Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_028999235.1 H537_RS0119920 acetolactate synthase 3 catalytic subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000430725.1:WP_028999235.1 Length = 590 Score = 906 bits (2341), Expect = 0.0 Identities = 439/573 (76%), Positives = 500/573 (87%), Gaps = 1/573 (0%) Query: 14 SAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAA 73 S + E+ G+EILV +L EGV+Y+WGYPGG+VLYIYD L+KQ +H+LVRHEQAAVHAA Sbjct: 18 SPSAELNGSEILVRSLQAEGVKYLWGYPGGSVLYIYDALYKQDSIQHVLVRHEQAAVHAA 77 Query: 74 DGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDT 133 DGYARATG+VGVALVTSGPGVTNAVTGIATAY+DSIPMV+ITG VPT AIG DAFQECDT Sbjct: 78 DGYARATGEVGVALVTSGPGVTNAVTGIATAYMDSIPMVIITGQVPTAAIGLDAFQECDT 137 Query: 134 VGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSI 193 VGITRPIVKHNFLVKDVR+LA T+KKAF IA TGRPGPVVVDIPKDVS + YP + Sbjct: 138 VGITRPIVKHNFLVKDVRELALTLKKAFHIARTGRPGPVVVDIPKDVSLKTAPFSYPDKV 197 Query: 194 DMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNT 253 +MRSYNPV KGH GQIRKAV LL A+RPYIY+GGGVVLANA+ ELR+LA L G+P TNT Sbjct: 198 EMRSYNPVRKGHGGQIRKAVQLLLQAKRPYIYSGGGVVLANAAAELRELADLLGYPCTNT 257 Query: 254 LMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARK 313 LMGLGA P + +F+GMLGMHGTYEANM MQ+CDVL+A+GARFDDRVIGNPAHF S RK Sbjct: 258 LMGLGAIPASDPKFLGMLGMHGTYEANMTMQHCDVLLAVGARFDDRVIGNPAHFASVERK 317 Query: 314 IIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRS 373 I+H+DIDPSSISKRVKVDIPIVG+VK+VLQELIAQI+ + +P ++A+A WW Q+ WR Sbjct: 318 IVHVDIDPSSISKRVKVDIPIVGDVKEVLQELIAQIREAQQRPDQQAMAHWWSQVNGWRQ 377 Query: 374 VDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSG 432 +CL Y SSE+IKPQYVV+K+ ELT+G D +I SDVGQHQM+AAQFY F+EPRRWINSG Sbjct: 378 RECLAYKNSSEVIKPQYVVQKLAELTRGRDTYITSDVGQHQMFAAQFYGFEEPRRWINSG 437 Query: 433 GLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYL 492 GLGTMGVGLPYAMGIK A PE +V ITGEGSIQMCIQELSTC QY TPVK+ SLNN YL Sbjct: 438 GLGTMGVGLPYAMGIKLAKPESDVFCITGEGSIQMCIQELSTCQQYKTPVKVISLNNRYL 497 Query: 493 GMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRT 552 GMVRQWQE++Y+ RYSHSYMDALPDFVKLAEAYGHVG+++E+ +DVEPALREA RL DRT Sbjct: 498 GMVRQWQELDYEGRYSHSYMDALPDFVKLAEAYGHVGLKIERPADVEPALREAIRLTDRT 557 Query: 553 VFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585 VFLD +TDPTENVWPMV+AGKGISEMLLG+EDL Sbjct: 558 VFLDIRTDPTENVWPMVKAGKGISEMLLGSEDL 590 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: 1051 Number of extensions: 31 Number of successful extensions: 2 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: 590 Length adjustment: 37 Effective length of query: 548 Effective length of database: 553 Effective search space: 303044 Effective search space used: 303044 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_028999235.1 H537_RS0119920 (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.3828266.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-257 840.0 0.1 4.8e-257 839.8 0.1 1.0 1 NCBI__GCF_000430725.1:WP_028999235.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000430725.1:WP_028999235.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 839.8 0.1 4.8e-257 4.8e-257 2 554 .. 24 584 .. 23 587 .. 0.98 Alignments for each domain: == domain 1 score: 839.8 bits; conditional E-value: 4.8e-257 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 +g+eilv+sl++egv++++GyPGG+vl iydaly ++ ++h+lvrheqaa+haadGyara+G+vGv+l+tsGP NCBI__GCF_000430725.1:WP_028999235.1 24 NGSEILVRSLQAEGVKYLWGYPGGSVLYIYDALYkQDSIQHVLVRHEQAAVHAADGYARATGEVGVALVTSGP 96 799*******************************9999*********************************** PP TIGR00118 74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146 G tn+vtgiatay+ds+P+v++tGqv+t++iG dafqe+d +Git+p++kh+flvk++++l+ +lk+af+ia NCBI__GCF_000430725.1:WP_028999235.1 97 GVTNAVTGIATAYMDSIPMVIITGQVPTAAIGLDAFQECDTVGITRPIVKHNFLVKDVRELALTLKKAFHIAR 169 ************************************************************************* PP TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeasee 219 tGrPGPv+vd+Pkdv+ ++ +++++kve+++y+p kgh qi+ka++l+ +ak+P ++ GgGv+ a+a +e NCBI__GCF_000430725.1:WP_028999235.1 170 TGRPGPVVVDIPKDVSLKTAPFSYPDKVEMRSYNPVRKGHGGQIRKAVQLLLQAKRPYIYSGGGVVLANAAAE 242 ************************************************************************* PP TIGR00118 220 lkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfap.e 291 l+ela+ l p t tl+GlGa+p+ +p++lgmlGmhGt+ean++++++d+l+avGarfddrv gn a+fa+ e NCBI__GCF_000430725.1:WP_028999235.1 243 LRELADLLGYPCTNTLMGLGAIPASDPKFLGMLGMHGTYEANMTMQHCDVLLAVGARFDDRVIGNPAHFASvE 315 *********************************************************************9757 PP TIGR00118 292 akiihididPaeigknvkvdipivGdakkvleellkklkee.....ekkekeWlekieewkkeyilkldeeee 359 ki+h+didP++i+k vkvdipivGd+k+vl+el+++++e ++ +W+++++ w+++ +l++++++e NCBI__GCF_000430725.1:WP_028999235.1 316 RKIVHVDIDPSSISKRVKVDIPIVGDVKEVLQELIAQIREAqqrpdQQAMAHWWSQVNGWRQRECLAYKNSSE 388 89***********************************999866663333445********************* PP TIGR00118 360 sikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetv 431 ikPq+v+++l +l+++ ++++t+dvGqhqm+aaqfy +++pr++i+sgGlGtmG GlP a+G+k+akpe++v NCBI__GCF_000430725.1:WP_028999235.1 389 VIKPQYVVQKLAELTRGrDTYITSDVGQHQMFAAQFYGFEEPRRWINSGGLGTMGVGLPYAMGIKLAKPESDV 461 ***************9989****************************************************** PP TIGR00118 432 vavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvk 504 ++tG+gs+qm +qelst+++y++pvk++ lnn++lGmv+qWqel ye+rys++++ + lpdfvklaeayG++ NCBI__GCF_000430725.1:WP_028999235.1 462 FCITGEGSIQMCIQELSTCQQYKTPVKVISLNNRYLGMVRQWQELDYEGRYSHSYMDA-LPDFVKLAEAYGHV 533 *********************************************************5.************** PP TIGR00118 505 giriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelv 554 g++ie+p+++e +l+ea++ + + v+ld++ d +e+v+Pmv G+g++e++ NCBI__GCF_000430725.1:WP_028999235.1 534 GLKIERPADVEPALREAIRLTdRTVFLDIRTDPTENVWPMVKAGKGISEML 584 ******************976599*************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (590 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: 00:00:00.02 # Mc/sec: 15.86 // [ok]
This GapMind analysis is from Jul 25 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