Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 5209298 Shew_1776 acetolactate synthase 3 catalytic subunit (RefSeq)
Query= BRENDA::P00893 (574 letters) >FitnessBrowser__PV4:5209298 Length = 573 Score = 868 bits (2242), Expect = 0.0 Identities = 422/575 (73%), Positives = 488/575 (84%), Gaps = 3/575 (0%) Query: 1 MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60 ME LSGA M+VRSLID+GVK +FGYPGG+VLDIYDALH GI+H+LVRHEQAAVHMADG Sbjct: 1 MEKLSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHQKSGIEHILVRHEQAAVHMADG 60 Query: 61 LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120 ARATG+VGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQV ++LIG DAFQECDM+G Sbjct: 61 YARATGKVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVPSNLIGNDAFQECDMIG 120 Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180 ISRPVVKHSFLV +DIP ++KKAF++A++GRPGPVVVD+PKD LNP Y +P+ + Sbjct: 121 ISRPVVKHSFLVTDAKDIPAIIKKAFYIASTGRPGPVVVDIPKDCLNPQILHEYQYPDEI 180 Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240 +MRSYNPTTTGHKGQI+R LQ L+ AKKPV+YVGGGA+ +G QQ+ + + L LPVV + Sbjct: 181 NMRSYNPTTTGHKGQIRRGLQALLKAKKPVLYVGGGAVISGADQQILKLSDRLGLPVVST 240 Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300 LMGLGAFP TH ++GMLGMHG YEANM MHNAD+IF +GVRFDDRTTNN+ KYCPNAT+ Sbjct: 241 LMGLGAFPGTHANSVGMLGMHGCYEANMAMHNADLIFGIGVRFDDRTTNNVEKYCPNATI 300 Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQE-SAHQPLDEIRDWWQQIEQWRA 359 LHIDIDP+SISKTV DIPIVG A VL+ ML LL E S I WW +I QWR+ Sbjct: 301 LHIDIDPSSISKTVRVDIPIVGSADSVLDDMLALLDDEPSMKNDEGAIDYWWSEINQWRS 360 Query: 360 RQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGG 419 R L YD SE+IKPQ VIETL +LT GDAYV SDVGQHQMFAALYYPF+KPRRWINSGG Sbjct: 361 RNSLAYDKSSERIKPQQVIETLHKLTNGDAYVASDVGQHQMFAALYYPFNKPRRWINSGG 420 Query: 420 LGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLG 479 LGTMGFGLPAA+GVKMA P+ETV+CVTGDGSIQMNIQELSTALQY+ PV ++NLNNR+LG Sbjct: 421 LGTMGFGLPAAMGVKMAKPDETVICVTGDGSIQMNIQELSTALQYDTPVKIINLNNRFLG 480 Query: 480 MVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNR 539 MVKQWQDMIYSGRHS SYM S+P+F ++AEAYGHVG+ IS P ELE+ L +AL ++ Sbjct: 481 MVKQWQDMIYSGRHSHSYMDSVPNFAKIAEAYGHVGMTISDPAELEAGLEKAL--AMKDK 538 Query: 540 LVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574 LVFVD++VD +EHVYPMQIRGGGM+EMWLSKTE++ Sbjct: 539 LVFVDISVDETEHVYPMQIRGGGMNEMWLSKTEKS 573 Lambda K H 0.319 0.135 0.403 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: 1087 Number of extensions: 33 Number of successful extensions: 3 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: 574 Length of database: 573 Length adjustment: 36 Effective length of query: 538 Effective length of database: 537 Effective search space: 288906 Effective search space used: 288906 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
Align candidate 5209298 Shew_1776 (acetolactate synthase 3 catalytic subunit (RefSeq))
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))
# 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/TIGR00118.hmm # target sequence database: /tmp/gapView.21855.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00118 [M=557] Accession: TIGR00118 Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-278 910.1 0.9 2.8e-278 909.9 0.9 1.0 1 lcl|FitnessBrowser__PV4:5209298 Shew_1776 acetolactate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209298 Shew_1776 acetolactate synthase 3 catalytic subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 909.9 0.9 2.8e-278 2.8e-278 1 556 [. 4 568 .. 4 569 .. 0.98 Alignments for each domain: == domain 1 score: 909.9 bits; conditional E-value: 2.8e-278 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatn 77 l+ga+++v+sl +egv+++fGyPGG+vl+iydal+ +s++ehilvrheqaa+h+adGyara+GkvGvvl+tsGPGatn lcl|FitnessBrowser__PV4:5209298 4 LSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHqKSGIEHILVRHEQAAVHMADGYARATGKVGVVLVTSGPGATN 81 689********************************99***************************************** PP TIGR00118 78 lvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlv 155 ++tgiatay+ds+Plvvl+Gqv+++liG+dafqe+d++Gi++pv+khsflv++a+d+p+i+k+af+iastGrPGPv+v lcl|FitnessBrowser__PV4:5209298 82 AITGIATAYMDSIPLVVLSGQVPSNLIGNDAFQECDMIGISRPVVKHSFLVTDAKDIPAIIKKAFYIASTGRPGPVVV 159 ****************************************************************************** PP TIGR00118 156 dlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipv 231 d+Pkd +++i e++ +++++++y+pt++ghk qi++ l+++ kakkPvl+vGgG++i++a++++ +l++rl +pv lcl|FitnessBrowser__PV4:5209298 160 DIPKDCLNPQILHEYQypDEINMRSYNPTTTGHKGQIRRGLQALLKAKKPVLYVGGGAVISGADQQILKLSDRLGLPV 237 ********9987666656************************************************************ PP TIGR00118 232 tttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvk 309 ++tl+GlGafp +h +++gmlGmhG++ean+a+++adl++++G+rfddr+t+n++k++p+a+i+hididP++i+k+v+ lcl|FitnessBrowser__PV4:5209298 238 VSTLMGLGAFPGTHANSVGMLGMHGCYEANMAMHNADLIFGIGVRFDDRTTNNVEKYCPNATILHIDIDPSSISKTVR 315 ****************************************************************************** PP TIGR00118 310 vdipivGdakkvleellkklkee.....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivt 381 vdipivG a +vl+++l+ l +e ++ ++ W+++i++w++++ l++d+++e ikPq+vi++l+kl++++a+v+ lcl|FitnessBrowser__PV4:5209298 316 VDIPIVGSADSVLDDMLALLDDEpsmknDEGAIDyWWSEINQWRSRNSLAYDKSSERIKPQQVIETLHKLTNGDAYVA 393 *******************9998876433333458******************************************* PP TIGR00118 382 tdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvki 459 +dvGqhqm+aa +y+++kpr++i+sgGlGtmGfGlPaa+G+k+akp+etv++vtGdgs+qmn+qelst+ +yd+pvki lcl|FitnessBrowser__PV4:5209298 394 SDVGQHQMFAALYYPFNKPRRWINSGGLGTMGFGLPAAMGVKMAKPDETVICVTGDGSIQMNIQELSTALQYDTPVKI 471 ****************************************************************************** PP TIGR00118 460 vilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdk 536 ++lnn++lGmvkqWq+++y++r+s++++ s +p+f+k+aeayG++g++i++p+ele+ l++al++k ++v++d++vd+ lcl|FitnessBrowser__PV4:5209298 472 INLNNRFLGMVKQWQDMIYSGRHSHSYMDS-VPNFAKIAEAYGHVGMTISDPAELEAGLEKALAMKdKLVFVDISVDE 548 *****************************5.********************************988799********* PP TIGR00118 537 eeevlPmvapGagldelvee 556 +e+v+Pm+++G+g++e++ + lcl|FitnessBrowser__PV4:5209298 549 TEHVYPMQIRGGGMNEMWLS 568 *****************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (573 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11.99 // [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