Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_027178079.1 G496_RS0103620 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000429985.1:WP_027178079.1 Length = 563 Score = 620 bits (1598), Expect = 0.0 Identities = 313/567 (55%), Positives = 408/567 (71%), Gaps = 10/567 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 E+ GA+IL+ L +EGV+ V+G+PGGAVL IY EL F+H+L RHEQ A+HAADGYA Sbjct: 2 ELTGAQILLECLKKEGVDVVFGFPGGAVLDIYHEL-PNFPFKHVLARHEQGAIHAADGYA 60 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 RATG VGV LVTSGPG TN VTGIATAY+DSIP+V++TG VPT IG DAFQE D VGIT Sbjct: 61 RATGDVGVCLVTSGPGATNTVTGIATAYMDSIPVVILTGQVPTALIGNDAFQEVDIVGIT 120 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RP KHN+LVKD+ +LA TI++AF++A +GRPGPV+VD+PKD+ + ++++P+ + +RS Sbjct: 121 RPCTKHNYLVKDINNLAYTIRQAFYLARSGRPGPVLVDLPKDIMQQITEFKWPEDVSLRS 180 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257 YNP H GQI+K L++ AERP IY GGGV+ + A ++L LA PVT TLMGL Sbjct: 181 YNPNLNPHYGQIKKVSKLIRKAERPLIYAGGGVISSGAQEDLIWLAKNLDIPVTATLMGL 240 Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317 G FPG ++GMLGMHGTY ANMA+ D+++AIGARFDDRV G + F A +H+ Sbjct: 241 GGFPGDDPLWLGMLGMHGTYAANMAVNTADLVLAIGARFDDRVTGKVSEFAPNA-TFVHV 299 Query: 318 DIDPSSISKRVKVDIPIVGNVKDVL----QELIAQIKASDIKPKREALAKWWEQIEQWRS 373 D+DP+SI K V V +PIV + K L + L I A+D + A A W +Q++ W + Sbjct: 300 DVDPTSIQKNVHVHVPIVADCKSFLMALRESLEPVIGATDFE---VAHAGWVKQVQDWST 356 Query: 374 VDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGG 433 L Y++ E IKPQ+VVEKI+E++KG+A I ++VGQ+QMWAAQFYKF +P+ +++SGG Sbjct: 357 AHPLHYNKGGEYIKPQHVVEKIYEISKGEAIIATEVGQNQMWAAQFYKFKKPKSFLSSGG 416 Query: 434 LGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLG 493 LGTMG G P A+G + A+P++ VV I G+GSIQM IQE+ T + + PVKI LNN YLG Sbjct: 417 LGTMGYGFPAAIGAQIAYPDRLVVNIAGDGSIQMNIQEMMTAVANNLPVKIVILNNRYLG 476 Query: 494 MVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTV 553 MVRQWQE+ YD YS + MDA PDFVKLAEAYG G R+ + D+E L+EAF + Sbjct: 477 MVRQWQELFYDRNYSETCMDAQPDFVKLAEAYGAAGFRITEEKDLESTLKEAF-ATPKPA 535 Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLL 580 +D DP ENV+PMV AG ++EMLL Sbjct: 536 IIDVIVDPEENVYPMVPAGCSLTEMLL 562 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: 931 Number of extensions: 29 Number of successful extensions: 4 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: 563 Length adjustment: 36 Effective length of query: 549 Effective length of database: 527 Effective search space: 289323 Effective search space used: 289323 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_027178079.1 G496_RS0103620 (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.12997.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-259 846.3 0.2 5.9e-259 846.1 0.2 1.0 1 lcl|NCBI__GCF_000429985.1:WP_027178079.1 G496_RS0103620 acetolactate synt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429985.1:WP_027178079.1 G496_RS0103620 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 846.1 0.2 5.9e-259 5.9e-259 1 554 [. 3 561 .. 3 563 .] 0.99 Alignments for each domain: == domain 1 score: 846.1 bits; conditional E-value: 5.9e-259 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 l+ga+il+e lkkegv++vfG+PGGavl+iy +l + ++h+l+rheq+a+haadGyara+G vGv+l+ lcl|NCBI__GCF_000429985.1:WP_027178079.1 3 LTGAQILLECLKKEGVDVVFGFPGGAVLDIYHELPNFPFKHVLARHEQGAIHAADGYARATGDVGVCLV 71 68******************************************************************* PP TIGR00118 70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138 tsGPGatn+vtgiatay+ds+P+v+ltGqv+t+liG+dafqe+di+Git+p+tkh++lvk+ ++l+ ++ lcl|NCBI__GCF_000429985.1:WP_027178079.1 72 TSGPGATNTVTGIATAYMDSIPVVILTGQVPTALIGNDAFQEVDIVGITRPCTKHNYLVKDINNLAYTI 140 ********************************************************************* PP TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207 ++af++a +GrPGPvlvdlPkd++++ +e++ +e+v+l++y+p++++h+ qikk+ +li+ka++P++++ lcl|NCBI__GCF_000429985.1:WP_027178079.1 141 RQAFYLARSGRPGPVLVDLPKDIMQQITEFKWPEDVSLRSYNPNLNPHYGQIKKVSKLIRKAERPLIYA 209 ********************************************************************* PP TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276 GgGvi ++a+e+l la++l+ipvt+tl+GlG+fp d+pl lgmlGmhGt++an+av+ adl++a+Gar lcl|NCBI__GCF_000429985.1:WP_027178079.1 210 GGGVISSGAQEDLIWLAKNLDIPVTATLMGLGGFPGDDPLWLGMLGMHGTYAANMAVNTADLVLAIGAR 278 ********************************************************************* PP TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee......ekkekeW 339 fddrvtg++++fap+a+ +h+d+dP++i+knv+v++piv d+k+ l l + l+ + e + W lcl|NCBI__GCF_000429985.1:WP_027178079.1 279 FDDRVTGKVSEFAPNATFVHVDVDPTSIQKNVHVHVPIVADCKSFLMALRESLEPVigatdfEVAHAGW 347 *************************************************9999998888776666666* PP TIGR00118 340 lekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408 ++++++w + ++l++++ e ikPq+v+++++++ k+eai++t+vGq+qmwaaqfyk+kkp++f++sgG lcl|NCBI__GCF_000429985.1:WP_027178079.1 348 VKQVQDWSTAHPLHYNKGGEYIKPQHVVEKIYEISKGEAIIATEVGQNQMWAAQFYKFKKPKSFLSSGG 416 ********************************************************************* PP TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477 lGtmG+G+Paa+Ga++a p+ vv+++Gdgs+qmn+qe+ t+v ++pvkivilnn++lGmv+qWqelf lcl|NCBI__GCF_000429985.1:WP_027178079.1 417 LGTMGYGFPAAIGAQIAYPDRLVVNIAGDGSIQMNIQEMMTAVANNLPVKIVILNNRYLGMVRQWQELF 485 ********************************************************************* PP TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvap 546 y++ yset++ + +pdfvklaeayG+ g ri+++++le+ lkea+++ +p+++dv vd ee+v+Pmv+ lcl|NCBI__GCF_000429985.1:WP_027178079.1 486 YDRNYSETCMDA-QPDFVKLAEAYGAAGFRITEEKDLESTLKEAFATPKPAIIDVIVDPEENVYPMVPA 553 ***********5.******************************************************** PP TIGR00118 547 Gagldelv 554 G++l+e++ lcl|NCBI__GCF_000429985.1:WP_027178079.1 554 GCSLTEML 561 ******98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (563 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: 9.20 // [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