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 7023118 Shewana3_0356 acetolactate synthase 2 catalytic subunit (RefSeq)
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__ANA3:7023118 Length = 557 Score = 723 bits (1866), Expect = 0.0 Identities = 357/547 (65%), Positives = 429/547 (78%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60 + GA V+ L A GV TVFGYPGGAIMP+YDALY VEHLL RHEQGAA AA+GYARA Sbjct: 7 IRGADAVIKVLAAHGVTTVFGYPGGAIMPIYDALYGSPVEHLLSRHEQGAAFAAVGYARA 66 Query: 61 TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120 +GKTGVC ATSGPGATNLIT LADALLDS+PVVAITGQVS IGTDAFQE+DVLG+SL+ Sbjct: 67 SGKTGVCFATSGPGATNLITSLADALLDSVPVVAITGQVSTAVIGTDAFQEIDVLGMSLS 126 Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180 CTKHSF+V + +L + +AF++A SGRPGPVLVDIPKDIQ+A + V NE Sbjct: 127 CTKHSFMVTDVNDLIPTLYQAFEIAASGRPGPVLVDIPKDIQIAQLEYRTPLLAVTNEPQ 186 Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEAD 240 +E++ AR +LA+A++PMLYVGGGVGMA AV LREF+ AT MP+ TLKGLG++ Sbjct: 187 ASASEIDAARALLAEAKQPMLYVGGGVGMAGAVDQLREFIKATGMPSVATLKGLGSIAHG 246 Query: 241 YPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAEM 300 P YLGMLGMHG KAAN AVQ+CDLL+ GARFDDRVTG+L TFA A VIH+DID AE+ Sbjct: 247 TPGYLGMLGMHGGKAANLAVQDCDLLVVAGARFDDRVTGRLATFANKAKVIHLDIDAAEL 306 Query: 301 NKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYAPLLLKQ 360 KLRQ VA+ GDL + PAL LN WQ L +H W Y HPG IYAP +L++ Sbjct: 307 GKLRQPDVAIAGDLRQIFPALAMALNITPWQAEVEHLARKHQWDYQHPGSLIYAPAMLRR 366 Query: 361 LSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQVARPND 420 L+++ P D VV DVGQHQMW AQH+ RPE+ ++S+GLGTMGFGLPAA+GAQVARP+ Sbjct: 367 LANKLPEDSVVCCDVGQHQMWVAQHMWFRRPEDHLSSAGLGTMGFGLPAAIGAQVARPDA 426 Query: 421 TVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD 480 TVV +SGDGSFMMNVQEL T+KR++LP+KI+L+DNQ+LGMV+QWQQLFF+ERYSET L+D Sbjct: 427 TVVTVSGDGSFMMNVQELTTIKRRKLPVKILLIDNQKLGMVKQWQQLFFEERYSETDLSD 486 Query: 481 NPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVPPGASN 540 NPDF+ LASAF I G+ I D+VE AL ML + GPYLLHV+ID+ NVWPLVPPGASN Sbjct: 487 NPDFVQLASAFDIPGRTIFSSDEVEEALTEMLAAKGPYLLHVAIDDAFNVWPLVPPGASN 546 Query: 541 SEMLEKL 547 S+M++++ Sbjct: 547 SDMMDEM 553 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: 925 Number of extensions: 29 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: 557 Length adjustment: 36 Effective length of query: 512 Effective length of database: 521 Effective search space: 266752 Effective search space used: 266752 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 7023118 Shewana3_0356 (acetolactate synthase 2 catalytic subunit (RefSeq))
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.7091.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-212 692.0 0.2 3.4e-212 691.7 0.2 1.0 1 lcl|FitnessBrowser__ANA3:7023118 Shewana3_0356 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7023118 Shewana3_0356 acetolactate synthase 2 catalytic subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 691.7 0.2 3.4e-212 3.4e-212 2 556 .. 8 552 .. 7 553 .. 0.97 Alignments for each domain: == domain 1 score: 691.7 bits; conditional E-value: 3.4e-212 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnl 78 +ga+++++ l ++gv tvfGyPGGa++piydaly s +eh+l rheq+aa aa GyarasGk+Gv++atsGPGatnl lcl|FitnessBrowser__ANA3:7023118 8 RGADAVIKVLAAHGVTTVFGYPGGAIMPIYDALYGSPVEHLLSRHEQGAAFAAVGYARASGKTGVCFATSGPGATNL 84 79*************************************************************************** PP TIGR00118 79 vtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlv 155 +t++a+a ldsvP+v++tGqv+t++iG+dafqeid+lG++l++tkhsf+v++++dl +l +afeia++GrPGPvlv lcl|FitnessBrowser__ANA3:7023118 85 ITSLADALLDSVPVVAITGQVSTAVIGTDAFQEIDVLGMSLSCTKHSFMVTDVNDLIPTLYQAFEIAASGRPGPVLV 161 ***************************************************************************** PP TIGR00118 156 dlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvt 232 d+Pkd++ a++e++++ l + + +++ i +a l+++ak+P+l+vGgGv +a+a ++l+e+ +++ +p + lcl|FitnessBrowser__ANA3:7023118 162 DIPKDIQIAQLEYRTP----LLAVTNEPQASASEIDAARALLAEAKQPMLYVGGGVGMAGAVDQLREFIKATGMPSV 234 ********99998877....5555566667788999999************************************** PP TIGR00118 233 ttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvk 309 +tl GlG++ + p lgmlGmhG k+anlav+++dll+ Garfddrvtg la+fa++ak+ih+did ae+gk ++ lcl|FitnessBrowser__ANA3:7023118 235 ATLKGLGSIAHGTPGYLGMLGMHGGKAANLAVQDCDLLVVAGARFDDRVTGRLATFANKAKVIHLDIDAAELGKLRQ 311 ***************************************************************************** PP TIGR00118 310 vdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGq 386 d++i Gd ++++ l +l+ + W +++e++ +++ +++ + i +++++l + l+++++v dvGq lcl|FitnessBrowser__ANA3:7023118 312 PDVAIAGDLRQIFPALAMALNI---T--PWQAEVEHLARKHQWDYQHPGSLIYAPAMLRRLANKLPEDSVVCCDVGQ 383 **********999998877654...3..3999*****9999999999999999999********************* PP TIGR00118 387 hqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkiviln 463 hqmw+aq+ +++p+ +++s+GlGtmGfGlPaa+Ga+va p++tvv+v+Gdgsf+mn+qel+ti++ ++pvki++++ lcl|FitnessBrowser__ANA3:7023118 384 HQMWVAQHMWFRRPEDHLSSAGLGTMGFGLPAAIGAQVARPDATVVTVSGDGSFMMNVQELTTIKRRKLPVKILLID 460 ***************************************************************************** PP TIGR00118 464 nellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeev 540 n+ lGmvkqWq+lf+eeryset l+ ++pdfv+la a+ + g +i + +e+ee+l+e+l+ k+p+ll v +d+ +v lcl|FitnessBrowser__ANA3:7023118 461 NQKLGMVKQWQQLFFEERYSETDLS-DNPDFVQLASAFDIPGRTIFSSDEVEEALTEMLAAKGPYLLHVAIDDAFNV 536 *************************.6************************************************** PP TIGR00118 541 lPmvapGagldelvee 556 +P+v+pGa+++++++e lcl|FitnessBrowser__ANA3:7023118 537 WPLVPPGASNSDMMDE 552 ************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (557 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: 7.80 // [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