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 Dsui_1925 Dsui_1925 acetolactate synthase, large subunit, biosynthetic type
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__PS:Dsui_1925 Length = 572 Score = 500 bits (1288), Expect = e-146 Identities = 269/553 (48%), Positives = 350/553 (63%), Gaps = 12/553 (2%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG-VEHLLCRHEQGAAMAAIGYAR 59 + GAQ VV L QGV TV G PGGAI+P YDAL + H+L RHEQGA A G AR Sbjct: 21 LTGAQIVVRLLERQGVTTVSGIPGGAILPFYDALSASEKIRHVLARHEQGAGFIAQGMAR 80 Query: 60 ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSL 119 A+G+ VC+A+SGPGATNL+T +ADA LDSIP+VAITGQV IGTDAFQEVD GLS+ Sbjct: 81 ASGQPAVCLASSGPGATNLLTAIADAKLDSIPLVAITGQVPRSMIGTDAFQEVDTYGLSI 140 Query: 120 ACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEV 179 TKH+FLV S EEL ++ AF +A SGRPGPVLVDIPKD+Q + ++ W + Sbjct: 141 PITKHNFLVNSAEELLEVIPRAFTLAASGRPGPVLVDIPKDVQAQAIEVSQWPAPGGRQA 200 Query: 180 --TFPHAEVEQARQMLAKAQKPMLYVGGGV---GMAQAVPALREFLAATKMPATCTLKGL 234 A +E+A M+ A++P+LY+GGGV G A+A AL E +P T TL L Sbjct: 201 PPAPDMAAIEKAAAMINAAERPILYLGGGVVHSGAAEAAVALAE---KASLPTTMTLMAL 257 Query: 235 GAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMD 294 GA+ D+P + MLGMHG + N ++ECDLLIAVGARFDDR TGK+ F P A +IH+D Sbjct: 258 GAMPVDHPLSIHMLGMHGARYTNLLLEECDLLIAVGARFDDRATGKVAAFCPKAQIIHID 317 Query: 295 IDPAEMNKLRQAHVALQGDLNALLPALQQPLNQY---DWQQHCAQLRDEHSWRYDHPGDA 351 IDP+E++K++ AHV + GD+ +L L + + W H LR + + D Sbjct: 318 IDPSELDKIKNAHVGIAGDVGEVLEKLSPLVEAHLRKRWLTHMGDLRSRFRLQRPNLEDP 377 Query: 352 IYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAV 411 L++ ++D + TDVGQHQMW AQ RP ++TS GLGTMGFG+PAA+ Sbjct: 378 RSHYGLIQAVADCLDDSAAIATDVGQHQMWVAQAYPLRRPRQWLTSGGLGTMGFGVPAAL 437 Query: 412 GAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQE 471 GA +A P TVVC +GDGS +MN+QEL T+ LKIVL++N LG+V Q Q+LF+ + Sbjct: 438 GAALAEPERTVVCFTGDGSILMNIQELATIAEAGANLKIVLMNNDALGLVYQQQELFYGK 497 Query: 472 RYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVW 531 RY + PDFL +A FGI + AAL L GP L+H ID E V+ Sbjct: 498 RYFASKFAGQPDFLKIAEGFGIDTLDLDTAADPRAALRQALQRPGPCLIHAFIDMNEKVY 557 Query: 532 PLVPPGASNSEML 544 P+VPPGA+N++M+ Sbjct: 558 PMVPPGAANTDMI 570 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: 842 Number of extensions: 28 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: 548 Length of database: 572 Length adjustment: 36 Effective length of query: 512 Effective length of database: 536 Effective search space: 274432 Effective search space used: 274432 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 Dsui_1925 Dsui_1925 (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.11970.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-210 685.4 0.0 3.1e-210 685.2 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_1925 Dsui_1925 acetolactate synthase, Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_1925 Dsui_1925 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 685.2 0.0 3.1e-210 3.1e-210 1 555 [. 21 571 .. 21 572 .] 0.98 Alignments for each domain: == domain 1 score: 685.2 bits; conditional E-value: 3.1e-210 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGat 76 l+ga+i+v+ l+++gv tv G+PGGa+lp+ydal +++++h+l+rheq+a +a+G+arasG++ v+la sGPGat lcl|FitnessBrowser__PS:Dsui_1925 21 LTGAQIVVRLLERQGVTTVSGIPGGAILPFYDALSaSEKIRHVLARHEQGAGFIAQGMARASGQPAVCLASSGPGAT 97 68*********************************8899************************************** PP TIGR00118 77 nlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPv 153 nl+t+ia+a lds+Plv++tGqv++s+iG+dafqe+d G+++p+tkh+flv++ae+l e++ +af++a++GrPGPv lcl|FitnessBrowser__PS:Dsui_1925 98 NLLTAIADAKLDSIPLVAITGQVPRSMIGTDAFQEVDTYGLSIPITKHNFLVNSAEELLEVIPRAFTLAASGRPGPV 174 ***************************************************************************** PP TIGR00118 154 lvdlPkdvteaeieleveekvelp.gykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlki 229 lvd+Pkdv++++ie+++ p g + ++ + i+ka+ +i++a++P+l+ GgGv++++a e + lae++ + lcl|FitnessBrowser__PS:Dsui_1925 175 LVDIPKDVQAQAIEVSQW---PAPgGRQAPPAPDMAAIEKAAAMINAAERPILYLGGGVVHSGAAEAAVALAEKASL 248 ************998876...4441555667889999**************************************** PP TIGR00118 230 pvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigk 306 p t+tl+ lGa+p dhpl++ mlGmhG++++nl ++e+dlliavGarfddr tg++a f+p+a+iihididP+e++k lcl|FitnessBrowser__PS:Dsui_1925 249 PTTMTLMALGAMPVDHPLSIHMLGMHGARYTNLLLEECDLLIAVGARFDDRATGKVAAFCPKAQIIHIDIDPSELDK 325 ***************************************************************************** PP TIGR00118 307 nvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttd 383 + ++++ i Gd+ +vle+l ++++ +k Wl ++ +++++ l+ + e++ +i+++ l+d+a ++td lcl|FitnessBrowser__PS:Dsui_1925 326 IKNAHVGIAGDVGEVLEKLSPLVEAHLRKR--WLTHMGDLRSRFRLQRPNLEDPRSHYGLIQAVADCLDDSAAIATD 400 *******************99998877666..********************************************* PP TIGR00118 384 vGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkiv 460 vGqhqmw+aq y+ ++pr+++tsgGlGtmGfG+PaalGa +a+pe tvv+ tGdgs+ mn+qel+ti+e++ ++kiv lcl|FitnessBrowser__PS:Dsui_1925 401 VGQHQMWVAQAYPLRRPRQWLTSGGLGTMGFGVPAALGAALAEPERTVVCFTGDGSILMNIQELATIAEAGANLKIV 477 ***************************************************************************** PP TIGR00118 461 ilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdke 537 ++nn+ lG+v+q qelfy +ry ++k+a ++pdf k+ae++G+ ++ + + ++ ++l++al+ +p l+ +d + lcl|FitnessBrowser__PS:Dsui_1925 478 LMNNDALGLVYQQQELFYGKRYFASKFA-GQPDFLKIAEGFGIDTLDLDTAADPRAALRQALQRPGPCLIHAFIDMN 553 ****************************.6*********************************************** PP TIGR00118 538 eevlPmvapGagldelve 555 e+v+Pmv+pGa+++++++ lcl|FitnessBrowser__PS:Dsui_1925 554 EKVYPMVPPGAANTDMIG 571 ***************985 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 12.46 // [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