLRDGNQALI PM+ ++K +F LL++ Sbjct: 8 KYRPYP----QVDLPNRIWPTKTITHAPIWCSVDLRDGNQALITPMNLDQKLSLFSLLLK 63 Query: 100 MGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGAKNV 159 +GFK IEVGFPSAS+ +FDF+R ++E+ +IPDDVT+QVLVQAREHLI +TFEA G K Sbjct: 64 LGFKNIEVGFPSASKVEFDFLRTLVEQKLIPDDVTVQVLVQAREHLIDKTFEALAGVKKA 123 Query: 160 IVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFTGTE 219 IVH YNSTS+ QR +VF ++ ++ LA + +++K A + D +YSPESFTGTE Sbjct: 124 IVHLYNSTSVAQRKIVFGKEQDEIIALALEGVDMVKERAAKH-DGEIMLEYSPESFTGTE 182 Query: 220 VEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSIILSL 279 +E+A + +AV + + E ++INLP+TVEM TPNVYAD IEWM R+L R+ +++S Sbjct: 183 LEFAARICNAVTDRWGISAERKVVINLPATVEMATPNVYADQIEWMSRHLTNREHVLIST 242 Query: 280 HPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLDFTD 339 H HNDRGT V A EL +AGADR+EG L NGERTGNV ++TLALNM TQGVDP+LDF+D Sbjct: 243 HTHNDRGTSVAATELALLAGADRVEGTLLSNGERTGNVDIITLALNMYTQGVDPELDFSD 302 Query: 340 IRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASSTEVS 399 + + VE C ++ ERHPY G+LV+TAFSGSHQDA+NKGL +K Sbjct: 303 LETVVRVVEECTDMKTHERHPYVGELVYTAFSGSHQDAINKGLAYQRSK----------- 351 Query: 400 WEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQVEF 459 D WEVPYLPIDP+DVGR+YE +IR+NSQSGKGGVAY+++ G +P+ M E Sbjct: 352 ----EDPFWEVPYLPIDPQDVGRNYEGIIRINSQSGKGGVAYVLEDKFGYSLPKKMHPEI 407 Query: 460 STVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAELIH 519 +VQ VTD G E+ S+ + DIF Y +E + V + + A E H Sbjct: 408 GRIVQQVTDEAGRELTSEEILDIFEKTYFGEPHDIEFVDYSVISESAKEHSAKCVLEYTH 467 Query: 520 NGKDVTVDGRGNGPLAAYANAL-EKLGIDVEIQEYNQHARTSGDDAEAAAYVLAEVNG-R 577 NGK + +G GNGP+ A NAL + + +I Y++H+R AEA AY+ + Sbjct: 468 NGKAIRSEGVGNGPIDACKNALMVEYSHNFKILSYSEHSRGELSSAEAVAYIEIQTESLE 527 Query: 578 KVWGVGIAGSITYASLKAVTSAVNRA 603 K +GVG IT AS+KA+ SA+NRA Sbjct: 528 KFFGVGCDNDITVASIKAMFSALNRA 553 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: 875 Number of extensions: 31 Number of successful extensions: 5 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: 555 Length adjustment: 37 Effective length of query: 579 Effective length of database: 518 Effective search space: 299922 Effective search space used: 299922 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 WP_013461086.1 SULKU_RS11215 (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.9533.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-227 740.6 0.0 6.7e-227 740.4 0.0 1.0 1 lcl|NCBI__GCF_000183725.1:WP_013461086.1 SULKU_RS11215 2-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183725.1:WP_013461086.1 SULKU_RS11215 2-isopropylmalate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 740.4 0.0 6.7e-227 6.7e-227 3 562 .. 7 553 .. 5 555 .] 0.96 Alignments for each domain: == domain 1 score: 740.4 bits; conditional E-value: 6.7e-227 TIGR00970 3 kkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfps 71 ky+p+ + l+nr wp k it+ap w+svdlrdGnqali pm+ ++k +f+ll+++Gfk+ievgfps lcl|NCBI__GCF_000183725.1:WP_013461086.1 7 GKYRPYPQVDLPNRIWPTKTITHAPIWCSVDLRDGNQALITPMNLDQKLSLFSLLLKLGFKNIEVGFPS 75 59******************************************************************* PP TIGR00970 72 asqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasr 140 as+ +fdf r ++eq lipddvt+qvl+q+re+li++t+eal+G kkaivhlyn+ts +r++vf +++ lcl|NCBI__GCF_000183725.1:WP_013461086.1 76 ASKVEFDFLRTLVEQKLIPDDVTVQVLVQAREHLIDKTFEALAGVKKAIVHLYNSTSVAQRKIVFGKEQ 144 ********************************************************************* PP TIGR00970 141 eevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnl 209 +e++ala+eg +vk+ a +++ + eyspesf++telefa ++c+av + + ++er ++ nl lcl|NCBI__GCF_000183725.1:WP_013461086.1 145 DEIIALALEG----VDMVKERAAKHDGEIMLEYSPESFTGTELEFAARICNAVTDRWGISAERKVVINL 209 **********....456677777888999**************************************** PP TIGR00970 210 patvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertG 278 patve+atpnvyad+ie++s+++++re+v++s+h+hndrGt+vaa+el llaGadr+eG l+ nGertG lcl|NCBI__GCF_000183725.1:WP_013461086.1 210 PATVEMATPNVYADQIEWMSRHLTNREHVLISTHTHNDRGTSVAATELALLAGADRVEGTLLSNGERTG 278 ********************************************************************* PP TIGR00970 279 nvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGlda 347 nvd++tlaln+ytqGv+p+ldfsdl+ ++rvve+c ++ herhpy G+lv+tafsGshqdai+kGl lcl|NCBI__GCF_000183725.1:WP_013461086.1 279 NVDIITLALNMYTQGVDPELDFSDLETVVRVVEECTDMKTHERHPYVGELVYTAFSGSHQDAINKGLAY 347 *******************************************************************87 PP TIGR00970 348 ldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkd 416 + k d+ w+vpylp+dp+dvgr+ye +ir+nsqsGkGGvayvl + G +lp+++ e +++v++ lcl|NCBI__GCF_000183725.1:WP_013461086.1 348 QRSK---EDPFWEVPYLPIDPQDVGRNYEGIIRINSQSGKGGVAYVLEDKFGYSLPKKMHPEIGRIVQQ 413 6554...468*********************************************************** PP TIGR00970 417 iadskGkelsskeisdlfkeeyllnveqlerislvdyaveddGteskvitavvkikgekkdi..eGsGn 483 ++d G+el+s+ei d+f+++y+ +++ i+ vdy+v ++ +++++ ++v++ + k i eG+Gn lcl|NCBI__GCF_000183725.1:WP_013461086.1 414 VTDEAGRELTSEEILDIFEKTYFG---EPHDIEFVDYSVISESAKEHSAKCVLEYTHNGKAIrsEGVGN 479 **********************99...678899*******************9986555554339**** PP TIGR00970 484 GplsalvdaladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsasl 552 Gp+ a +al + +++++ yseh+ g ++a+a +y+e+ + +++GvG ++d+t as+ lcl|NCBI__GCF_000183725.1:WP_013461086.1 480 GPIDACKNALMVEYSHNFKILSYSEHSRGELSSAEAVAYIEIQTESLE-----KFFGVGCDNDITVASI 543 *****************************************9876655.....79************** PP TIGR00970 553 ravlsavnra 562 +a++sa+nra lcl|NCBI__GCF_000183725.1:WP_013461086.1 544 KAMFSALNRA 553 ********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (564 nodes) Target sequences: 1 (555 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 9.20 // [ok]
This GapMind analysis is from Apr 10 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