Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate SMc01431 SMc01431 acetolactate synthase 3 catalytic subunit
Query= metacyc::MONOMER-18810 (585 letters) >FitnessBrowser__Smeli:SMc01431 Length = 592 Score = 629 bits (1623), Expect = 0.0 Identities = 314/575 (54%), Positives = 418/575 (72%), Gaps = 6/575 (1%) Query: 13 SSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHA 72 S +M GAEI++ AL + GVE+++GYPGGAVL IYDE+ +Q +HILVRHEQ A H Sbjct: 2 SGTENQMTGAEIVLQALKDNGVEHIFGYPGGAVLPIYDEIFQQEDIQHILVRHEQGAGHM 61 Query: 73 ADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECD 132 A+GYAR+TGKVGV LVTSGPG TNAVT + A +DSIP+V I+G VPT IG DAFQECD Sbjct: 62 AEGYARSTGKVGVMLVTSGPGATNAVTPLQDALMDSIPLVCISGQVPTSLIGSDAFQECD 121 Query: 133 TVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKS 192 T+GITRP KHN+LV+DV +LA I +AF +A +GRPGPVVVDIPKDV Y P + Sbjct: 122 TIGITRPCTKHNWLVRDVNELARVIHEAFRVAQSGRPGPVVVDIPKDVQFATGTYTPPSA 181 Query: 193 I-DMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHP 249 + +SY P +G +I +AVAL++ A +P IY+GGGV+ + A+ LR+L LTG P Sbjct: 182 VPTQKSYQPKTQGDLKKIEEAVALMKTARQPVIYSGGGVINSGPQAAHFLRELVELTGFP 241 Query: 250 VTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTS 309 +T+TLMGLGA+P + K ++GMLGMHGTYEAN+AM +CDV+I IGARFDDR+ G F+ Sbjct: 242 ITSTLMGLGAYPASGKNWLGMLGMHGTYEANLAMHDCDVMICIGARFDDRITGRLNAFSP 301 Query: 310 QARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIE 369 ++K IHIDIDPSSI+K V+VD+PI+G+V VL+++I +A+ + L WW+ I Sbjct: 302 NSKK-IHIDIDPSSINKNVRVDVPIIGDVAAVLEDMIRLWRAAAKTVDQTRLGDWWKSIS 360 Query: 370 QWRSVDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRW 428 +WR+ + L Y S+++I PQY +++++ELTK D +I ++VGQHQMWAAQF+ F+EP RW Sbjct: 361 KWRARNSLAYTPSADVIMPQYAIQRLYELTKDRDTYITTEVGQHQMWAAQFFGFEEPNRW 420 Query: 429 INSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLN 488 + SGGLGTMG G P A+G++ A PE V+ I G+ SIQMCIQE+S +QY PVKI LN Sbjct: 421 MTSGGLGTMGYGFPAAVGVQVAHPESLVIDIAGDASIQMCIQEMSCAVQYGLPVKIFILN 480 Query: 489 NGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRL 548 N Y+GMVRQWQ++ + NR SHSY +A+PDFVKLAEAYG VG+R EK +++ A+R+ Sbjct: 481 NQYMGMVRQWQQLLHGNRLSHSYTEAMPDFVKLAEAYGGVGIRCEKPGELDDAIRQMIDT 540 Query: 549 KDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAE 583 +F D + N +PM+ +GK +EMLL E Sbjct: 541 PAPVIF-DCRVANLANCFPMIPSGKAHNEMLLPDE 574 Lambda K H 0.319 0.135 0.407 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: 964 Number of extensions: 37 Number of successful extensions: 6 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: 585 Length of database: 592 Length adjustment: 37 Effective length of query: 548 Effective length of database: 555 Effective search space: 304140 Effective search space used: 304140 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 SMc01431 SMc01431 (acetolactate synthase 3 catalytic 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.10827.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-244 798.2 0.1 2.1e-244 798.0 0.1 1.0 1 lcl|FitnessBrowser__Smeli:SMc01431 SMc01431 acetolactate synthase 3 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc01431 SMc01431 acetolactate synthase 3 catalytic subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 798.0 0.1 2.1e-244 2.1e-244 1 555 [. 8 571 .. 8 573 .. 0.97 Alignments for each domain: == domain 1 score: 798.0 bits; conditional E-value: 2.1e-244 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPG 74 ++gaei++++lk++gve++fGyPGGavlpiyd+++ +++++hilvrheq+a h+a+Gyar++GkvGv+l+tsGPG lcl|FitnessBrowser__Smeli:SMc01431 8 MTGAEIVLQALKDNGVEHIFGYPGGAVLPIYDEIFqQEDIQHILVRHEQGAGHMAEGYARSTGKVGVMLVTSGPG 82 79*********************************999************************************* PP TIGR00118 75 atnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGr 149 atn+vt++ +a +ds+Plv ++Gqv+tsliGsdafqe+d +Git+p+tkh++lv+++++l+++++eaf +a++Gr lcl|FitnessBrowser__Smeli:SMc01431 83 ATNAVTPLQDALMDSIPLVCISGQVPTSLIGSDAFQECDTIGITRPCTKHNWLVRDVNELARVIHEAFRVAQSGR 157 *************************************************************************** PP TIGR00118 150 PGPvlvdlPkdvteaeieleveekv.elpgykptvkghklqikkaleliekakkPvllvGgGviia..easeelk 221 PGPv+vd+Pkdv+ a+ +++ ++ v + ++y+p+++g+ ++i++a+ l+++a++Pv++ GgGvi + +a + l+ lcl|FitnessBrowser__Smeli:SMc01431 158 PGPVVVDIPKDVQFATGTYTPPSAVpTQKSYQPKTQGDLKKIEEAVALMKTARQPVIYSGGGVINSgpQAAHFLR 232 ******************99997763679***********************************883357789** PP TIGR00118 222 elaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiih 296 el+e + p+t+tl+GlGa+p+ ++ lgmlGmhGt+eanla++++d++i++Garfddr+tg l+ f+p++k ih lcl|FitnessBrowser__Smeli:SMc01431 233 ELVELTGFPITSTLMGLGAYPASGKNWLGMLGMHGTYEANLAMHDCDVMICIGARFDDRITGRLNAFSPNSKKIH 307 *************************************************************************** PP TIGR00118 297 ididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.WlekieewkkeyilkldeeeesikPqkv 366 ididP++i+knv+vd+pi+Gd+ vle++++ ++ +++ W+++i++w++++ l++ + + i Pq+ lcl|FitnessBrowser__Smeli:SMc01431 308 IDIDPSSINKNVRVDVPIIGDVAAVLEDMIRLWRAAaktvDQTRLGdWWKSISKWRARNSLAYTPSADVIMPQYA 382 *****************************998776655553444336**************************** PP TIGR00118 367 ikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsf 440 i++l++l+kd ++++tt+vGqhqmwaaqf+ +++p++++tsgGlGtmG+G+Paa+G++va+pe+ v++++Gd+s+ lcl|FitnessBrowser__Smeli:SMc01431 383 IQRLYELTKDrDTYITTEVGQHQMWAAQFFGFEEPNRWMTSGGLGTMGYGFPAAVGVQVAHPESLVIDIAGDASI 457 *********999*************************************************************** PP TIGR00118 441 qmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeele 515 qm +qe+s +v+y++pvki ilnn+++Gmv+qWq+l++ +r s+++ ++ +pdfvklaeayG +gir ekp el+ lcl|FitnessBrowser__Smeli:SMc01431 458 QMCIQEMSCAVQYGLPVKIFILNNQYMGMVRQWQQLLHGNRLSHSYTEA-MPDFVKLAEAYGGVGIRCEKPGELD 531 ************************************************5.************************* PP TIGR00118 516 eklkealeskepvlldvevdkeeevlPmvapGagldelve 555 +++++++ + +pv++d +v++ ++++Pm+++G++ +e++ lcl|FitnessBrowser__Smeli:SMc01431 532 DAIRQMIDTPAPVIFDCRVANLANCFPMIPSGKAHNEMLL 571 *************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (592 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.33 // [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