Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_077244874.1 B1A74_RS12995 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_001995255.1:WP_077244874.1 Length = 572 Score = 798 bits (2062), Expect = 0.0 Identities = 384/568 (67%), Positives = 463/568 (81%), Gaps = 1/568 (0%) Query: 13 SSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHA 72 S+++ + GAEI V +L EGV+ V+GYPGGAVL+IYD L++Q++ H+LVRHEQ AVHA Sbjct: 5 SASSTAITGAEIFVRSLQAEGVDLVFGYPGGAVLHIYDALYQQSEVSHVLVRHEQGAVHA 64 Query: 73 ADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECD 132 A+GYA+++ + GVALVTSGPG TNA+TGIA AY+DS+P+VV TG VPT IG DAFQE D Sbjct: 65 AEGYAKSSDRPGVALVTSGPGATNAITGIADAYMDSVPLVVFTGQVPTSMIGNDAFQEVD 124 Query: 133 TVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKS 192 TVGITRP VKHNFLVKDV+DLA TIKKAF+IA TGRPGPVVVDIPKDV+ ++C++EYP+S Sbjct: 125 TVGITRPCVKHNFLVKDVKDLATTIKKAFYIATTGRPGPVVVDIPKDVTADSCEFEYPES 184 Query: 193 IDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTN 252 I MRSYNP +GH+GQIR+AV L+ A++P IYTGGGVVL S+ L + G+P+TN Sbjct: 185 IHMRSYNPKVRGHTGQIRRAVELILSAKQPMIYTGGGVVLGRGSEALTEFTRKLGYPITN 244 Query: 253 TLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQAR 312 TLMGLGA+P + QF+GMLGMHGTYEANMAM + DVLIAIGARFDDRV GN F A Sbjct: 245 TLMGLGAYPASDDQFLGMLGMHGTYEANMAMHHADVLIAIGARFDDRVTGNIEKFCPHA- 303 Query: 313 KIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWR 372 KI+H+D+DP+SISK VKVD+PIVG V+ VL+ELI ++ + +P +AL WW+QI +WR Sbjct: 304 KIVHVDVDPASISKNVKVDVPIVGEVEPVLRELIRALEENGGQPDADALKAWWDQIREWR 363 Query: 373 SVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSG 432 DCLKYDR SE+IKPQYVV+K WELT GDAF+ SDVGQHQMWAAQFY FD+P RWINSG Sbjct: 364 GQDCLKYDRDSELIKPQYVVQKFWELTGGDAFVTSDVGQHQMWAAQFYGFDKPNRWINSG 423 Query: 433 GLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYL 492 GLGTMGVGLP+AMG++ A P+ V ITGE SIQMC+QELSTC QY P+KI +LNN YL Sbjct: 424 GLGTMGVGLPFAMGVQFAHPDATVGCITGEASIQMCMQELSTCYQYQLPLKILNLNNRYL 483 Query: 493 GMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRT 552 GMVRQWQE Y RY+ SYMDALPDFVKLAEAYGHVGMR++K +DVE AL+EA KDR Sbjct: 484 GMVRQWQEFFYQGRYAMSYMDALPDFVKLAEAYGHVGMRIDKPADVEGALKEALAQKDRL 543 Query: 553 VFLDFQTDPTENVWPMVQAGKGISEMLL 580 VFLDF TD +ENV+PM+ AG G +EM+L Sbjct: 544 VFLDFITDQSENVYPMIPAGAGQNEMIL 571 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: 1046 Number of extensions: 35 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: 572 Length adjustment: 36 Effective length of query: 549 Effective length of database: 536 Effective search space: 294264 Effective search space used: 294264 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_077244874.1 B1A74_RS12995 (acetolactate synthase, large subunit, biosynthetic type)
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.12020.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-264 865.0 0.2 1.3e-264 864.8 0.2 1.0 1 lcl|NCBI__GCF_001995255.1:WP_077244874.1 B1A74_RS12995 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001995255.1:WP_077244874.1 B1A74_RS12995 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 864.8 0.2 1.3e-264 1.3e-264 2 555 .. 12 571 .. 11 572 .] 0.99 Alignments for each domain: == domain 1 score: 864.8 bits; conditional E-value: 1.3e-264 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 +gaei+v+sl++egv+ vfGyPGGavl+iydaly +se++h+lvrheq+a+haa+Gya++s ++Gv+l+ lcl|NCBI__GCF_001995255.1:WP_077244874.1 12 TGAEIFVRSLQAEGVDLVFGYPGGAVLHIYDALYqQSEVSHVLVRHEQGAVHAAEGYAKSSDRPGVALV 80 89********************************99********************************* PP TIGR00118 70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138 tsGPGatn++tgia+ay+dsvPlvv+tGqv+ts+iG+dafqe+d +Git+p++kh+flvk+++dl++++ lcl|NCBI__GCF_001995255.1:WP_077244874.1 81 TSGPGATNAITGIADAYMDSVPLVVFTGQVPTSMIGNDAFQEVDTVGITRPCVKHNFLVKDVKDLATTI 149 ********************************************************************* PP TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207 k+af+ia+tGrPGPv+vd+Pkdvt+ ++e+e++e++++++y+p+v+gh+ qi++a+eli +ak+P+++ lcl|NCBI__GCF_001995255.1:WP_077244874.1 150 KKAFYIATTGRPGPVVVDIPKDVTADSCEFEYPESIHMRSYNPKVRGHTGQIRRAVELILSAKQPMIYT 218 ********************************************************************* PP TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276 GgGv+ + +se l+e++ +l p+t tl+GlGa+p+ + ++lgmlGmhGt+ean+a+++ad+lia+Gar lcl|NCBI__GCF_001995255.1:WP_077244874.1 219 GGGVVLGRGSEALTEFTRKLGYPITNTLMGLGAYPASDDQFLGMLGMHGTYEANMAMHHADVLIAIGAR 287 ********************************************************************* PP TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wl 340 fddrvtgn++kf+p+aki+h+d+dPa+i+knvkvd+pivG+++ vl+el+++l+e+ + + + W+ lcl|NCBI__GCF_001995255.1:WP_077244874.1 288 FDDRVTGNIEKFCPHAKIVHVDVDPASISKNVKVDVPIVGEVEPVLRELIRALEENggqpDADALKaWW 356 ******************************************************9998864555557** PP TIGR00118 341 ekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGl 409 ++i+ew+ + +lk+d+++e ikPq+v+++ ++l+ ++a+vt+dvGqhqmwaaqfy ++kp+++i+sgGl lcl|NCBI__GCF_001995255.1:WP_077244874.1 357 DQIREWRGQDCLKYDRDSELIKPQYVVQKFWELTGGDAFVTSDVGQHQMWAAQFYGFDKPNRWINSGGL 425 ********************************************************************* PP TIGR00118 410 GtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfy 478 GtmG GlP a+G++ a+p++tv ++tG++s+qm +qelst+ +y++p+ki++lnn++lGmv+qWqe+fy lcl|NCBI__GCF_001995255.1:WP_077244874.1 426 GTMGVGLPFAMGVQFAHPDATVGCITGEASIQMCMQELSTCYQYQLPLKILNLNNRYLGMVRQWQEFFY 494 ********************************************************************* PP TIGR00118 479 eerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvap 546 ++ry+ +++ + lpdfvklaeayG++g+ri kp+++e +lkeal++k ++v+ld+ d++e+v+Pm++ lcl|NCBI__GCF_001995255.1:WP_077244874.1 495 QGRYAMSYMDA-LPDFVKLAEAYGHVGMRIDKPADVEGALKEALAQKdRLVFLDFITDQSENVYPMIPA 562 **********5.********************************998799******************* PP TIGR00118 547 Gagldelve 555 Gag +e++ lcl|NCBI__GCF_001995255.1:WP_077244874.1 563 GAGQNEMIL 571 *******85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (572 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 7.49 // [ok]
This GapMind analysis is from Apr 10 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