Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_085635848.1 MGEO_RS06270 acetolactate synthase 3 large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_002115805.1:WP_085635848.1 Length = 584 Score = 601 bits (1549), Expect = e-176 Identities = 303/567 (53%), Positives = 400/567 (70%), Gaps = 5/567 (0%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 +M GA+++V AL ++GV+ V+GYPGGAVL IYDE+ +Q H LVRHEQ AVHAA+GYA Sbjct: 4 QMTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFQQNGIRHYLVRHEQGAVHAAEGYA 63 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 RATGK GV LVTSGPG TNAVTG+ A +DSIP+VV+TG VPT IG DAFQE DTVGIT Sbjct: 64 RATGKPGVVLVTSGPGATNAVTGLTDALMDSIPIVVLTGQVPTFMIGSDAFQEADTVGIT 123 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RP KHN+LVKD L+ I +AF +A +GRPGPV++DIPKDV + Y + Sbjct: 124 RPCTKHNWLVKDTDTLSGIIHEAFHVATSGRPGPVLIDIPKDVQFASGAYTEKAKASVSH 183 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255 Y P KG I + V ++ AERP YTGGGVV + AS LR+L TG P+T+TLM Sbjct: 184 YQPQVKGDMETITQLVEAIETAERPVFYTGGGVVNSGPGASQLLRELVDATGIPITSTLM 243 Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315 GLG +P + K ++GMLGMHG YEAN+AM CD++I +GARFDDR+ G F+ ++RK Sbjct: 244 GLGCYPASGKNWLGMLGMHGLYEANLAMHGCDLMINVGARFDDRITGRLDAFSPKSRK-A 302 Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375 HIDIDPSSI+K ++VD+PI+G+V VL++++ KA K REA+ KWW +IE+WR VD Sbjct: 303 HIDIDPSSINKVIRVDMPIIGDVGHVLEDVLKVWKARGRKVNREAIQKWWARIEEWRKVD 362 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434 CLKY S + I+PQ+ ++++ LTKG D +IC++VGQHQMWAAQ+ F++P RW+ SGGL Sbjct: 363 CLKYKPSGKTIRPQHALDRLEALTKGRDRYICTEVGQHQMWAAQYLGFEDPNRWMTSGGL 422 Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494 GTMG G P ++G++ A P+ V+ + GE S M +QE+ T +QY PVK LNN LGM Sbjct: 423 GTMGYGTPASIGVQVAHPDALVINVAGEASWLMNMQEMGTAVQYRLPVKQFILNNERLGM 482 Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554 VRQWQE+ + RYSHS+ +ALPDFVKLAEA+G G+ +D++ A+ E D V Sbjct: 483 VRQWQELLHGERYSHSWSEALPDFVKLAEAFGCKGILCSDPADLDDAIMEMLDY-DGPVI 541 Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLG 581 D + EN +PM+ +G+ ++MLLG Sbjct: 542 FDCLVEKHENCFPMIPSGEPHNKMLLG 568 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: 989 Number of extensions: 31 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: 585 Length of database: 584 Length adjustment: 37 Effective length of query: 548 Effective length of database: 547 Effective search space: 299756 Effective search space used: 299756 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_085635848.1 MGEO_RS06270 (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.2982043.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-236 769.9 0.0 8e-236 769.7 0.0 1.0 1 NCBI__GCF_002115805.1:WP_085635848.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085635848.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 769.7 0.0 8e-236 8e-236 1 554 [. 5 566 .. 5 569 .. 0.98 Alignments for each domain: == domain 1 score: 769.7 bits; conditional E-value: 8e-236 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 ++ga+++v++lk++gv+tvfGyPGGavlpiyd+++ +++++h lvrheq+a+haa+Gyara+Gk+Gvvl+tsG NCBI__GCF_002115805.1:WP_085635848.1 5 MTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFqQNGIRHYLVRHEQGAVHAAEGYARATGKPGVVLVTSG 77 79*********************************999*********************************** PP TIGR00118 73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145 PGatn+vtg+++a +ds+P+vvltGqv+t +iGsdafqe+d +Git+p+tkh++lvk+++ l+ i++eaf++a NCBI__GCF_002115805.1:WP_085635848.1 78 PGATNAVTGLTDALMDSIPIVVLTGQVPTFMIGSDAFQEADTVGITRPCTKHNWLVKDTDTLSGIIHEAFHVA 150 ************************************************************************* PP TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviia..ea 216 ++GrPGPvl+d+Pkdv+ a+ ++ ++k ++ y+p+vkg+ i +++e+ie+a++Pv + GgGv+ + +a NCBI__GCF_002115805.1:WP_085635848.1 151 TSGRPGPVLIDIPKDVQFASGAYTEKAKASVSHYQPQVKGDMETITQLVEAIETAERPVFYTGGGVVNSgpGA 223 *******************************************************************873369 PP TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289 s+ l+el++++ ip+t+tl+GlG++p+ ++ lgmlGmhG +eanla++ +dl+i vGarfddr+tg l+ f+ NCBI__GCF_002115805.1:WP_085635848.1 224 SQLLRELVDATGIPITSTLMGLGCYPASGKNWLGMLGMHGLYEANLAMHGCDLMINVGARFDDRITGRLDAFS 296 9************************************************************************ PP TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldee 357 p+++ hididP++i+k+++vd+pi+Gd+ +vle++lk k++ +++ ++ W+++ieew+k +lk++ + NCBI__GCF_002115805.1:WP_085635848.1 297 PKSRKAHIDIDPSSINKVIRVDMPIIGDVGHVLEDVLKVWKARgrkvNREAIQkWWARIEEWRKVDCLKYKPS 369 *************************************98877766666666677******************* PP TIGR00118 358 eesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpee 429 ++i+Pq+ +++l l+k+ + ++ t+vGqhqmwaaq++ ++ p++++tsgGlGtmG+G Pa++G++va+p++ NCBI__GCF_002115805.1:WP_085635848.1 370 GKTIRPQHALDRLEALTKGrDRYICTEVGQHQMWAAQYLGFEDPNRWMTSGGLGTMGYGTPASIGVQVAHPDA 442 ******************9899*************************************************** PP TIGR00118 430 tvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502 v++v+G++s mn+qe+ t+v+y +pvk ilnne lGmv+qWqel++ erys++ ++ lpdfvklaea+G NCBI__GCF_002115805.1:WP_085635848.1 443 LVINVAGEASWLMNMQEMGTAVQYRLPVKQFILNNERLGMVRQWQELLHGERYSHSWSEA-LPDFVKLAEAFG 514 ********************************************************9995.************ PP TIGR00118 503 vkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554 kgi ++p++l++++ e+l ++pv++d v+k+e+++Pm+++G ++++ NCBI__GCF_002115805.1:WP_085635848.1 515 CKGILCSDPADLDDAIMEMLDYDGPVIFDCLVEKHENCFPMIPSGEPHNKML 566 **********************************************999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (584 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: 00:00:00.01 # Mc/sec: 24.84 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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