Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_037576554.1 BS73_RS26265 2-isopropylmalate synthase
Query= BRENDA::P9WQB3 (644 letters) >NCBI__GCF_000744815.1:WP_037576554.1 Length = 582 Score = 665 bits (1715), Expect = 0.0 Identities = 351/617 (56%), Positives = 429/617 (69%), Gaps = 58/617 (9%) Query: 36 QRASSMPVNRYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARK 95 Q+ S MP RY+PF + L +RTWP +VI +AP W + DLRDGNQALIDPMSPARK Sbjct: 14 QKPSGMPFQRYKPFGT----VDLPDRTWPGKVITKAPRWLSTDLRDGNQALIDPMSPARK 69 Query: 96 RRMFDLLVRMGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTF 155 R MFDLLVR+GYKEIEVGFPS+ QTDFDFVR IIE+GAIP+DVTI VLTQ R +LIERT Sbjct: 70 RAMFDLLVRLGYKEIEVGFPSSGQTDFDFVRSIIEEGAIPEDVTISVLTQAREDLIERTV 129 Query: 156 QACSGAPRAIVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKYPG--TQWRF 213 ++ GAPRA VH YN+T+ L RRVVFRA+R EV+ IA DG ++ A + G T + + Sbjct: 130 ESLVGAPRATVHMYNATAPLFRRVVFRASRDEVRQIAVDGTGHVMKYAEQLLGEDTVFGY 189 Query: 214 EYSPESYTGTELEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRN 273 +YSPE + TEL++A +VC+AV +V P R II NLP TVE TPNVYAD IEWMSRN Sbjct: 190 QYSPEIFVDTELDFALEVCEAVMDVWQPEEGREIILNLPTTVERCTPNVYADQIEWMSRN 249 Query: 274 LANRESVILSLHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFS 333 L+ RE + LS HPHNDRGT VA+AEL AGADR+EGCLFG GERTGN+ +VT+G+NLFS Sbjct: 250 LSRREFIALSSHPHNDRGTGVASAELAIMAGADRVEGCLFGQGERTGNLDIVTVGMNLFS 309 Query: 334 RGVDPQIDFSNIDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLD 393 +GVDP +DFS+IDEIRR EYCNQ+ V ERHPY GDLVYT+FSGSHQDAI KG +A++ D Sbjct: 310 QGVDPMVDFSDIDEIRRVYEYCNQMTVPERHPYVGDLVYTSFSGSHQDAIKKGFEALEKD 369 Query: 394 ADAADCDVDDMLWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRL 453 A+AA V W VPYLPIDP+DVGR+YEAVIRVNSQSGKGG++Y++K++H L LPRR+ Sbjct: 370 AEAAGVPVGQQTWGVPYLPIDPKDVGRSYEAVIRVNSQSGKGGISYVLKSEHQLDLPRRM 429 Query: 454 QIEFSQVIQKIAEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLE------RIRQHVDAADD 507 Q+EFS++IQ T EGGEV+P E+W F +EYL P E R+R H + Sbjct: 430 QVEFSKIIQ---TKTDTEGGEVTPAEIWSIFEDEYL----PTESAWGRIRLRSHQSSTTT 482 Query: 508 DGGTTSITATVKINGVETEISGSGNGPLAAFVHALADVGFDVAVLDYYEHAMSAGDDAQA 567 DG + V ++G +T + G+GNGP+ AF AL VG DV +LDY EH S G AQA Sbjct: 483 DGRDELVVDAV-VDGEDTVLKGAGNGPIDAFFDALGAVGVDVRLLDYVEHTRSQGAAAQA 541 Query: 568 AAYVEASVTIASPAQPGEAGRHASDPVTIASPAQPGEAGRHASDPVTSKTVWGVGIAPSI 627 AAYVE +V GE K VWGVG+ +I Sbjct: 542 AAYVECAV--------GE------------------------------KVVWGVGVDNNI 563 Query: 628 TTASLRAVVSAVNRAAR 644 ASL+A +SAVNRA + Sbjct: 564 VRASLKAAISAVNRAEK 580 Lambda K H 0.317 0.133 0.399 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: 962 Number of extensions: 41 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 644 Length of database: 582 Length adjustment: 37 Effective length of query: 607 Effective length of database: 545 Effective search space: 330815 Effective search space used: 330815 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 (21.7 bits) S2: 53 (25.0 bits)
Align candidate WP_037576554.1 BS73_RS26265 (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.1608477.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-253 828.7 0.0 1.3e-253 828.5 0.0 1.0 1 NCBI__GCF_000744815.1:WP_037576554.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037576554.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 828.5 0.0 1.3e-253 1.3e-253 1 563 [. 20 579 .. 20 580 .. 0.97 Alignments for each domain: == domain 1 score: 828.5 bits; conditional E-value: 1.3e-253 TIGR00970 1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfpsas 73 p ++ykpf ++ l++r+wp kvit+aprwls+dlrdGnqalidpms++rk+ +f+llvr+G+keievgfps+ NCBI__GCF_000744815.1:WP_037576554.1 20 PFQRYKPFGTVDLPDRTWPGKVITKAPRWLSTDLRDGNQALIDPMSPARKRAMFDLLVRLGYKEIEVGFPSSG 92 779********************************************************************** PP TIGR00970 74 qtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasreevlal 146 qtdfdfvr iie+g+ip+dvti+vltq+re+li+rtve+l Ga++a+vh+ynat++lfr+vvfrasr+ev ++ NCBI__GCF_000744815.1:WP_037576554.1 93 QTDFDFVRSIIEEGAIPEDVTISVLTQAREDLIERTVESLVGAPRATVHMYNATAPLFRRVVFRASRDEVRQI 165 ************************************************************************* PP TIGR00970 147 avegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatvevatpn 219 av+g+ v k +++ + ++t ++++yspe f dtel+fa+evceav +v++p e r ii+nlp+tve +tpn NCBI__GCF_000744815.1:WP_037576554.1 166 AVDGTGHVMKYAEQLL-GEDTVFGYQYSPEIFVDTELDFALEVCEAVMDVWQPEEGREIILNLPTTVERCTPN 237 **********999876.5789**************************************************** PP TIGR00970 220 vyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnvdlvtlalnlytq 292 vyad+ie++s+n++ re + ls hphndrGt+va+ael ++aGadr+eGclfG+GertGn+d+vt+++nl++q NCBI__GCF_000744815.1:WP_037576554.1 238 VYADQIEWMSRNLSRREFIALSSHPHNDRGTGVASAELAIMAGADRVEGCLFGQGERTGNLDIVTVGMNLFSQ 310 ************************************************************************* PP TIGR00970 293 GvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldkkkaaa.....dtlwk 360 Gv+p +dfsd+dei+rv e+cn++ v erhpy Gdlv+t+fsGshqdaikkG++al+k+++aa ++ w NCBI__GCF_000744815.1:WP_037576554.1 311 GVDPMVDFSDIDEIRRVYEYCNQMTVPERHPYVGDLVYTSFSGSHQDAIKKGFEALEKDAEAAgvpvgQQTWG 383 ***********************************************************99988999999*** PP TIGR00970 361 vpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdl 433 vpylp+dpkdvgr yeavirvnsqsGkGG++yvlk ++ ldlprr+q+efs++++ +d++G+e+++ ei+ + NCBI__GCF_000744815.1:WP_037576554.1 384 VPYLPIDPKDVGRSYEAVIRVNSQSGKGGISYVLKSEHQLDLPRRMQVEFSKIIQTKTDTEGGEVTPAEIWSI 456 ************************************************************************* PP TIGR00970 434 fkeeyllnveqlerislvdyaveddGteskvitavvkikgekkdieGsGnGplsalvdaladllnvdvavady 506 f++eyl ++ +ri+l++++ + + ++ + ++ge + ++G+GnGp+ a+ dal ++ vdv ++dy NCBI__GCF_000744815.1:WP_037576554.1 457 FEDEYLPTESAWGRIRLRSHQSSTTTDGRDELVVDAVVDGEDTVLKGAGNGPIDAFFDALGAVG-VDVRLLDY 528 *************9998777666555555555555556789999******************99.******** PP TIGR00970 507 sehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsaslravlsavnraa 563 eh+ + G a+aa+yve +v ++ vwGvG+++++ asl+a +savnra NCBI__GCF_000744815.1:WP_037576554.1 529 VEHTRSQGAAAQAAAYVECAVGEKV------VWGVGVDNNIVRASLKAAISAVNRAE 579 *******************998877......************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (564 nodes) Target sequences: 1 (582 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 23.67 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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