Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate GFF543 HP15_531 acetolactate synthase, large subunit, biosynthetic type
Query= BRENDA::P00893 (574 letters) >FitnessBrowser__Marino:GFF543 Length = 572 Score = 749 bits (1935), Expect = 0.0 Identities = 353/573 (61%), Positives = 446/573 (77%), Gaps = 2/573 (0%) Query: 1 MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60 ME+LSGA+M++RSL D+G++ ++GYPGGA L IYDAL + H+LVRHEQAAVHMADG Sbjct: 1 MELLSGADMLIRSLQDEGIEYIYGYPGGAALHIYDALFRQDKVKHILVRHEQAAVHMADG 60 Query: 61 LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120 ARATG+ G VLVTSGPGATN ITGIATA+MDSIP+VVL GQVA++LIG DAFQE DM+G Sbjct: 61 YARATGKPGTVLVTSGPGATNTITGIATAFMDSIPMVVLCGQVASTLIGEDAFQETDMMG 120 Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180 +SRPVVKH+ V+ E+IP++++KA+++AA+GRPGPVVVD+PKD+ P + Y +P+ V Sbjct: 121 VSRPVVKHNLSVRHPEEIPEIIRKAYYIAATGRPGPVVVDIPKDMTTPNERYEYAYPKKV 180 Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240 +RSYNP GH GQIK+A+ ++AAK+P++Y GGG + QL E V L P+ + Sbjct: 181 KLRSYNPAIRGHAGQIKKAVDMMLAAKRPIIYAGGGVVLGKASDQLTELVRLLGYPITNT 240 Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300 LMG+G +PA+ +Q LG LGMHGTYEANM MH++D+I VG RFDDR TN K+CP A + Sbjct: 241 LMGIGCYPASDKQHLGWLGMHGTYEANMAMHHSDLILCVGARFDDRVTNATEKFCPGARI 300 Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360 +HIDIDP SISKTV AD+PIVG VL++ML L+ + + D I WW+QI++WRA Sbjct: 301 IHIDIDPASISKTVDADVPIVGPVDAVLKEMLSLVKEANEKPDADAIASWWKQIDEWRAF 360 Query: 361 QCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL 420 ++Y+T + IKPQ VIE L RLT G+A+VTSDVGQHQMFAA YY FDKP RWINSGGL Sbjct: 361 HGMRYETSPDVIKPQEVIEMLCRLTNGEAFVTSDVGQHQMFAAQYYKFDKPNRWINSGGL 420 Query: 421 GTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGM 480 GTMGFGLPAA+GVK+ P++ V+C+TG+GSIQMNIQELST QY LPV ++NLNN+ LGM Sbjct: 421 GTMGFGLPAAMGVKLTHPDDEVLCITGEGSIQMNIQELSTCKQYNLPVKIINLNNQALGM 480 Query: 481 VKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRL 540 VKQWQDM Y RH++SYM+SLPDF++LAEAYGH G++I +LE+KL E L + L Sbjct: 481 VKQWQDMNYESRHAESYMESLPDFIKLAEAYGHKGVRIEKKEDLETKLKEVL--AMKDEL 538 Query: 541 VFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTER 573 VFVD+ VD EHVYPMQ+ G M +MWLSKTER Sbjct: 539 VFVDIYVDRFEHVYPMQVARGSMKDMWLSKTER 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: 1012 Number of extensions: 25 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 GFF543 HP15_531 (acetolactate synthase, large subunit, biosynthetic type)
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.16253.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-262 855.3 0.4 1.1e-261 855.1 0.4 1.0 1 lcl|FitnessBrowser__Marino:GFF543 HP15_531 acetolactate synthase, Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF543 HP15_531 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 855.1 0.4 1.1e-261 1.1e-261 1 556 [. 4 567 .. 4 568 .. 0.97 Alignments for each domain: == domain 1 score: 855.1 bits; conditional E-value: 1.1e-261 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGa 75 l+ga++l++sl++eg+e+++GyPGGa l+iydal+ +++++hilvrheqaa+h+adGyara+Gk+G vl+tsGPGa lcl|FitnessBrowser__Marino:GFF543 4 LSGADMLIRSLQDEGIEYIYGYPGGAALHIYDALFrQDKVKHILVRHEQAAVHMADGYARATGKPGTVLVTSGPGA 79 68*********************************99*************************************** PP TIGR00118 76 tnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPG 151 tn++tgiata++ds+P+vvl Gqva++liG+dafqe d++G+++pv+kh++ v+++e++pei+++a++ia+tGrPG lcl|FitnessBrowser__Marino:GFF543 80 TNTITGIATAFMDSIPMVVLCGQVASTLIGEDAFQETDMMGVSRPVVKHNLSVRHPEEIPEIIRKAYYIAATGRPG 155 **************************************************************************** PP TIGR00118 152 PvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelae 225 Pv+vd+Pkd+t+++ ++e+ +kv+l++y+p ++gh qikka++++ +ak+P++++GgGv+ ++as++l+el+ lcl|FitnessBrowser__Marino:GFF543 156 PVVVDIPKDMTTPNERYEYAypKKVKLRSYNPAIRGHAGQIKKAVDMMLAAKRPIIYAGGGVVLGKASDQLTELVR 231 ***********99988877666****************************************************** PP TIGR00118 226 rlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididP 301 l p+t tl+G+G++p+ +++ lg lGmhGt+ean+a++++dl+++vGarfddrvt+ +kf+p a+iihididP lcl|FitnessBrowser__Marino:GFF543 232 LLGYPITNTLMGIGCYPASDKQHLGWLGMHGTYEANMAMHHSDLILCVGARFDDRVTNATEKFCPGARIIHIDIDP 307 **************************************************************************** PP TIGR00118 302 aeigknvkvdipivGdakkvleellkklkee....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelsk 372 a+i+k+v +d+pivG + vl+e+l+ +ke + + + W+++i+ew++ + ++++++ + ikPq+vi+ l++ lcl|FitnessBrowser__Marino:GFF543 308 ASISKTVDADVPIVGPVDAVLKEMLSLVKEAnekpDADAIAsWWKQIDEWRAFHGMRYETSPDVIKPQEVIEMLCR 383 *************************99998865543333447********************************** PP TIGR00118 373 llkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqels 448 l+++ea+vt+dvGqhqm+aaq+yk++kp+++i+sgGlGtmGfGlPaa+G+k+++p+++v+++tG+gs+qmn+qels lcl|FitnessBrowser__Marino:GFF543 384 LTNGEAFVTSDVGQHQMFAAQYYKFDKPNRWINSGGLGTMGFGLPAAMGVKLTHPDDEVLCITGEGSIQMNIQELS 459 **************************************************************************** PP TIGR00118 449 tiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkeales 524 t+++y++pvki++lnn+ lGmvkqWq++ ye r++e++++s lpdf+klaeayG+kg+riek+e+le klke+l++ lcl|FitnessBrowser__Marino:GFF543 460 TCKQYNLPVKIINLNNQALGMVKQWQDMNYESRHAESYMES-LPDFIKLAEAYGHKGVRIEKKEDLETKLKEVLAM 534 ****************************************5.********************************98 PP TIGR00118 525 k.epvlldvevdkeeevlPmvapGagldelvee 556 k e+v++d+ vd+ e+v+Pm++ +++++++ + lcl|FitnessBrowser__Marino:GFF543 535 KdELVFVDIYVDRFEHVYPMQVARGSMKDMWLS 567 879*******************9999**99975 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: 8.57 // [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