Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate BPHYT_RS06545 BPHYT_RS06545 acetolactate synthase
Query= metacyc::MONOMER-18810 (585 letters) >FitnessBrowser__BFirm:BPHYT_RS06545 Length = 587 Score = 953 bits (2464), Expect = 0.0 Identities = 458/585 (78%), Positives = 523/585 (89%) Query: 1 MPSAEFSHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEH 60 MPSAEFS +D+ + IGA +L+ ALA+E VE+VWGYPGG+VLYIYDEL+KQ KF+H Sbjct: 3 MPSAEFSTSDTTPHPEADSIGATVLMKALADEDVEFVWGYPGGSVLYIYDELYKQDKFQH 62 Query: 61 ILVRHEQAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPT 120 ILVRHEQAAVHAAD Y+R+TGKVGV LVTSGPGVTNAVTGIATAY+DSIPMVVI+G VPT Sbjct: 63 ILVRHEQAAVHAADAYSRSTGKVGVCLVTSGPGVTNAVTGIATAYMDSIPMVVISGQVPT 122 Query: 121 HAIGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDV 180 AIGQDAFQECDTVGITRP VKHNFLVKDVRDLAAT+KKAFFIA TGRPGPV++DIPKDV Sbjct: 123 AAIGQDAFQECDTVGITRPCVKHNFLVKDVRDLAATVKKAFFIARTGRPGPVLIDIPKDV 182 Query: 181 SRNACKYEYPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELR 240 S+ C+YE K++ +RSYNPV KGHSGQIRKAV+LL A+RPYIYTGGG++LA+AS EL Sbjct: 183 SKAPCQYEPLKTVSLRSYNPVTKGHSGQIRKAVSLLLSAKRPYIYTGGGIILADASRELN 242 Query: 241 QLAALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRV 300 Q A L G+PVTNTLMGLG + + K+F+GMLGMHGTYEANMAMQ+CDVLIAIGARFDDRV Sbjct: 243 QFADLLGYPVTNTLMGLGGYRASDKKFLGMLGMHGTYEANMAMQHCDVLIAIGARFDDRV 302 Query: 301 IGNPAHFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREA 360 IG+PAHF+S+ RKIIHIDIDPSSISKRVKVDIPIVG+VK+VL+ELI Q++ ++ P A Sbjct: 303 IGDPAHFSSRPRKIIHIDIDPSSISKRVKVDIPIVGDVKEVLKELIEQLQTAEHGPDTAA 362 Query: 361 LAKWWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFY 420 LA WW+ IE WR+ DCLK+DR S+IIKPQYVVEK WELT G+AF+CSDVGQHQMWAAQFY Sbjct: 363 LADWWKDIEAWRAKDCLKFDRKSDIIKPQYVVEKAWELTDGNAFVCSDVGQHQMWAAQFY 422 Query: 421 KFDEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDT 480 +F++PRRWINSGGLGTMG GLP AMG+K A P+ +V+ ITGEGSIQMCIQELSTC QY+T Sbjct: 423 RFNKPRRWINSGGLGTMGFGLPAAMGVKMAHPDDDVLCITGEGSIQMCIQELSTCKQYET 482 Query: 481 PVKICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEP 540 PVKI SLNN YLGMVRQWQ+IEY RYSHSYMDALPDFVKLAEAYGHVGMR+E+T+DVEP Sbjct: 483 PVKIISLNNRYLGMVRQWQQIEYSKRYSHSYMDALPDFVKLAEAYGHVGMRIERTADVEP 542 Query: 541 ALREAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585 AL+EA RLKDRTVFLDFQTDPTENVWPMVQAGKGI+EML+G+EDL Sbjct: 543 ALKEALRLKDRTVFLDFQTDPTENVWPMVQAGKGITEMLMGSEDL 587 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: 1061 Number of extensions: 25 Number of successful extensions: 1 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: 587 Length adjustment: 37 Effective length of query: 548 Effective length of database: 550 Effective search space: 301400 Effective search space used: 301400 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 BPHYT_RS06545 BPHYT_RS06545 (acetolactate synthase)
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.6330.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-261 852.8 0.0 6.5e-261 852.5 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS06545 BPHYT_RS06545 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS06545 BPHYT_RS06545 acetolactate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 852.5 0.0 6.5e-261 6.5e-261 3 554 .. 23 581 .. 21 584 .. 0.98 Alignments for each domain: == domain 1 score: 852.5 bits; conditional E-value: 6.5e-261 TIGR00118 3 gaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlats 71 ga++l+++l +e+ve v+GyPGG+vl iyd+ly +++++hilvrheqaa+haad y+r++GkvGv+l+ts lcl|FitnessBrowser__BFirm:BPHYT_RS06545 23 GATVLMKALADEDVEFVWGYPGGSVLYIYDELYkQDKFQHILVRHEQAAVHAADAYSRSTGKVGVCLVTS 92 899******************************999********************************** PP TIGR00118 72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkea 141 GPG tn+vtgiatay+ds+P+vv++Gqv+t++iG+dafqe+d +Git+p++kh+flvk+++dl++++k+a lcl|FitnessBrowser__BFirm:BPHYT_RS06545 93 GPGVTNAVTGIATAYMDSIPMVVISGQVPTAAIGQDAFQECDTVGITRPCVKHNFLVKDVRDLAATVKKA 162 ********************************************************************** PP TIGR00118 142 feiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGv 211 f ia tGrPGPvl+d+Pkdv++a +++e ++v+l++y+p +kgh qi+ka+ l+ +ak+P ++ GgG+ lcl|FitnessBrowser__BFirm:BPHYT_RS06545 163 FFIARTGRPGPVLIDIPKDVSKAPCQYEPLKTVSLRSYNPVTKGHSGQIRKAVSLLLSAKRPYIYTGGGI 232 ********************************************************************** PP TIGR00118 212 iiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrv 281 i a+as+el+++a+ l pvt tl+GlG++ + ++++lgmlGmhGt+ean+a++++d+lia+Garfddrv lcl|FitnessBrowser__BFirm:BPHYT_RS06545 233 ILADASRELNQFADLLGYPVTNTLMGLGGYRASDKKFLGMLGMHGTYEANMAMQHCDVLIAIGARFDDRV 302 ********************************************************************** PP TIGR00118 282 tgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekiee 345 g+ a+f+++ kiihididP++i+k vkvdipivGd+k+vl+el+++l++ ++ W++ ie lcl|FitnessBrowser__BFirm:BPHYT_RS06545 303 IGDPAHFSSRPrKIIHIDIDPSSISKRVKVDIPIVGDVKEVLKELIEQLQTAehgpDTAALAdWWKDIEA 372 *******998627***********************************999866653333335******* PP TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfG 415 w+++ +lk+d++++ ikPq+v+++ ++l++++a+v +dvGqhqmwaaqfy+++kpr++i+sgGlGtmGfG lcl|FitnessBrowser__BFirm:BPHYT_RS06545 373 WRAKDCLKFDRKSDIIKPQYVVEKAWELTDGNAFVCSDVGQHQMWAAQFYRFNKPRRWINSGGLGTMGFG 442 ********************************************************************** PP TIGR00118 416 lPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeeryset 485 lPaa+G+k+a+p+++v+++tG+gs+qm +qelst+++y++pvki+ lnn++lGmv+qWq++ y++rys++ lcl|FitnessBrowser__BFirm:BPHYT_RS06545 443 LPAAMGVKMAHPDDDVLCITGEGSIQMCIQELSTCKQYETPVKIISLNNRYLGMVRQWQQIEYSKRYSHS 512 ********************************************************************** PP TIGR00118 486 klaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelv 554 ++ + lpdfvklaeayG++g+rie+ +++e +lkeal+ k + v+ld++ d +e+v+Pmv G+g++e++ lcl|FitnessBrowser__BFirm:BPHYT_RS06545 513 YMDA-LPDFVKLAEAYGHVGMRIERTADVEPALKEALRLKdRTVFLDFQTDPTENVWPMVQAGKGITEML 581 ***5.********************************988689*************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (587 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: 00:00:00.03 # Mc/sec: 8.45 // [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