Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate BWI76_RS00960 BWI76_RS00960 acetolactate synthase 2 catalytic subunit
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__Koxy:BWI76_RS00960 Length = 548 Score = 990 bits (2559), Expect = 0.0 Identities = 488/548 (89%), Positives = 518/548 (94%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60 MNGA+WVVHALRAQGV+TVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA Sbjct: 1 MNGARWVVHALRAQGVDTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60 Query: 61 TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120 TGKTGVCIATSGPGATNLITGLADALLDS+PVVAITGQV+APFIGTDAFQEVDVLGLSLA Sbjct: 61 TGKTGVCIATSGPGATNLITGLADALLDSVPVVAITGQVAAPFIGTDAFQEVDVLGLSLA 120 Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180 CTKHSFLVQSLEELPRI+AEAF VA SGRPGPVLVDIPKDIQLA GDL+P F+ V ++V Sbjct: 121 CTKHSFLVQSLEELPRIIAEAFHVANSGRPGPVLVDIPKDIQLAQGDLDPHFSMVADDVD 180 Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEAD 240 FP+A++E A QML ++QKPMLYVGGGVGMAQAVPALREFL T+MPAT TLKGLG V AD Sbjct: 181 FPYADIEYALQMLTQSQKPMLYVGGGVGMAQAVPALREFLTVTQMPATATLKGLGVVAAD 240 Query: 241 YPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAEM 300 YPYYLGMLGMHGTKAAN AVQECDLLIAVGARFDDRVTGKLNTFAPHA VIHMDIDPAE+ Sbjct: 241 YPYYLGMLGMHGTKAANLAVQECDLLIAVGARFDDRVTGKLNTFAPHAKVIHMDIDPAEL 300 Query: 301 NKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYAPLLLKQ 360 NKLRQAH+ L GDLN +LPALQQPL+ W+Q AQLR EH+WRYDHPG+AIYAPLLLKQ Sbjct: 301 NKLRQAHIGLTGDLNVMLPALQQPLSIDAWRQRNAQLRAEHAWRYDHPGEAIYAPLLLKQ 360 Query: 361 LSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQVARPND 420 LS+RKPADCVVTTDVGQHQMW+AQH+ +TRPENFITSSGLGTMGFGLPAAVGAQVARP+D Sbjct: 361 LSERKPADCVVTTDVGQHQMWSAQHMTYTRPENFITSSGLGTMGFGLPAAVGAQVARPDD 420 Query: 421 TVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD 480 TV+CISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD Sbjct: 421 TVICISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD 480 Query: 481 NPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVPPGASN 540 NPDFL LASAFGI GQHITRKDQVEAALDTML+S GPYLLHVSIDELENVWPLVPPGASN Sbjct: 481 NPDFLTLASAFGIPGQHITRKDQVEAALDTMLSSQGPYLLHVSIDELENVWPLVPPGASN 540 Query: 541 SEMLEKLS 548 +EMLEKLS Sbjct: 541 AEMLEKLS 548 Lambda K H 0.320 0.135 0.410 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: 1059 Number of extensions: 27 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: 548 Length of database: 548 Length adjustment: 36 Effective length of query: 512 Effective length of database: 512 Effective search space: 262144 Effective search space used: 262144 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 BWI76_RS00960 BWI76_RS00960 (acetolactate synthase 2 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.3342.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-221 721.3 0.0 4.1e-221 721.1 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS00960 BWI76_RS00960 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS00960 BWI76_RS00960 acetolactate synthase 2 catalytic subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 721.1 0.0 4.1e-221 4.1e-221 1 555 [. 1 545 [. 1 547 [. 0.97 Alignments for each domain: == domain 1 score: 721.1 bits; conditional E-value: 4.1e-221 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlats 71 ++ga+ +v++l+++gv+tvfGyPGGa++p+ydalyd+++eh+l rheq+aa aa Gyara+Gk+Gv++ats lcl|FitnessBrowser__Koxy:BWI76_RS00960 1 MNGARWVVHALRAQGVDTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATGKTGVCIATS 71 789******************************************************************** PP TIGR00118 72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeaf 142 GPGatnl+tg+a+a ldsvP+v++tGqva+ iG+dafqe+d+lG++l++tkhsflv++ e+lp+i+ eaf lcl|FitnessBrowser__Koxy:BWI76_RS00960 72 GPGATNLITGLADALLDSVPVVAITGQVAAPFIGTDAFQEVDVLGLSLACTKHSFLVQSLEELPRIIAEAF 142 *********************************************************************** PP TIGR00118 143 eiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGvii 213 ++a++GrPGPvlvd+Pkd++ a+ +l+ + ++ + +v ++ i+ al+++++++kP+l+vGgGv + lcl|FitnessBrowser__Koxy:BWI76_RS00960 143 HVANSGRPGPVLVDIPKDIQLAQGDLDPH--FSM--VADDVDFPYADIEYALQMLTQSQKPMLYVGGGVGM 209 ***********************999887..444..4567778899************************* PP TIGR00118 214 aeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgn 284 a+a l+e+ +++p t+tl GlG + +d p lgmlGmhGtk+anlav+e+dlliavGarfddrvtg+ lcl|FitnessBrowser__Koxy:BWI76_RS00960 210 AQAVPALREFLTVTQMPATATLKGLGVVAADYPYYLGMLGMHGTKAANLAVQECDLLIAVGARFDDRVTGK 280 *********************************************************************** PP TIGR00118 285 lakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkld 355 l++fap+ak+ih+didPae++k ++++i + Gd + +l l + l + + W ++ +++++e+ ++d lcl|FitnessBrowser__Koxy:BWI76_RS00960 281 LNTFAPHAKVIHMDIDPAELNKLRQAHIGLTGDLNVMLPALQQPL----SID-AWRQRNAQLRAEHAWRYD 346 *********************************877776665444....333.4***************** PP TIGR00118 356 eeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvak 426 + e+i ++k+ls+ + + +vttdvGqhqmw+aq+ ++++p++fits+GlGtmGfGlPaa+Ga+va lcl|FitnessBrowser__Koxy:BWI76_RS00960 347 HPGEAIYAPLLLKQLSERKPADCVVTTDVGQHQMWSAQHMTYTRPENFITSSGLGTMGFGLPAAVGAQVAR 417 *******99************************************************************** PP TIGR00118 427 peetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvkl 497 p++tv++++Gdgsf+mn+qel t+++ ++p+kiv+l+n+ lGmv+qWq+lf++eryset+l+ ++pdf l lcl|FitnessBrowser__Koxy:BWI76_RS00960 418 PDDTVICISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLT-DNPDFLTL 487 **************************************************************.6******* PP TIGR00118 498 aeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555 a a+G+ g++i++++++e++l+ +l+s++p+ll v++d+ e+v+P+v+pGa+++e++e lcl|FitnessBrowser__Koxy:BWI76_RS00960 488 ASAFGIPGQHITRKDQVEAALDTMLSSQGPYLLHVSIDELENVWPLVPPGASNAEMLE 545 ********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (548 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10.58 // [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