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 WP_012585806.1 C665_RS00880 acetolactate synthase, large subunit, biosynthetic type
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000310185.1:WP_012585806.1 Length = 555 Score = 488 bits (1255), Expect = e-142 Identities = 257/551 (46%), Positives = 351/551 (63%), Gaps = 8/551 (1%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG-VEHLLCRHEQGAAMAAIGYAR 59 M GAQ +V L QGV TV G PGGAI+P YDAL + H+L RHEQGA A G AR Sbjct: 4 MTGAQLMVRLLERQGVRTVAGIPGGAILPFYDALSGSEHIHHVLARHEQGAGFIAQGMAR 63 Query: 60 ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSL 119 +G VCIA+SGPGATNL+T +ADA LDSIP+V ITGQV IGTDAFQEVD+ G+++ Sbjct: 64 VSGVPQVCIASSGPGATNLVTAIADACLDSIPMVVITGQVPQAMIGTDAFQEVDIYGITV 123 Query: 120 ACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQ--LASGDLEPWFTTVEN 177 TKH+FLV+S +EL ++ +AF +A SGRPGPVL+D+PKD+Q L + P + Sbjct: 124 PITKHNFLVRSAQELLEVIPDAFRIAMSGRPGPVLIDVPKDVQNQLVAVAEFPAPAVADP 183 Query: 178 EVTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAV 237 A VE A +M+ +A++P+LY+GGGV + A P + +P T TL LGA+ Sbjct: 184 APQLDLAAVELAAKMINEAEQPVLYLGGGVVASGAAPLAVQLAEQAGLPTTMTLMALGAM 243 Query: 238 EADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDP 297 D+P +GMLGMHG + NF ++E D+L+ VGARFDDR G+ F P+A ++H+DID Sbjct: 244 PMDHPLSIGMLGMHGARYTNFVLEEADVLVCVGARFDDRAIGRAAQFCPNAKIVHIDIDR 303 Query: 298 AEMNKLRQAHVALQGD----LNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIY 353 +E++K++ AHVA+ + L ALLP +Q L + W H L+ ++ D Sbjct: 304 SELHKIKNAHVAIHANVKCALEALLPRVQATLRKR-WLSHVDSLKTRFPMQFPGQDDPRT 362 Query: 354 APLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGA 413 L++ ++ +V TDVGQHQMW AQ RP ++TS GLGTMGFGLP+A+GA Sbjct: 363 HYGLIQAVAAALDDRAIVATDVGQHQMWVAQAYPFRRPRQWLTSGGLGTMGFGLPSALGA 422 Query: 414 QVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERY 473 +A P TVVC +GDGSF MN+QEL T+ + L +KIVL++N LG+V Q Q LF+ +R Sbjct: 423 ALAEPGRTVVCFTGDGSFKMNIQELATLAEEGLNVKIVLMNNNALGLVYQQQTLFYGQRL 482 Query: 474 SETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPL 533 + PDF+ +A FG+ + D AAL L+ GP L+H +ID + V+P+ Sbjct: 483 FASKYRTEPDFVKIAEGFGVPAVDLDLADNPRAALAEALHRPGPCLIHATIDREQFVYPM 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: 816 Number of extensions: 22 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: 555 Length adjustment: 36 Effective length of query: 512 Effective length of database: 519 Effective search space: 265728 Effective search space used: 265728 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_012585806.1 C665_RS00880 (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.32623.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-206 671.6 0.2 4.9e-206 671.4 0.2 1.0 1 lcl|NCBI__GCF_000310185.1:WP_012585806.1 C665_RS00880 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_012585806.1 C665_RS00880 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 671.4 0.2 4.9e-206 4.9e-206 1 555 [. 4 554 .. 4 555 .] 0.97 Alignments for each domain: == domain 1 score: 671.4 bits; conditional E-value: 4.9e-206 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 ++ga+++v+ l+++gv tv G+PGGa+lp+ydal +++++h+l+rheq+a +a+G+ar+sG + v++ lcl|NCBI__GCF_000310185.1:WP_012585806.1 4 MTGAQLMVRLLERQGVRTVAGIPGGAILPFYDALSgSEHIHHVLARHEQGAGFIAQGMARVSGVPQVCI 72 79*********************************9999****************************** PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 a sGPGatnlvt+ia+a lds+P+vv+tGqv++++iG+dafqe+di Git+p+tkh+flv++a++l e+ lcl|NCBI__GCF_000310185.1:WP_012585806.1 73 ASSGPGATNLVTAIADACLDSIPMVVITGQVPQAMIGTDAFQEVDIYGITVPITKHNFLVRSAQELLEV 141 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206 + +af ia +GrPGPvl+d+Pkdv+++ + + + p + + + ++ a+++i++a++Pvl+ lcl|NCBI__GCF_000310185.1:WP_012585806.1 142 IPDAFRIAMSGRPGPVLIDVPKDVQNQLVAVAEFPAPAVAD--PAPQLDLAAVELAAKMINEAEQPVLY 208 **************************998877664444444..444556677999************** PP TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275 GgGv++++a ++lae++ +p t+tl+ lGa+p dhpl++gmlGmhG++++n+ ++ead+l++vGa lcl|NCBI__GCF_000310185.1:WP_012585806.1 209 LGGGVVASGAAPLAVQLAEQAGLPTTMTLMALGAMPMDHPLSIGMLGMHGARYTNFVLEEADVLVCVGA 277 ********************************************************************* PP TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekie 344 rfddr g a+f+p+aki+hidid +e+ k+ +++++i ++k le ll +++++ +k Wl++++ lcl|NCBI__GCF_000310185.1:WP_012585806.1 278 RFDDRAIGRAAQFCPNAKIVHIDIDRSELHKIKNAHVAIHANVKCALEALLPRVQATLRKR--WLSHVD 344 ******************************************************9988877..****** PP TIGR00118 345 ewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmG 413 ++k++ ++++ ++++ +i+++ l+d aiv+tdvGqhqmw+aq y++++pr+++tsgGlGtmG lcl|NCBI__GCF_000310185.1:WP_012585806.1 345 SLKTRFPMQFPGQDDPRTHYGLIQAVAAALDDRAIVATDVGQHQMWVAQAYPFRRPRQWLTSGGLGTMG 413 ********************************************************************* PP TIGR00118 414 fGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeery 482 fGlP+alGa +a+p tvv+ tGdgsf+mn+qel+t++e +++vkiv++nn+ lG+v+q q lfy +r lcl|NCBI__GCF_000310185.1:WP_012585806.1 414 FGLPSALGAALAEPGRTVVCFTGDGSFKMNIQELATLAEEGLNVKIVLMNNNALGLVYQQQTLFYGQRL 482 ********************************************************************* PP TIGR00118 483 setklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagld 551 ++k + pdfvk+ae++Gv ++ + ++ ++l+eal+ +p l+ ++d+e+ v+Pmv+pGa+++ lcl|NCBI__GCF_000310185.1:WP_012585806.1 483 FASKYRT-EPDFVKIAEGFGVPAVDLDLADNPRAALAEALHRPGPCLIHATIDREQFVYPMVPPGAANT 550 *****95.9************************************************************ PP TIGR00118 552 elve 555 e+++ lcl|NCBI__GCF_000310185.1:WP_012585806.1 551 EMIG 554 **95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (555 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: 00:00:00.04 # Mc/sec: 7.24 // [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