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 17731 b3671 acetolactate synthase large subunit (NCBI)
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__Keio:17731 Length = 562 Score = 499 bits (1286), Expect = e-146 Identities = 258/550 (46%), Positives = 356/550 (64%), Gaps = 12/550 (2%) Query: 3 GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG-VEHLLCRHEQGAAMAAIGYARAT 61 GA+++VH L QG+ V G PGG+I+PVYDAL + H+L RHEQGA A G AR Sbjct: 15 GAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHEQGAGFIAQGMARTD 74 Query: 62 GKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLAC 121 GK VC+A SGPGATNL+T +ADA LDSIP++ ITGQV A IGTDAFQEVD G+S+ Sbjct: 75 GKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTDAFQEVDTYGISIPI 134 Query: 122 TKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT- 180 TKH++LV+ +EELP++M++AF +A SGRPGPV +DIPKD+Q A ++E E Sbjct: 135 TKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFEIETQPAMAEKAAAP 194 Query: 181 -FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEA 239 F + A M+ A++P+LY+GGGV A A +RE ++P T TL LG + Sbjct: 195 AFSEESIRDAAAMINAAKRPVLYLGGGVINAPA--RVRELAEKAQLPTTMTLMALGMLPK 252 Query: 240 DYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAE 299 +P LGMLGMHG ++ N+ +QE DLLI +GARFDDR GK F P+A +IH+DID AE Sbjct: 253 AHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPNAKIIHVDIDRAE 312 Query: 300 MNKLRQAHVALQGDLNALLPAL-----QQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYA 354 + K++Q HVA+Q D++ +L L QP + +W Q A L+ E D + Sbjct: 313 LGKIKQPHVAIQADVDDVLAQLIPLVEAQP--RAEWHQLVADLQREFPCPIPKACDPLSH 370 Query: 355 PLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQ 414 L+ ++ + ++TTDVGQHQMW AQ RP ++TS GLGTMGFGLPAA+GA Sbjct: 371 YGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMGFGLPAAIGAA 430 Query: 415 VARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYS 474 +A P+ V+C SGDGS MMN+QE+ T QL +KI+L++N+ LG+V Q Q LF+++ Sbjct: 431 LANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALGLVHQQQSLFYEQGVF 490 Query: 475 ETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLV 534 T +F+ +A+ FG+ + + +A+L ++N GP L+HV ID E V+P+V Sbjct: 491 AATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHVRIDAEEKVYPMV 550 Query: 535 PPGASNSEML 544 PPGA+N+EM+ Sbjct: 551 PPGAANTEMV 560 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: 828 Number of extensions: 34 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: 548 Length of database: 562 Length adjustment: 36 Effective length of query: 512 Effective length of database: 526 Effective search space: 269312 Effective search space used: 269312 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 17731 b3671 (acetolactate synthase large subunit (NCBI))
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.17536.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-206 670.7 0.4 9.2e-206 670.5 0.4 1.0 1 lcl|FitnessBrowser__Keio:17731 b3671 acetolactate synthase larg Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17731 b3671 acetolactate synthase large subunit (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 670.5 0.4 9.2e-206 9.2e-206 2 555 .. 14 561 .. 13 562 .] 0.98 Alignments for each domain: == domain 1 score: 670.5 bits; conditional E-value: 9.2e-206 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnlv 79 +gae +v+ l+++g+++v G+PGG++lp+ydal + +++hil+rheq+a +a+G+ar+ Gk+ v++a sGPGatnlv lcl|FitnessBrowser__Keio:17731 14 TGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSqSTQIRHILARHEQGAGFIAQGMARTDGKPAVCMACSGPGATNLV 92 79*******************************97889***************************************** PP TIGR00118 80 tgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdlP 158 t+ia+a lds+Pl+ +tGqv++s+iG+dafqe+d Gi++p+tkh++lv++ e+lp+++ +af ia++GrPGPv +d+P lcl|FitnessBrowser__Keio:17731 93 TAIADARLDSIPLICITGQVPASMIGTDAFQEVDTYGISIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIP 171 ******************************************************************************* PP TIGR00118 159 kdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttllG 237 kdv++a +e+e++ + ++ +p ++ i+ a+ +i++ak+Pvl+ GgGvi a +++++elae++++p t+tl+ lcl|FitnessBrowser__Keio:17731 172 KDVQTAVFEIETQPAMAEKAAAPAF--SEESIRDAAAMINAAKRPVLYLGGGVINA--PARVRELAEKAQLPTTMTLMA 246 ********99999888777777766..5678***********************65..6789***************** PP TIGR00118 238 lGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivG 316 lG +p+ hpl+lgmlGmhG + +n+ ++eadlli +Garfddr g+ ++f+p+akiih+did ae+gk+ + +++i lcl|FitnessBrowser__Keio:17731 247 LGMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPNAKIIHVDIDRAELGKIKQPHVAIQA 325 ******************************************************************************* PP TIGR00118 317 dakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfy 395 d+ vl++l+ ++++ + e W + ++++++e + + + +++ +i+++ ++d+ai+ttdvGqhqmw+aq y lcl|FitnessBrowser__Keio:17731 326 DVDDVLAQLIPLVEAQPRAE--WHQLVADLQREFPCPIPKACDPLSHYGLINAVAACVDDNAIITTDVGQHQMWTAQAY 402 **************999999..********************************************************* PP TIGR00118 396 ktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474 + ++pr+++tsgGlGtmGfGlPaa+Ga +a+p+ +v++ +Gdgs++mn+qe++t++e +++vki+++nne lG+v+q q lcl|FitnessBrowser__Keio:17731 403 PLNRPRQWLTSGGLGTMGFGLPAAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALGLVHQQQ 481 ******************************************************************************* PP TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldel 553 +lfye+ +++ ++ +f+++a ++G+++ ++++++ ++ l+e+++ +p+l+ v++d ee+v+Pmv+pGa+++e+ lcl|FitnessBrowser__Keio:17731 482 SLFYEQGVFAATYP-GKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHVRIDAEEKVYPMVPPGAANTEM 559 *****998887777.58************************************************************** PP TIGR00118 554 ve 555 v+ lcl|FitnessBrowser__Keio:17731 560 VG 561 96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (562 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: 7.85 // [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