Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 6937877 Sama_2018 acetolactate synthase 3 catalytic subunit (RefSeq)
Query= BRENDA::P00893 (574 letters) >FitnessBrowser__SB2B:6937877 Length = 573 Score = 895 bits (2312), Expect = 0.0 Identities = 434/575 (75%), Positives = 498/575 (86%), Gaps = 3/575 (0%) Query: 1 MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60 ME LSGA M+VRSLID+GVK +FGYPGG+VLDIYDALH I+H+LVRHEQAAVHMADG Sbjct: 1 MEKLSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHESSNIEHILVRHEQAAVHMADG 60 Query: 61 LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120 ARATG+VGVVLVTSGPGATNAITGIATAYMDS+PLV+LSGQV +SLIG DAFQECDM+G Sbjct: 61 YARATGDVGVVLVTSGPGATNAITGIATAYMDSVPLVILSGQVPSSLIGNDAFQECDMIG 120 Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180 ISRP+VKHSFLVK +IP+ +KKAF++AA+GRPGPVVVDLPKD LNPA K Y +P V Sbjct: 121 ISRPIVKHSFLVKDPTEIPETIKKAFYIAATGRPGPVVVDLPKDTLNPALKFDYEYPSEV 180 Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240 MRSYNPT TGHKGQI+R LQ L+ AKKPV+YVGGGAI + C +Q+ E LN+PVV + Sbjct: 181 KMRSYNPTVTGHKGQIRRGLQALLNAKKPVLYVGGGAIISSCDKQILALSERLNIPVVNT 240 Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300 LMGLGAFP TH +GMLGMHGTYEANMTMHN+D+IF +GVRFDDRTTNN+ KYCPNATV Sbjct: 241 LMGLGAFPGTHPNNIGMLGMHGTYEANMTMHNSDLIFGIGVRFDDRTTNNVQKYCPNATV 300 Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRD-WWQQIEQWRA 359 LHIDIDP+SISKTV A IPIVG A +VL++ML LL ++ + + D WW I QWR+ Sbjct: 301 LHIDIDPSSISKTVQAHIPIVGSADKVLDEMLSLLDGDTEMRNDEGAIDCWWNDINQWRS 360 Query: 360 RQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGG 419 R+CL Y+T+SEKIKPQ VIETL+RLTKGDAYV+SDVGQHQMFAALYYPFDKPRRWINSGG Sbjct: 361 RKCLAYETNSEKIKPQQVIETLYRLTKGDAYVSSDVGQHQMFAALYYPFDKPRRWINSGG 420 Query: 420 LGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLG 479 LGTMGFGLPAA+GVKMA+P+ETVVCVTGDGSIQMNIQELSTALQY++PV ++NLNNR+LG Sbjct: 421 LGTMGFGLPAAMGVKMAMPDETVVCVTGDGSIQMNIQELSTALQYDVPVKIINLNNRFLG 480 Query: 480 MVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNR 539 MVKQWQDMIYSGRHS SYM S+PDF ++AEAYGHVGI IS P ELE KL+EAL +R Sbjct: 481 MVKQWQDMIYSGRHSHSYMDSVPDFAKIAEAYGHVGITISRPEELEPKLAEALSM--TDR 538 Query: 540 LVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574 LVFVD+ VD +EHVYPMQIRGG M++MWLSKTER+ Sbjct: 539 LVFVDINVDETEHVYPMQIRGGAMNDMWLSKTERS 573 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: 1086 Number of extensions: 37 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: 573 Length adjustment: 36 Effective length of query: 538 Effective length of database: 537 Effective search space: 288906 Effective search space used: 288906 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 6937877 Sama_2018 (acetolactate synthase 3 catalytic subunit (RefSeq))
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.6676.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-280 916.7 0.2 2.7e-280 916.5 0.2 1.0 1 lcl|FitnessBrowser__SB2B:6937877 Sama_2018 acetolactate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937877 Sama_2018 acetolactate synthase 3 catalytic subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 916.5 0.2 2.7e-280 2.7e-280 1 556 [. 4 568 .. 4 569 .. 0.97 Alignments for each domain: == domain 1 score: 916.5 bits; conditional E-value: 2.7e-280 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGat 76 l+ga+++v+sl +egv+++fGyPGG+vl+iydal+ +s++ehilvrheqaa+h+adGyara+G vGvvl+tsGPGat lcl|FitnessBrowser__SB2B:6937877 4 LSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHeSSNIEHILVRHEQAAVHMADGYARATGDVGVVLVTSGPGAT 80 689********************************999*************************************** PP TIGR00118 77 nlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPv 153 n++tgiatay+dsvPlv+l+Gqv++sliG+dafqe+d++Gi++p++khsflvk++ ++pe++k+af+ia+tGrPGPv lcl|FitnessBrowser__SB2B:6937877 81 NAITGIATAYMDSVPLVILSGQVPSSLIGNDAFQECDMIGISRPIVKHSFLVKDPTEIPETIKKAFYIAATGRPGPV 157 ***************************************************************************** PP TIGR00118 154 lvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlk 228 +vdlPkd+ ++++++++e ++v++++y+ptv+ghk qi++ l+++ +akkPvl+vGgG+ii+ +++++ l+erl+ lcl|FitnessBrowser__SB2B:6937877 158 VVDLPKDTLNPALKFDYEypSEVKMRSYNPTVTGHKGQIRRGLQALLNAKKPVLYVGGGAIISSCDKQILALSERLN 234 **********9988877766********************************************************* PP TIGR00118 229 ipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeig 305 ipv+ tl+GlGafp +hp+ +gmlGmhGt+ean++++++dl++++G+rfddr+t+n++k++p+a+++hididP++i+ lcl|FitnessBrowser__SB2B:6937877 235 IPVVNTLMGLGAFPGTHPNNIGMLGMHGTYEANMTMHNSDLIFGIGVRFDDRTTNNVQKYCPNATVLHIDIDPSSIS 311 ***************************************************************************** PP TIGR00118 306 knvkvdipivGdakkvleellkklkee.....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkd 376 k+v+++ipivG a kvl+e+l+ l ++ ++ W++ i++w+++++l++++++e+ikPq+vi++l++l+k+ lcl|FitnessBrowser__SB2B:6937877 312 KTVQAHIPIVGSADKVLDEMLSLLDGDtemrnDEGAIDcWWNDINQWRSRKCLAYETNSEKIKPQQVIETLYRLTKG 388 *********************998765555433333458************************************** PP TIGR00118 377 eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstivey 453 +a+v++dvGqhqm+aa +y+++kpr++i+sgGlGtmGfGlPaa+G+k+a+p+etvv+vtGdgs+qmn+qelst+ +y lcl|FitnessBrowser__SB2B:6937877 389 DAYVSSDVGQHQMFAALYYPFDKPRRWINSGGLGTMGFGLPAAMGVKMAMPDETVVCVTGDGSIQMNIQELSTALQY 465 ***************************************************************************** PP TIGR00118 454 dipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvl 529 d+pvki++lnn++lGmvkqWq+++y++r+s++++ s +pdf+k+aeayG++gi+i++peele kl+eal+++ ++v+ lcl|FitnessBrowser__SB2B:6937877 466 DVPVKIINLNNRFLGMVKQWQDMIYSGRHSHSYMDS-VPDFAKIAEAYGHVGITISRPEELEPKLAEALSMTdRLVF 541 ***********************************5.********************************987699** PP TIGR00118 530 ldvevdkeeevlPmvapGagldelvee 556 +d++vd++e+v+Pm+++G+++++++ + lcl|FitnessBrowser__SB2B:6937877 542 VDINVDETEHVYPMQIRGGAMNDMWLS 568 ************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (573 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: 9.97 // [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