Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_086511579.1 BZY95_RS19630 acetolactate synthase 3 large subunit
Query= BRENDA::P00893 (574 letters) >NCBI__GCF_002151265.1:WP_086511579.1 Length = 574 Score = 692 bits (1785), Expect = 0.0 Identities = 335/577 (58%), Positives = 430/577 (74%), Gaps = 6/577 (1%) Query: 1 MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60 ME+LSGA+M+ R L D+GV+ ++GYPGGA L IYDAL + H+LVRHEQAA H ADG Sbjct: 1 MELLSGADMIARFLQDEGVEYIYGYPGGAALHIYDALFRQDKVKHILVRHEQAATHAADG 60 Query: 61 LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120 ARA+G+ GVVLVTSGPGATNA+TGIATAYMDSIP+VVL GQV + LIG DAFQE D++G Sbjct: 61 YARASGKPGVVLVTSGPGATNAVTGIATAYMDSIPMVVLCGQVMSHLIGDDAFQETDIIG 120 Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180 ++RP+VKHSF +K +IP+VLKKAF+LA++GRPGPVVVD+PKD+ P + YV+P+ V Sbjct: 121 VTRPIVKHSFSIKHPTEIPEVLKKAFYLASTGRPGPVVVDIPKDMTAPTERYEYVYPKKV 180 Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240 +RSYNP GH GQIK+A++ ++ AK+PV Y GGG IT + L + V+ L P+ + Sbjct: 181 KLRSYNPVARGHTGQIKKAVEMMLKAKRPVFYTGGGVITGRACEGLTDLVKRLGYPITTT 240 Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300 LMG+GA+P + RQ LG LGMHG+YE+NM MH+AD+I A+G RFDDR TNN +K+CP A + Sbjct: 241 LMGIGAYPQSDRQCLGWLGMHGSYESNMAMHHADLIIAIGARFDDRVTNNTSKFCPTAKI 300 Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360 +H+DIDP+S+SKTV AD+PIVG A V+++M+ L+ + P + + +WWQ+I+ WR Sbjct: 301 IHVDIDPSSVSKTVRADVPIVGPAASVIDEMISLVQGKEIAHP-EALTEWWQKIDGWREE 359 Query: 361 QCLKYDTHS---EKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINS 417 + K S E++KPQ VIE L +T+G+AYVT+DVGQHQMFAA YY FDKP R+I S Sbjct: 360 RRGKLYEPSKPGEQLKPQEVIEALCEITRGEAYVTTDVGQHQMFAAQYYKFDKPNRFITS 419 Query: 418 GGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRY 477 GGLGTMGFG PAA+G+K PEETVVCVTG+GS QM +QELST Q+ V ++NLNN Sbjct: 420 GGLGTMGFGFPAAMGIKQNFPEETVVCVTGEGSFQMMMQELSTCKQFGGGVKIINLNNAS 479 Query: 478 LGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRN 537 LGMV+QWQD+ Y RH+ SYM+SLPDF +L EAYG +++ EL L Sbjct: 480 LGMVRQWQDLNYKSRHAHSYMESLPDFAKLIEAYGFTALRVETMDELRPALERTFAD--K 537 Query: 538 NRLVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574 + LVFVDV VD EHVYPMQ+ G M +M LSKTERT Sbjct: 538 HELVFVDVIVDPREHVYPMQVPLGSMRDMLLSKTERT 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: 1004 Number of extensions: 33 Number of successful extensions: 5 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 WP_086511579.1 BZY95_RS19630 (acetolactate synthase 3 large subunit)
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.30927.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-251 821.9 0.1 1.4e-251 821.7 0.1 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086511579.1 BZY95_RS19630 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511579.1 BZY95_RS19630 acetolactate synthase 3 large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 821.7 0.1 1.4e-251 1.4e-251 1 556 [. 4 569 .. 4 570 .. 0.96 Alignments for each domain: == domain 1 score: 821.7 bits; conditional E-value: 1.4e-251 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 l+ga+++ + l++egve+++GyPGGa l+iydal+ +++++hilvrheqaa+haadGyarasGk+Gvvl lcl|NCBI__GCF_002151265.1:WP_086511579.1 4 LSGADMIARFLQDEGVEYIYGYPGGAALHIYDALFrQDKVKHILVRHEQAATHAADGYARASGKPGVVL 72 68*********************************99******************************** PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 +tsGPGatn+vtgiatay+ds+P+vvl Gqv+++liG dafqe di+G+t+p++khsf +k++ ++pe+ lcl|NCBI__GCF_002151265.1:WP_086511579.1 73 VTSGPGATNAVTGIATAYMDSIPMVVLCGQVMSHLIGDDAFQETDIIGVTRPIVKHSFSIKHPTEIPEV 141 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPv 204 lk+af++astGrPGPv+vd+Pkd+t+++ ++e+ +kv+l++y+p +gh+ qikka+e++ kak+Pv lcl|NCBI__GCF_002151265.1:WP_086511579.1 142 LKKAFYLASTGRPGPVVVDIPKDMTAPTERYEYVypKKVKLRSYNPVARGHTGQIKKAVEMMLKAKRPV 210 *************************99888877666********************************* PP TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273 + GgGvi++ a e l++l++rl p+tttl+G+Ga+p+ +++ lg lGmhG++e+n+a+++adl+ia+ lcl|NCBI__GCF_002151265.1:WP_086511579.1 211 FYTGGGVITGRACEGLTDLVKRLGYPITTTLMGIGAYPQSDRQCLGWLGMHGSYESNMAMHHADLIIAI 279 ********************************************************************* PP TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338 Garfddrvt+n +kf+p akiih+didP++++k+v++d+pivG a +v++e+++ ++ + + +e lcl|NCBI__GCF_002151265.1:WP_086511579.1 280 GARFDDRVTNNTSKFCPTAKIIHVDIDPSSVSKTVRADVPIVGPAASVIDEMISLVQGKeiahPEALTE 348 ******************************************************999886663333456 PP TIGR00118 339 Wlekieewkkeyilk...ldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404 W++ki+ w++e k ++ e++kPq+vi++l++++++ea+vttdvGqhqm+aaq+yk++kp++fi lcl|NCBI__GCF_002151265.1:WP_086511579.1 349 WWQKIDGWREERRGKlyePSKPGEQLKPQEVIEALCEITRGEAYVTTDVGQHQMFAAQYYKFDKPNRFI 417 *********9987762113444567******************************************** PP TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473 tsgGlGtmGfG+Paa+G+k peetvv+vtG+gsfqm +qelst+++++ vki++lnn+ lGmv+qW lcl|NCBI__GCF_002151265.1:WP_086511579.1 418 TSGGLGTMGFGFPAAMGIKQNFPEETVVCVTGEGSFQMMMQELSTCKQFGGGVKIINLNNASLGMVRQW 486 ********************************************************************* PP TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevl 541 q+l y+ r+++++++s lpdf+kl eayG +++r+e+ +el +l++ ++ k e+v++dv vd +e+v+ lcl|NCBI__GCF_002151265.1:WP_086511579.1 487 QDLNYKSRHAHSYMES-LPDFAKLIEAYGFTALRVETMDELRPALERTFADKhELVFVDVIVDPREHVY 554 ***************5.*****************************99987769*************** PP TIGR00118 542 PmvapGagldelvee 556 Pm++p +++ +++ + lcl|NCBI__GCF_002151265.1:WP_086511579.1 555 PMQVPLGSMRDMLLS 569 *********999865 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 7.80 // [ok]
This GapMind analysis is from Apr 10 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