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 209294 DVU0360 acetolactate synthase, large subunit, biosynthetic type
Query= SwissProt::P0DP90 (548 letters) >MicrobesOnline__882:209294 Length = 563 Score = 492 bits (1266), Expect = e-143 Identities = 261/551 (47%), Positives = 354/551 (64%), Gaps = 8/551 (1%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDAL-YDGGVEHLLCRHEQGAAMAAIGYAR 59 M+GA+ V+ L QG++ + G PGGA +P+YDAL + + H+L RHEQGA A G AR Sbjct: 4 MSGAELVIRLLERQGIDCISGIPGGANLPLYDALSHSKRIRHVLARHEQGAGFIAQGMAR 63 Query: 60 ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSL 119 +TG+ V ATSGPGATN +T +ADA LDS+PV+ ITGQV IG+DAFQEVD+ G+S+ Sbjct: 64 STGRPAVFFATSGPGATNTLTAIADAKLDSVPVICITGQVPRSMIGSDAFQEVDIYGMSI 123 Query: 120 ACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPW-FTTVENE 178 TKH+FLV+S+E+L ++ EAF +A SGRPGPVLVDIPKD+Q A E W T + Sbjct: 124 PVTKHNFLVRSVEDLLTVIPEAFRIATSGRPGPVLVDIPKDVQTAEVAFEAWPETGGPDP 183 Query: 179 VTFPHAE-VEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAV 237 P E + +A +MLA+A++P+L++GGGV + A R F T +P +L GLG + Sbjct: 184 AEAPDMEGLARAARMLAEAERPILFIGGGVVASGAGEVARVFAERTGLPTAMSLLGLGTL 243 Query: 238 EADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDP 297 ++P LGMLGMHG + N ++ECDLL+ VGARFDDR TG++ F PHAS+IH+DIDP Sbjct: 244 PPEHPLTLGMLGMHGARCTNMLLEECDLLMVVGARFDDRATGRIEQFCPHASIIHVDIDP 303 Query: 298 AEMNKLRQAHVALQGD----LNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIY 353 +E++KLR AHVA+ GD L ALLP L +P+++ W H A+++ H D Sbjct: 304 SEIDKLRTAHVAITGDAGRVLEALLPML-EPVDRKAWHGHVARMKAAHPLLTPGADDPRT 362 Query: 354 APLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGA 413 L+ + ++ TDVGQHQM AQ R ++TS GLGTMGFGLPAA+GA Sbjct: 363 PYGLVTCTAACLDDSAIIATDVGQHQMRTAQAYPLRRTRQWLTSGGLGTMGFGLPAAIGA 422 Query: 414 QVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERY 473 +A P TVVC +GDGS MN+QEL T +KIVL +N LG+V+Q Q LF+ R Sbjct: 423 ALANPERTVVCFTGDGSLQMNIQELATAAETGANVKIVLANNNALGLVQQQQDLFYGRRI 482 Query: 474 SETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPL 533 + T DF+ +A FG+ + R + L L + GP L+HV + ENV+P+ Sbjct: 483 FASDFTHRIDFVRIAEGFGVPAVDLGRSADPKRDLARALRAKGPCLIHVPVAVEENVYPM 542 Query: 534 VPPGASNSEML 544 VPPGA+N+EM+ Sbjct: 543 VPPGAANTEMI 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: 874 Number of extensions: 43 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: 563 Length adjustment: 36 Effective length of query: 512 Effective length of database: 527 Effective search space: 269824 Effective search space used: 269824 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 209294 DVU0360 (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.25052.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-205 670.0 0.0 1.5e-205 669.8 0.0 1.0 1 lcl|MicrobesOnline__882:209294 DVU0360 acetolactate synthase, l Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:209294 DVU0360 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 669.8 0.0 1.5e-205 1.5e-205 1 555 [. 4 554 .. 4 556 .. 0.98 Alignments for each domain: == domain 1 score: 669.8 bits; conditional E-value: 1.5e-205 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnl 78 ++gae++++ l+++g++ + G+PGGa lp+ydal ++ ++h+l+rheq+a +a+G+ar++G++ v +atsGPGatn+ lcl|MicrobesOnline__882:209294 4 MSGAELVIRLLERQGIDCISGIPGGANLPLYDALShSKRIRHVLARHEQGAGFIAQGMARSTGRPAVFFATSGPGATNT 82 79********************************75889**************************************** PP TIGR00118 79 vtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdl 157 +t+ia+a ldsvP++ +tGqv++s+iGsdafqe+di G+++pvtkh+flv+++edl +++ eaf ia++GrPGPvlvd+ lcl|MicrobesOnline__882:209294 83 LTAIADAKLDSVPVICITGQVPRSMIGSDAFQEVDIYGMSIPVTKHNFLVRSVEDLLTVIPEAFRIATSGRPGPVLVDI 161 ******************************************************************************* PP TIGR00118 158 PkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttll 236 Pkdv++ae+ +e e g p ++ +++a+ ++++a++P+l++GgGv++++a e + +aer+ +p +++ll lcl|MicrobesOnline__882:209294 162 PKDVQTAEVAFEAWP--ETGGPDPAEAPDMEGLARAARMLAEAERPILFIGGGVVASGAGEVARVFAERTGLPTAMSLL 238 **********99885..556889999999************************************************** PP TIGR00118 237 GlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipiv 315 GlG++p +hpl+lgmlGmhG++ +n+ ++e+dll+ vGarfddr tg +++f+p+a iih+didP+ei+k ++++++i lcl|MicrobesOnline__882:209294 239 GLGTLPPEHPLTLGMLGMHGARCTNMLLEECDLLMVVGARFDDRATGRIEQFCPHASIIHVDIDPSEIDKLRTAHVAIT 317 ******************************************************************************* PP TIGR00118 316 GdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqf 394 Gda +vle ll l+ +++k W +++++k+ ++l +++ P ++ l+d+ai++tdvGqhqm +aq lcl|MicrobesOnline__882:209294 318 GDAGRVLEALLPMLEPVDRKA--WHGHVARMKAAHPLLTPGADDPRTPYGLVTCTAACLDDSAIIATDVGQHQMRTAQA 394 ****************99998..******************************************************** PP TIGR00118 395 yktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473 y+ +++r+++tsgGlGtmGfGlPaa+Ga +a+pe tvv+ tGdgs+qmn+qel+t++e + +vkiv+ nn+ lG+v+q lcl|MicrobesOnline__882:209294 395 YPLRRTRQWLTSGGLGTMGFGLPAAIGAALANPERTVVCFTGDGSLQMNIQELATAAETGANVKIVLANNNALGLVQQQ 473 ******************************************************************************* PP TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552 q+lfy +r ++ +++ dfv++ae++Gv ++ + + ++ + l++al+ k+p l+ v v+ ee+v+Pmv+pGa+++e lcl|MicrobesOnline__882:209294 474 QDLFYGRRIFASDFTH-RIDFVRIAEGFGVPAVDLGRSADPKRDLARALRAKGPCLIHVPVAVEENVYPMVPPGAANTE 551 ***************5.9************************************************************* PP TIGR00118 553 lve 555 +++ lcl|MicrobesOnline__882:209294 552 MIG 554 *96 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: 8.15 // [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