Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 201429 SO2279 acetolactate synthase III, large subunit (NCBI ptt file)
Query= BRENDA::P00893 (574 letters) >FitnessBrowser__MR1:201429 Length = 572 Score = 885 bits (2287), Expect = 0.0 Identities = 425/573 (74%), Positives = 492/573 (85%), Gaps = 2/573 (0%) Query: 1 MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60 ME LSGA M+VRSLID+GVK +FGYPGG+VLDIYDALH + GI+H+LVRHEQAAVHMADG Sbjct: 1 MEKLSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHLIPGIEHILVRHEQAAVHMADG 60 Query: 61 LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120 ARATG+VGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQV ++LIG DAFQECDM+G Sbjct: 61 YARATGKVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVPSNLIGNDAFQECDMIG 120 Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180 ISRPVVKHSFLV+ IP+++KKAF++A++GRPGPVVVDLPKD LNPA Y++PES+ Sbjct: 121 ISRPVVKHSFLVQDPTQIPEIIKKAFYIASTGRPGPVVVDLPKDCLNPALLHDYIYPESI 180 Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240 MRSYNPTT+GHKGQI+R LQ L+AAKKPV+YVGGGAI +G +Q+ E LN+PV+ + Sbjct: 181 KMRSYNPTTSGHKGQIRRGLQALLAAKKPVLYVGGGAIISGSEKQILTLAEKLNIPVIST 240 Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300 LMGLGAFP TH+ +LGMLGMHG YEANM MHN D+IF +GVRFDDRTTNN+ KYCPNAT+ Sbjct: 241 LMGLGAFPGTHKNSLGMLGMHGRYEANMAMHNCDLIFGIGVRFDDRTTNNIEKYCPNATI 300 Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360 LHIDIDP+SISKTV DIPIVG A VL+ +L LL + S I WWQ+I WR R Sbjct: 301 LHIDIDPSSISKTVRVDIPIVGSADIVLDSILALLDEASETNDFVAINQWWQEITTWRNR 360 Query: 361 QCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL 420 QCL YD S +IKPQ VIETL++LT G+AYV SDVGQHQMFAALYYPFDKPRRWINSGGL Sbjct: 361 QCLAYDKESNRIKPQQVIETLYKLTNGEAYVASDVGQHQMFAALYYPFDKPRRWINSGGL 420 Query: 421 GTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGM 480 GTMGFGLPAA+GVKMA+P+ETVVCVTGDGSIQMNIQELSTALQY+ PV ++NLNNR+LGM Sbjct: 421 GTMGFGLPAAMGVKMAMPDETVVCVTGDGSIQMNIQELSTALQYDTPVKIINLNNRFLGM 480 Query: 481 VKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRL 540 VKQWQDMIYSGRHS SYM S+P+F ++AEAYGHVG+ IS P ELESK++EAL +RL Sbjct: 481 VKQWQDMIYSGRHSHSYMDSVPNFAKIAEAYGHVGMTISDPAELESKMAEAL--AMKDRL 538 Query: 541 VFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTER 573 VF+D+ VD +EHVYPM IRGG M+EMWLSKTE+ Sbjct: 539 VFIDIMVDETEHVYPMLIRGGAMNEMWLSKTEK 571 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: 1088 Number of extensions: 30 Number of successful extensions: 2 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: 572 Length adjustment: 36 Effective length of query: 538 Effective length of database: 536 Effective search space: 288368 Effective search space used: 288368 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 201429 SO2279 (acetolactate synthase III, large subunit (NCBI ptt file))
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.5689.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-277 905.6 0.5 6.4e-277 905.4 0.5 1.0 1 lcl|FitnessBrowser__MR1:201429 SO2279 acetolactate synthase III Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:201429 SO2279 acetolactate synthase III, large subunit (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 905.4 0.5 6.4e-277 6.4e-277 1 556 [. 4 567 .. 4 568 .. 0.97 Alignments for each domain: == domain 1 score: 905.4 bits; conditional E-value: 6.4e-277 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnl 78 l+ga+++v+sl +egv+++fGyPGG+vl+iydal+ ++ehilvrheqaa+h+adGyara+GkvGvvl+tsGPGatn+ lcl|FitnessBrowser__MR1:201429 4 LSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHlIPGIEHILVRHEQAAVHMADGYARATGKVGVVLVTSGPGATNA 82 689********************************999***************************************** PP TIGR00118 79 vtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdl 157 +tgiatay+ds+Plvvl+Gqv+++liG+dafqe+d++Gi++pv+khsflv+++ ++pei+k+af+iastGrPGPv+vdl lcl|FitnessBrowser__MR1:201429 83 ITGIATAYMDSIPLVVLSGQVPSNLIGNDAFQECDMIGISRPVVKHSFLVQDPTQIPEIIKKAFYIASTGRPGPVVVDL 161 ******************************************************************************* PP TIGR00118 158 Pkdvteaei..eleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvttt 234 Pkd ++++ ++ ++e++++++y+pt++ghk qi++ l+++ +akkPvl+vGgG+ii+++++++ lae+l+ipv++t lcl|FitnessBrowser__MR1:201429 162 PKDCLNPALlhDYIYPESIKMRSYNPTTSGHKGQIRRGLQALLAAKKPVLYVGGGAIISGSEKQILTLAEKLNIPVIST 240 ******9972255666*************************************************************** PP TIGR00118 235 llGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdip 313 l+GlGafp +h+++lgmlGmhG++ean+a++++dl++++G+rfddr+t+n++k++p+a+i+hididP++i+k+v+vdip lcl|FitnessBrowser__MR1:201429 241 LMGLGAFPGTHKNSLGMLGMHGRYEANMAMHNCDLIFGIGVRFDDRTTNNIEKYCPNATILHIDIDPSSISKTVRVDIP 319 ******************************************************************************* PP TIGR00118 314 ivGdakkvleellkklkee.ekke....keWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqh 387 ivG a vl+ +l+ l e e+++ ++W+++i+ w+++++l++d+e++ ikPq+vi++l+kl+++ea+v++dvGqh lcl|FitnessBrowser__MR1:201429 320 IVGSADIVLDSILALLDEAsETNDfvaiNQWWQEITTWRNRQCLAYDKESNRIKPQQVIETLYKLTNGEAYVASDVGQH 398 **************9999843333333246************************************************* PP TIGR00118 388 qmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnel 466 qm+aa +y+++kpr++i+sgGlGtmGfGlPaa+G+k+a+p+etvv+vtGdgs+qmn+qelst+ +yd+pvki++lnn++ lcl|FitnessBrowser__MR1:201429 399 QMFAALYYPFDKPRRWINSGGLGTMGFGLPAAMGVKMAMPDETVVCVTGDGSIQMNIQELSTALQYDTPVKIINLNNRF 477 ******************************************************************************* PP TIGR00118 467 lGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmv 544 lGmvkqWq+++y++r+s++++ s +p+f+k+aeayG++g++i++p+ele+k++eal++k ++v++d+ vd++e+v+Pm+ lcl|FitnessBrowser__MR1:201429 478 LGMVKQWQDMIYSGRHSHSYMDS-VPNFAKIAEAYGHVGMTISDPAELESKMAEALAMKdRLVFIDIMVDETEHVYPML 555 **********************5.********************************988799***************** PP TIGR00118 545 apGagldelvee 556 ++G++++e++ + lcl|FitnessBrowser__MR1:201429 556 IRGGAMNEMWLS 567 *********976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (572 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: 9.37 // [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