Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate GFF1003 Psest_1036 acetolactate synthase, large subunit, biosynthetic type
Query= BRENDA::P00893 (574 letters) >FitnessBrowser__psRCH2:GFF1003 Length = 574 Score = 748 bits (1930), Expect = 0.0 Identities = 359/576 (62%), Positives = 446/576 (77%), Gaps = 4/576 (0%) Query: 1 MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60 ME+LSGAEMVVRSL D+GVK ++GYPGGAVL IYDAL I+H+LVRHEQAA HMADG Sbjct: 1 MELLSGAEMVVRSLRDEGVKYIYGYPGGAVLHIYDALFKEKAIEHILVRHEQAATHMADG 60 Query: 61 LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120 ARATG+ GVVLVTSGPGATNAITGIATA+MDSIP+VV+SGQV ++++G DAFQE DM+G Sbjct: 61 YARATGKAGVVLVTSGPGATNAITGIATAFMDSIPMVVISGQVPSTMVGTDAFQETDMIG 120 Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180 ISRP+VKHSF++K +IP+V+KKAF+LA SGRPGPVV+D+PKD+ NPA K YV+P+ Sbjct: 121 ISRPIVKHSFMIKHPSEIPEVMKKAFYLAESGRPGPVVIDIPKDMTNPAEKFEYVYPKKA 180 Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240 +RSY+P GH GQI++A + L+ AK+P++Y GGG I QL E + LNLPV + Sbjct: 181 KLRSYSPAVRGHSGQIRKAAELLLGAKRPIIYAGGGVILGKASAQLTELAKMLNLPVTNT 240 Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300 LMGLG +P RQ +GMLGMHG+Y AN+ MH++DVI AVG RFDDR N +K+CPNA + Sbjct: 241 LMGLGCYPGGDRQFVGMLGMHGSYTANLAMHHSDVILAVGARFDDRVINGASKFCPNAKI 300 Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360 +HIDIDP SISKT+ ADIPIVG VL +M+ ++ + + + WW+QI++WR Sbjct: 301 IHIDIDPASISKTIKADIPIVGPVDSVLTEMVAIVKEIGQAPNAETVASWWKQIDEWRGN 360 Query: 361 QCL--KYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSG 418 L + IKPQA IE L +TKG+AYV SDVGQHQMFA YY FDKP RW+NSG Sbjct: 361 GRLFPYNEGDGSIIKPQAAIEVLCEVTKGEAYVASDVGQHQMFACQYYKFDKPNRWLNSG 420 Query: 419 GLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYL 478 GLGTMGFGLPAA+GVK+ PE V VTG+GSIQMNIQELST LQY+LPV ++NLNN L Sbjct: 421 GLGTMGFGLPAAMGVKLNFPEADVAVVTGEGSIQMNIQELSTCLQYDLPVKIINLNNGAL 480 Query: 479 GMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNN 538 GMV+QWQDM+Y+ R+S SYM+SLPDFV+LAEAYGHVG++I+ +L+ + EA + Sbjct: 481 GMVRQWQDMVYNSRYSHSYMESLPDFVKLAEAYGHVGMRITDLKDLKPMMEEAF--AMKD 538 Query: 539 RLVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574 RLVF+D+ VD +EHVYPMQI+ G M +MWLSKTERT Sbjct: 539 RLVFLDIAVDTAEHVYPMQIKDGAMRDMWLSKTERT 574 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: 1031 Number of extensions: 34 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: 574 Length adjustment: 36 Effective length of query: 538 Effective length of database: 538 Effective search space: 289444 Effective search space used: 289444 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 GFF1003 Psest_1036 (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.20690.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-259 846.1 1.6 6.7e-259 845.9 1.6 1.0 1 lcl|FitnessBrowser__psRCH2:GFF1003 Psest_1036 acetolactate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1003 Psest_1036 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 845.9 1.6 6.7e-259 6.7e-259 1 556 [. 4 569 .. 4 570 .. 0.97 Alignments for each domain: == domain 1 score: 845.9 bits; conditional E-value: 6.7e-259 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPG 74 l+gae++v+sl++egv++++GyPGGavl+iydal+ ++ +ehilvrheqaa+h+adGyara+Gk+Gvvl+tsGPG lcl|FitnessBrowser__psRCH2:GFF1003 4 LSGAEMVVRSLRDEGVKYIYGYPGGAVLHIYDALFkEKAIEHILVRHEQAATHMADGYARATGKAGVVLVTSGPG 78 68*********************************8889************************************ PP TIGR00118 75 atnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGr 149 atn++tgiata++ds+P+vv++Gqv+++++G+dafqe d++Gi++p++khsf++k+++++pe++k+af++a++Gr lcl|FitnessBrowser__psRCH2:GFF1003 79 ATNAITGIATAFMDSIPMVVISGQVPSTMVGTDAFQETDMIGISRPIVKHSFMIKHPSEIPEVMKKAFYLAESGR 153 *************************************************************************** PP TIGR00118 150 PGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelke 222 PGPv++d+Pkd+t+++ ++e+ +k +l++y p v+gh qi+ka+el+ ak+P++++GgGvi ++as++l+e lcl|FitnessBrowser__psRCH2:GFF1003 154 PGPVVIDIPKDMTNPAEKFEYVypKKAKLRSYSPAVRGHSGQIRKAAELLLGAKRPIIYAGGGVILGKASAQLTE 228 *************99888777666*************************************************** PP TIGR00118 223 laerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihi 297 la++l++pvt tl+GlG++p +++++gmlGmhG+++anla++++d+++avGarfddrv + +kf+p+akiihi lcl|FitnessBrowser__psRCH2:GFF1003 229 LAKMLNLPVTNTLMGLGCYPGGDRQFVGMLGMHGSYTANLAMHHSDVILAVGARFDDRVINGASKFCPNAKIIHI 303 *************************************************************************** PP TIGR00118 298 didPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilk.ldeeees.ikPqk 365 didPa+i+k++k+dipivG + +vl+e+++ +ke + ++ W+++i+ew+ + l ++e ++s ikPq+ lcl|FitnessBrowser__psRCH2:GFF1003 304 DIDPASISKTIKADIPIVGPVDSVLTEMVAIVKEIgqapNAETVAsWWKQIDEWRGNGRLFpYNEGDGSiIKPQA 378 *****************************99998877764444446*********9987765777776669**** PP TIGR00118 366 vikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsf 440 i+ l++++k+ea+v++dvGqhqm+a q+yk++kp+++++sgGlGtmGfGlPaa+G+k+ pe++v vtG+gs+ lcl|FitnessBrowser__psRCH2:GFF1003 379 AIEVLCEVTKGEAYVASDVGQHQMFACQYYKFDKPNRWLNSGGLGTMGFGLPAAMGVKLNFPEADVAVVTGEGSI 453 *************************************************************************** PP TIGR00118 441 qmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeele 515 qmn+qelst+ +yd+pvki++lnn lGmv+qWq+++y+ rys+++++s lpdfvklaeayG++g+ri++ ++l+ lcl|FitnessBrowser__psRCH2:GFF1003 454 QMNIQELSTCLQYDLPVKIINLNNGALGMVRQWQDMVYNSRYSHSYMES-LPDFVKLAEAYGHVGMRITDLKDLK 527 ************************************************5.************************* PP TIGR00118 516 eklkealesk.epvlldvevdkeeevlPmvapGagldelvee 556 ++ea+++k ++v+ld+ vd+ e+v+Pm+++ +++ +++ + lcl|FitnessBrowser__psRCH2:GFF1003 528 PMMEEAFAMKdRLVFLDIAVDTAEHVYPMQIKDGAMRDMWLS 569 ******9988799**************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (574 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.67 // [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