Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate H281DRAFT_04551 H281DRAFT_04551 acetolactate synthase, large subunit
Query= metacyc::MONOMER-18810 (585 letters) >FitnessBrowser__Burk376:H281DRAFT_04551 Length = 587 Score = 951 bits (2458), Expect = 0.0 Identities = 455/585 (77%), Positives = 522/585 (89%) Query: 1 MPSAEFSHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEH 60 MPSAEFS +D+ + IGA +L+ ALA+E VE+VWGYPGG+VLYIYDEL+KQ KF+H Sbjct: 3 MPSAEFSTSDTTPQHEADSIGATVLMKALADEDVEFVWGYPGGSVLYIYDELYKQDKFQH 62 Query: 61 ILVRHEQAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPT 120 ILVRHEQAAVHAAD Y+R+TGKVGV LVTSGPGVTNAVTGIATAY+DSIPMVVI+G VPT Sbjct: 63 ILVRHEQAAVHAADAYSRSTGKVGVCLVTSGPGVTNAVTGIATAYMDSIPMVVISGQVPT 122 Query: 121 HAIGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDV 180 AIGQDAFQECDTVGITRP VKHNFLVKDVRDLAAT+KKAF+IA TGRPGPV++DIPKDV Sbjct: 123 AAIGQDAFQECDTVGITRPCVKHNFLVKDVRDLAATVKKAFYIARTGRPGPVLIDIPKDV 182 Query: 181 SRNACKYEYPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELR 240 S+ C+YE K++ +RSYNPV KGHSGQIRKAV+LL A+RPYIYTGGG++LA+AS EL Sbjct: 183 SKAPCQYEPIKTVSLRSYNPVTKGHSGQIRKAVSLLLSAKRPYIYTGGGIILADASRELN 242 Query: 241 QLAALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRV 300 Q A L G+P+TNTLMGLG + + K+F+GMLGMHGTYEANMAMQ+CDVLIAIGARFDDRV Sbjct: 243 QFADLLGYPITNTLMGLGGYRASDKKFLGMLGMHGTYEANMAMQHCDVLIAIGARFDDRV 302 Query: 301 IGNPAHFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREA 360 IG+PAHF S+ RKIIHIDIDPSSISKRVKVDIPIVG+VK+VL+ELI Q++ ++ P A Sbjct: 303 IGDPAHFASRPRKIIHIDIDPSSISKRVKVDIPIVGDVKEVLKELIEQLQTAEHGPDTAA 362 Query: 361 LAKWWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFY 420 LA WW+ IE WR+ DCLK+DR S++IKPQYVVEK WELT G+AF+CSDVGQHQMWAAQFY Sbjct: 363 LADWWKDIEAWRAKDCLKFDRKSDVIKPQYVVEKAWELTDGNAFVCSDVGQHQMWAAQFY 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: 1064 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 H281DRAFT_04551 H281DRAFT_04551 (acetolactate synthase, 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.28093.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-261 854.3 0.0 2.2e-261 854.1 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04551 H281DRAFT_04551 acetolactate syn Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04551 H281DRAFT_04551 acetolactate synthase, large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 854.1 0.0 2.2e-261 2.2e-261 3 554 .. 23 581 .. 21 584 .. 0.98 Alignments for each domain: == domain 1 score: 854.1 bits; conditional E-value: 2.2e-261 TIGR00118 3 gaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvv 67 ga++l+++l +e+ve v+GyPGG+vl iyd+ly +++++hilvrheqaa+haad y+r++GkvGv+ lcl|FitnessBrowser__Burk376:H281DRAFT_04551 23 GATVLMKALADEDVEFVWGYPGGSVLYIYDELYkQDKFQHILVRHEQAAVHAADAYSRSTGKVGVC 88 899******************************999****************************** PP TIGR00118 68 latsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaed 133 l+tsGPG tn+vtgiatay+ds+P+vv++Gqv+t++iG+dafqe+d +Git+p++kh+flvk+++d lcl|FitnessBrowser__Burk376:H281DRAFT_04551 89 LVTSGPGVTNAVTGIATAYMDSIPMVVISGQVPTAAIGQDAFQECDTVGITRPCVKHNFLVKDVRD 154 ****************************************************************** PP TIGR00118 134 lpeilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliek 199 l++++k+af+ia tGrPGPvl+d+Pkdv++a +++e ++v+l++y+p +kgh qi+ka+ l+ + lcl|FitnessBrowser__Burk376:H281DRAFT_04551 155 LAATVKKAFYIARTGRPGPVLIDIPKDVSKAPCQYEPIKTVSLRSYNPVTKGHSGQIRKAVSLLLS 220 ****************************************************************** PP TIGR00118 200 akkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavs 265 ak+P ++ GgG+i a+as+el+++a+ l p+t tl+GlG++ + ++++lgmlGmhGt+ean+a++ lcl|FitnessBrowser__Burk376:H281DRAFT_04551 221 AKRPYIYTGGGIILADASRELNQFADLLGYPITNTLMGLGGYRASDKKFLGMLGMHGTYEANMAMQ 286 ****************************************************************** PP TIGR00118 266 eadlliavGarfddrvtgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklk 330 ++d+lia+Garfddrv g+ a+fa++ kiihididP++i+k vkvdipivGd+k+vl+el+++l+ lcl|FitnessBrowser__Burk376:H281DRAFT_04551 287 HCDVLIAIGARFDDRVIGDPAHFASRPrKIIHIDIDPSSISKRVKVDIPIVGDVKEVLKELIEQLQ 352 ************************98626***********************************99 PP TIGR00118 331 ee....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwa 391 + ++ W++ ie w+++ +lk+d++++ ikPq+v+++ ++l++++a+v +dvGqhqmwa lcl|FitnessBrowser__Burk376:H281DRAFT_04551 353 TAehgpDTAALAdWWKDIEAWRAKDCLKFDRKSDVIKPQYVVEKAWELTDGNAFVCSDVGQHQMWA 418 9866653333335***************************************************** PP TIGR00118 392 aqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipv 457 aqfy+++kpr++i+sgGlGtmGfGlPaa+G+k+a+p+++v+++tG+gs+qm +qelst+++y++pv lcl|FitnessBrowser__Burk376:H281DRAFT_04551 419 AQFYRFNKPRRWINSGGLGTMGFGLPAAMGVKMAHPDDDVLCITGEGSIQMCIQELSTCKQYETPV 484 ****************************************************************** PP TIGR00118 458 kivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkeale 523 ki+ lnn++lGmv+qWq++ y++rys++++ + lpdfvklaeayG++g+rie+ +++e +lkeal+ lcl|FitnessBrowser__Burk376:H281DRAFT_04551 485 KIISLNNRYLGMVRQWQQIEYSKRYSHSYMDA-LPDFVKLAEAYGHVGMRIERTADVEPALKEALR 549 *******************************5.********************************9 PP TIGR00118 524 sk.epvlldvevdkeeevlPmvapGagldelv 554 k + v+ld++ d +e+v+Pmv G+g++e++ lcl|FitnessBrowser__Burk376:H281DRAFT_04551 550 LKdRTVFLDFQTDPTENVWPMVQAGKGITEML 581 88689*************************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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11.35 // [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