Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Pf1N1B4_2878 Acetolactate synthase large subunit (EC 2.2.1.6)
Query= BRENDA::P00893 (574 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 Length = 566 Score = 749 bits (1933), Expect = 0.0 Identities = 359/568 (63%), Positives = 444/568 (78%), Gaps = 4/568 (0%) Query: 9 MVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLARATGEV 68 M+VR L D+GVK ++GYPGGA+L +YDAL + H+LVRHEQAA HMADG ARATG+ Sbjct: 1 MLVRFLRDEGVKYIYGYPGGALLHVYDALFKEPEVTHILVRHEQAATHMADGYARATGKA 60 Query: 69 GVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVGISRPVVKH 128 GVVLVTSGPGATNAITGIATAYMDSIP+V++SGQV ++++G DAFQE DM+GISRP+VKH Sbjct: 61 GVVLVTSGPGATNAITGIATAYMDSIPMVIISGQVPSTMVGTDAFQETDMIGISRPIVKH 120 Query: 129 SFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESVSMRSYNPT 188 SF++K +IP+V+KKAF+LA SGRPGPVVVD+PKD+ NPA K Y++P+ +RSY+P Sbjct: 121 SFMIKHASEIPEVMKKAFYLAQSGRPGPVVVDIPKDMTNPAEKFEYIFPKKAKLRSYSPA 180 Query: 189 TTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCSLMGLGAFP 248 GH GQI++A + L+AAK+PV+Y GGG I G L E + LNLPV +LMGLGA+P Sbjct: 181 VRGHSGQIRKAAEMLLAAKRPVLYSGGGVILGGGSAPLTELAKMLNLPVTNTLMGLGAYP 240 Query: 249 ATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATVLHIDIDPT 308 T RQ +GMLGMHG+Y AN+ MH+ADVI AVG RFDDR N AK+CPNA ++HIDIDP Sbjct: 241 GTDRQFIGMLGMHGSYTANLAMHHADVILAVGARFDDRVINGPAKFCPNAKIIHIDIDPA 300 Query: 309 SISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRA-RQCLKYDT 367 SISKT+ AD+PIVG VL +M+ +L + + + WW+Q+++WR R YD Sbjct: 301 SISKTIKADVPIVGPVESVLTEMVAILKEIGETPNKESVASWWKQVDEWRGDRGLFPYDK 360 Query: 368 -HSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGLGTMGFG 426 IKPQ VIETL +TKGDA+VTSDVGQHQMFAA YY F+KP RWINSGGLGTMGFG Sbjct: 361 GDGSVIKPQTVIETLCEVTKGDAFVTSDVGQHQMFAAQYYTFNKPNRWINSGGLGTMGFG 420 Query: 427 LPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGMVKQWQD 486 LPAA+G+K++ P++ V CVTG+GSIQMNIQELST LQY LPV +V LNN LGMV+QWQD Sbjct: 421 LPAAMGIKLSFPDDDVACVTGEGSIQMNIQELSTCLQYGLPVKIVILNNGVLGMVRQWQD 480 Query: 487 MIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRLVFVDVT 546 M Y RHS SYM+SLPDFV+LAEAYGHVG++I+ +L+SK+ EA +RLV +D++ Sbjct: 481 MSYGSRHSHSYMESLPDFVKLAEAYGHVGVRITESKDLKSKMEEAF--AMKDRLVVIDIS 538 Query: 547 VDGSEHVYPMQIRGGGMDEMWLSKTERT 574 VD SEHVYPMQI+ G M +MWLSKTERT Sbjct: 539 VDTSEHVYPMQIKDGSMRDMWLSKTERT 566 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: 1015 Number of extensions: 32 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: 566 Length adjustment: 36 Effective length of query: 538 Effective length of database: 530 Effective search space: 285140 Effective search space used: 285140 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 Pf1N1B4_2878 (Acetolactate synthase large subunit (EC 2.2.1.6))
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.22717.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-258 845.0 0.9 1.4e-258 844.8 0.9 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 Acetolactate synthase large subu Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 Acetolactate synthase large subunit (EC 2.2.1.6) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 844.8 0.9 1.4e-258 1.4e-258 6 556 .. 1 561 [. 1 562 [. 0.97 Alignments for each domain: == domain 1 score: 844.8 bits; conditional E-value: 1.4e-258 TIGR00118 6 ilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 +lv+ l++egv++++GyPGGa+l++ydal+ + e++hilvrheqaa+h+adGyara+Gk+Gvvl lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 1 MLVRFLRDEGVKYIYGYPGGALLHVYDALFkEPEVTHILVRHEQAATHMADGYARATGKAGVVL 64 7899**************************889******************************* PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkae 132 +tsGPGatn++tgiatay+ds+P+v+++Gqv+++++G+dafqe d++Gi++p++khsf++k+a+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 65 VTSGPGATNAITGIATAYMDSIPMVIISGQVPSTMVGTDAFQETDMIGISRPIVKHSFMIKHAS 128 **************************************************************** PP TIGR00118 133 dlpeilkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkal 194 ++pe++k+af++a++GrPGPv+vd+Pkd+t+++ ++e+ +k +l++y p v+gh qi+ka+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 129 EIPEVMKKAFYLAQSGRPGPVVVDIPKDMTNPAEKFEYIfpKKAKLRSYSPAVRGHSGQIRKAA 192 *******************************9988888777*********************** PP TIGR00118 195 eliekakkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtk 258 e++ +ak+Pvl+ GgGvi +++s+ l+ela++l++pvt tl+GlGa+p ++++++gmlGmhG++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 193 EMLLAAKRPVLYSGGGVILGGGSAPLTELAKMLNLPVTNTLMGLGAYPGTDRQFIGMLGMHGSY 256 **************************************************************** PP TIGR00118 259 eanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvl 322 +anla+++ad+++avGarfddrv + akf+p+akiihididPa+i+k++k+d+pivG +++vl lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 257 TANLAMHHADVILAVGARFDDRVINGPAKFCPNAKIIHIDIDPASISKTIKADVPIVGPVESVL 320 **************************************************************** PP TIGR00118 323 eellkklkee....ekkeke.Wlekieewkkeyilk.ldeeees.ikPqkvikelskllkdeai 379 +e+++ lke +k++ W+++++ew+ + l +d+ ++s ikPq+vi++l++++k++a+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 321 TEMVAILKEIgetpNKESVAsWWKQVDEWRGDRGLFpYDKGDGSvIKPQTVIETLCEVTKGDAF 384 ***999888777764444446*********999877688888777******************* PP TIGR00118 380 vttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmn 443 vt+dvGqhqm+aaq+y+++kp+++i+sgGlGtmGfGlPaa+G+k++ p+++v +vtG+gs+qmn lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 385 VTSDVGQHQMFAAQYYTFNKPNRWINSGGLGTMGFGLPAAMGIKLSFPDDDVACVTGEGSIQMN 448 **************************************************************** PP TIGR00118 444 lqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgir 507 +qelst+ +y++pvkivilnn +lGmv+qWq++ y r+s+++++s lpdfvklaeayG++g+r lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 449 IQELSTCLQYGLPVKIVILNNGVLGMVRQWQDMSYGSRHSHSYMES-LPDFVKLAEAYGHVGVR 511 *********************************************5.***************** PP TIGR00118 508 iekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelvee 556 i++ ++l++k++ea+++k ++v++d++vd++e+v+Pm+++ +++ +++ + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 512 ITESKDLKSKMEEAFAMKdRLVVIDISVDTSEHVYPMQIKDGSMRDMWLS 561 **************9988799**************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (566 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.95 // [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