Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_052306284.1 BPHY_RS37050 biosynthetic-type acetolactate synthase large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000020045.1:WP_052306284.1 Length = 584 Score = 760 bits (1963), Expect = 0.0 Identities = 364/565 (64%), Positives = 441/565 (78%), Gaps = 2/565 (0%) Query: 21 GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80 GA+I++ L EGV+ VWGYPGGAVL +YD L + H+LVRHEQAAVHAADG+ARAT Sbjct: 20 GAQIVLSVLRAEGVDTVWGYPGGAVLPLYDALQETVDITHLLVRHEQAAVHAADGFARAT 79 Query: 81 GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140 GKVGVALVTSGPGVTN VTGIATAY DSIPMVVI+GNVPTH+IG DAFQECD VGITR I Sbjct: 80 GKVGVALVTSGPGVTNTVTGIATAYFDSIPMVVISGNVPTHSIGTDAFQECDAVGITRSI 139 Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200 VKHNFLV D+ LA T+K AF+IA TGRPGPV+VDIPKDV + +S+ +RSY P Sbjct: 140 VKHNFLVLDISQLAKTLKSAFYIARTGRPGPVLVDIPKDVLQAKTPLSIAESVALRSYRP 199 Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260 + H GQ+R+A L + RP I GGG V + AS+E+ +L PVTNTLM LGAF Sbjct: 200 RTEPHVGQVRRAAEALARSRRPCILVGGGAVASAASEEIAELVRRLDAPVTNTLMALGAF 259 Query: 261 PGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHIDID 320 P + ++ +GM G+HGTYEAN+AMQ+CDVLIA+GARFDDRVIGN F S R IIH+DID Sbjct: 260 PASDRRCLGMPGLHGTYEANLAMQHCDVLIALGARFDDRVIGNTGEFQSDRRTIIHVDID 319 Query: 321 PSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCLKYD 380 P++I KRV+VDIPIVG+VK + ++ Q++A I WW++I WR CL Y+ Sbjct: 320 PATIDKRVQVDIPIVGDVKTAARAILEQLRAQRINDGNR--NDWWKEIGNWREKRCLAYE 377 Query: 381 RSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMGVG 440 +++IKPQ+V++++WE T GDA+ICSDVGQHQMWAAQ Y FD+PRRWINSGGLGTMGVG Sbjct: 378 PDADVIKPQFVIQQLWEATGGDAYICSDVGQHQMWAAQLYGFDKPRRWINSGGLGTMGVG 437 Query: 441 LPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQWQE 500 LPYAMG+K+A P+ +VV +TG+GSIQMCIQELSTC QYD VKI SLNNGYLGMVRQ Q Sbjct: 438 LPYAMGVKRALPDADVVAVTGDGSIQMCIQELSTCRQYDLGVKIVSLNNGYLGMVRQLQH 497 Query: 501 IEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDFQTD 560 + Y +RYSHSYMDALPDFV LA AYGHVG R+E+ DVEP LREA +K RTVF+DF D Sbjct: 498 VNYRDRYSHSYMDALPDFVALARAYGHVGFRIERPCDVEPVLREALAMKQRTVFMDFAID 557 Query: 561 PTENVWPMVQAGKGISEMLLGAEDL 585 P+ENVWPMV+AG G+++ML+ + D+ Sbjct: 558 PSENVWPMVRAGAGLTDMLMNSRDV 582 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: 1005 Number of extensions: 26 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: 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_052306284.1 BPHY_RS37050 (biosynthetic-type 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.4020244.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-240 785.6 0.0 1.5e-240 785.3 0.0 1.0 1 NCBI__GCF_000020045.1:WP_052306284.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000020045.1:WP_052306284.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 785.3 0.0 1.5e-240 1.5e-240 2 555 .. 19 577 .. 18 579 .. 0.98 Alignments for each domain: == domain 1 score: 785.3 bits; conditional E-value: 1.5e-240 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 +ga+i+++ l++egv+tv+GyPGGavlp+ydal + +++h+lvrheqaa+haadG+ara+GkvGv+l+tsGP NCBI__GCF_000020045.1:WP_052306284.1 19 SGAQIVLSVLRAEGVDTVWGYPGGAVLPLYDALQeTVDITHLLVRHEQAAVHAADGFARATGKVGVALVTSGP 91 79********************************889************************************ PP TIGR00118 74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146 G tn+vtgiatay ds+P+vv++G v+t+ iG+dafqe+d +Git++++kh+flv + ++l+++lk af+ia NCBI__GCF_000020045.1:WP_052306284.1 92 GVTNTVTGIATAYFDSIPMVVISGNVPTHSIGTDAFQECDAVGITRSIVKHNFLVLDISQLAKTLKSAFYIAR 164 ************************************************************************* PP TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeasee 219 tGrPGPvlvd+Pkdv +a++ l++ e+v l++y+p++++h q+++a+e+++++++P +lvGgG++++ asee NCBI__GCF_000020045.1:WP_052306284.1 165 TGRPGPVLVDIPKDVLQAKTPLSIAESVALRSYRPRTEPHVGQVRRAAEALARSRRPCILVGGGAVASAASEE 237 ************************************************************************* PP TIGR00118 220 lkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapea 292 + el+ rl++pvt tl+ lGafp+ +++ lgm G+hGt+eanla++++d+lia+Garfddrv gn +f ++ NCBI__GCF_000020045.1:WP_052306284.1 238 IAELVRRLDAPVTNTLMALGAFPASDRRCLGMPGLHGTYEANLAMQHCDVLIALGARFDDRVIGNTGEFQSDR 310 *********************************************************************9876 PP TIGR00118 293 k.iihididPaeigknvkvdipivGdakkvleellkklkee..ekkeke.Wlekieewkkeyilkldeeeesi 361 + iih+didPa i+k v+vdipivGd+k+ + +l++l+++ ++ +++ W+++i +w+++ +l+++ + + i NCBI__GCF_000020045.1:WP_052306284.1 311 RtIIHVDIDPATIDKRVQVDIPIVGDVKTAARAILEQLRAQriNDGNRNdWWKEIGNWREKRCLAYEPDADVI 383 559*********************************99999653333335*********************** PP TIGR00118 362 kPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvav 434 kPq vi++l++ + ++a++ +dvGqhqmwaaq y ++kpr++i+sgGlGtmG GlP a+G+k a p+++vvav NCBI__GCF_000020045.1:WP_052306284.1 384 KPQFVIQQLWEATGGDAYICSDVGQHQMWAAQLYGFDKPRRWINSGGLGTMGVGLPYAMGVKRALPDADVVAV 456 ************************************************************************* PP TIGR00118 435 tGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgir 507 tGdgs+qm +qelst+++yd+ vkiv lnn +lGmv+q q++ y++rys++++ + lpdfv+la+ayG++g r NCBI__GCF_000020045.1:WP_052306284.1 457 TGDGSIQMCIQELSTCRQYDLGVKIVSLNNGYLGMVRQLQHVNYRDRYSHSYMDA-LPDFVALARAYGHVGFR 528 ******************************************************5.***************** PP TIGR00118 508 iekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelve 555 ie+p ++e l+eal++k + v++d+ +d +e+v+Pmv Gagl++++ NCBI__GCF_000020045.1:WP_052306284.1 529 IERPCDVEPVLREALAMKqRTVFMDFAIDPSENVWPMVRAGAGLTDMLM 577 ***************988689*************************985 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: 30.25 // [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