Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate 206818 DVU1376 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-18810 (585 letters) >MicrobesOnline__882:206818 Length = 563 Score = 608 bits (1568), Expect = e-178 Identities = 313/565 (55%), Positives = 401/565 (70%), Gaps = 6/565 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 ++ GA+IL+ L +EGV+ +GYPGGAV+ IYDE+ + + H+LVRHEQAAVHAADGYA Sbjct: 2 QLNGAQILLECLKKEGVDVFFGYPGGAVIDIYDEIPRHPELHHVLVRHEQAAVHAADGYA 61 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 RA+GKVGV LVTSGPG TN VTGIATAY DSIP+V++TG VPT IG DAFQE D VGIT Sbjct: 62 RASGKVGVCLVTSGPGATNTVTGIATAYSDSIPVVILTGQVPTPLIGNDAFQEVDIVGIT 121 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RP KHN+LV+DV++LA +++AF++A TGRPGPV+VD+PKDV + + +P+ + MRS Sbjct: 122 RPCTKHNYLVRDVKELATVVRQAFYLARTGRPGPVLVDLPKDVMQAKTDFVWPEDVSMRS 181 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257 YNP K + QIR+A AERP ++ GGGVV+++AS+EL A PV +TLMGL Sbjct: 182 YNPTYKPNLNQIRRAADAFFEAERPLLFVGGGVVMSDASEELGWFARTLRIPVASTLMGL 241 Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317 GAFPG ++GMLGMHGTY AN A+ N D+++A+GARFDDRV G + F S+AR IIHI Sbjct: 242 GAFPGDDPLWLGMLGMHGTYAANKAVNNADLIVAVGARFDDRVTGRLSAFASKAR-IIHI 300 Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPK--REALAKWWEQIEQWRSVD 375 DIDP+SI K V+V IP+VG+ + L I +I ++ K A A+W EQ+ WR Sbjct: 301 DIDPTSIRKNVQVGIPVVGDCRQSLAN-IREILVPRLEEKDWGAAHARWLEQLASWRVEQ 359 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435 L + R IKPQ V+E+++ +T+GDA I ++VGQ+QMW AQFY F +PR I SGGLG Sbjct: 360 PLGFSREGG-IKPQQVIEQLFAITRGDAIITTEVGQNQMWTAQFYTFRKPRTLITSGGLG 418 Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495 TMG G P A+G + AFP+K VV + G+GSIQM IQEL+T + PVKI LNNGYLGMV Sbjct: 419 TMGYGFPAAIGAQFAFPDKLVVDVAGDGSIQMNIQELATAVCNKLPVKILILNNGYLGMV 478 Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555 RQWQE+ Y Y + MDA PDFVKLAEAYG G R+ + +E LREA + Sbjct: 479 RQWQELFYQRNYCSTCMDAQPDFVKLAEAYGAEGYRITEVESLESTLREAL-ASPHPAII 537 Query: 556 DFQTDPTENVWPMVQAGKGISEMLL 580 D + + ENV+PMV AG + EMLL Sbjct: 538 DVRVEREENVYPMVPAGAALDEMLL 562 Lambda K H 0.319 0.135 0.407 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: 896 Number of extensions: 29 Number of successful extensions: 5 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: 585 Length of database: 563 Length adjustment: 36 Effective length of query: 549 Effective length of database: 527 Effective search space: 289323 Effective search space used: 289323 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 206818 DVU1376 (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.32103.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-257 841.7 0.0 1.4e-257 841.5 0.0 1.0 1 lcl|MicrobesOnline__882:206818 DVU1376 acetolactate synthase, l Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:206818 DVU1376 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 841.5 0.0 1.4e-257 1.4e-257 1 554 [. 3 561 .. 3 563 .] 0.97 Alignments for each domain: == domain 1 score: 841.5 bits; conditional E-value: 1.4e-257 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnl 78 l+ga+il+e lkkegv++ fGyPGGav++iyd++ + el+h+lvrheqaa+haadGyarasGkvGv+l+tsGPGatn+ lcl|MicrobesOnline__882:206818 3 LNGAQILLECLKKEGVDVFFGYPGGAVIDIYDEIPrHPELHHVLVRHEQAAVHAADGYARASGKVGVCLVTSGPGATNT 81 579*******************************9899***************************************** PP TIGR00118 79 vtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdl 157 vtgiatay ds+P+v+ltGqv+t liG+dafqe+di+Git+p+tkh++lv+++++l++++++af++a tGrPGPvlvdl lcl|MicrobesOnline__882:206818 82 VTGIATAYSDSIPVVILTGQVPTPLIGNDAFQEVDIVGITRPCTKHNYLVRDVKELATVVRQAFYLARTGRPGPVLVDL 160 ******************************************************************************* PP TIGR00118 158 PkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttll 236 Pkdv++a++++ +e+v++++y+pt k++ +qi++a+++ +a++P+l+vGgGv++++aseel +a +l+ipv++tl+ lcl|MicrobesOnline__882:206818 161 PKDVMQAKTDFVWPEDVSMRSYNPTYKPNLNQIRRAADAFFEAERPLLFVGGGVVMSDASEELGWFARTLRIPVASTLM 239 ******************************************************************************* PP TIGR00118 237 GlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipiv 315 GlGafp d+pl lgmlGmhGt++an av++adl++avGarfddrvtg l+ fa++a+iihididP++i knv+v ip+v lcl|MicrobesOnline__882:206818 240 GLGAFPGDDPLWLGMLGMHGTYAANKAVNNADLIVAVGARFDDRVTGRLSAFASKARIIHIDIDPTSIRKNVQVGIPVV 318 ******************************************************************************* PP TIGR00118 316 Gdakkvleellkklkee......ekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhq 388 Gd+++ l+++ + l + + +Wle++++w+ e++l +++ e+ ikPq+vi++l +++++ai+tt+vGq+q lcl|MicrobesOnline__882:206818 319 GDCRQSLANIREILVPRleekdwGAAHARWLEQLASWRVEQPLGFSR-EGGIKPQQVIEQLFAITRGDAIITTEVGQNQ 396 *******9987766555433355445567*************99975.689**************************** PP TIGR00118 389 mwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnell 467 mw+aqfy+++kpr+ itsgGlGtmG+G+Paa+Ga+ a p++ vv+v+Gdgs+qmn+qel+t+v ++pvki+ilnn +l lcl|MicrobesOnline__882:206818 397 MWTAQFYTFRKPRTLITSGGLGTMGYGFPAAIGAQFAFPDKLVVDVAGDGSIQMNIQELATAVCNKLPVKILILNNGYL 475 ******************************************************************************* PP TIGR00118 468 GmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvap 546 Gmv+qWqelfy++ y +t++ + +pdfvklaeayG++g ri++ e le+ l+eal+s +p+++dv+v++ee+v+Pmv+ lcl|MicrobesOnline__882:206818 476 GMVRQWQELFYQRNYCSTCMDA-QPDFVKLAEAYGAEGYRITEVESLESTLREALASPHPAIIDVRVEREENVYPMVPA 553 *********************5.******************************************************** PP TIGR00118 547 Gagldelv 554 Ga+lde++ lcl|MicrobesOnline__882:206818 554 GAALDEML 561 *******8 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 12.39 // [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