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 BWI76_RS27815 BWI76_RS27815 acetolactate synthase catalytic subunit
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__Koxy:BWI76_RS27815 Length = 562 Score = 505 bits (1301), Expect = e-147 Identities = 269/552 (48%), Positives = 359/552 (65%), Gaps = 16/552 (2%) Query: 3 GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG-VEHLLCRHEQGAAMAAIGYARAT 61 GAQ VVH L QG+ TV G PGG+I+P+YDAL + H+L RHEQGA A G AR Sbjct: 15 GAQLVVHLLERQGITTVSGIPGGSILPIYDALSQSTQIRHILARHEQGAGFIAQGMARTE 74 Query: 62 GKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLAC 121 GK VC+A SGPGATNLIT +ADA LDSIP+V ITGQV A IGTDAFQEVD G+S+ Sbjct: 75 GKPAVCMACSGPGATNLITAIADARLDSIPLVCITGQVPASMIGTDAFQEVDTYGISIPI 134 Query: 122 TKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDL----EPWFTTVEN 177 TKH++LV+++ ELP++M++AF +A SGRPGPV +DIPKD+Q A+ +L EP Sbjct: 135 TKHNYLVRNIAELPQVMSDAFRIAQSGRPGPVWIDIPKDVQAATIELDALPEPGARMAAP 194 Query: 178 EVTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAV 237 E F A V +A M+ AQ+P+LY+GGGV A +R+ +P T TL LG + Sbjct: 195 E--FDSASVREAAAMINAAQRPVLYLGGGV--INAPEHIRQLAEKANLPTTQTLMALGML 250 Query: 238 EADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDP 297 +P LGMLGMHG ++ NF +QE DLL+ +GARFDDR GK F P+A +IH+DID Sbjct: 251 PKAHPLSLGMLGMHGARSTNFILQEADLLVVLGARFDDRAIGKTEQFCPNAKIIHVDIDR 310 Query: 298 AEMNKLRQAHVALQGD----LNALLPALQ-QPLNQYDWQQHCAQLRDEHSWRYDHPGDAI 352 +E+ K++QAHVA+QGD L L+P ++ QP + W Q A L+ E D + Sbjct: 311 SELGKIKQAHVAIQGDVGEVLEQLIPQVEAQPRSA--WLQLVADLQREFPCTIPQEQDPL 368 Query: 353 YAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVG 412 L+ ++ + +VTTDVGQHQMW AQ RP ++TS GLGTMGFGLPAAVG Sbjct: 369 SHYGLINAVAACVDDEAIVTTDVGQHQMWVAQAYPLNRPRQWLTSGGLGTMGFGLPAAVG 428 Query: 413 AQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQER 472 A +A P V+C SGDGS MMN+QE+ T QL +KI+L++N+ LG+V Q Q LF+++ Sbjct: 429 AALANPQRKVICFSGDGSLMMNIQEMATAAENQLDVKIILMNNEALGLVYQQQSLFYKQG 488 Query: 473 YSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWP 532 T +F+ +AS FG+ + + +AAL +++ GP L+HV ID E V+P Sbjct: 489 VFAATYPGMVNFMQIASGFGLQTCDLNNEADPQAALQAIIDRPGPALIHVRIDAEEKVYP 548 Query: 533 LVPPGASNSEML 544 +VPPGA+N+EM+ Sbjct: 549 MVPPGAANTEMV 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: 32 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 BWI76_RS27815 BWI76_RS27815 (acetolactate synthase catalytic subunit)
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.6732.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-205 669.8 0.8 1.6e-205 669.6 0.8 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS27815 BWI76_RS27815 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS27815 BWI76_RS27815 acetolactate synthase catalytic subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 669.6 0.8 1.6e-205 1.6e-205 2 555 .. 14 561 .. 13 562 .] 0.97 Alignments for each domain: == domain 1 score: 669.6 bits; conditional E-value: 1.6e-205 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlats 71 +ga+++v+ l+++g+ tv G+PGG++lpiydal + +++hil+rheq+a +a+G+ar+ Gk+ v++a s lcl|FitnessBrowser__Koxy:BWI76_RS27815 14 TGAQLVVHLLERQGITTVSGIPGGSILPIYDALSqSTQIRHILARHEQGAGFIAQGMARTEGKPAVCMACS 84 79*******************************97889********************************* PP TIGR00118 72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeaf 142 GPGatnl+t+ia+a lds+Plv +tGqv++s+iG+dafqe+d Gi++p+tkh++lv++ ++lp+++ +af lcl|FitnessBrowser__Koxy:BWI76_RS27815 85 GPGATNLITAIADARLDSIPLVCITGQVPASMIGTDAFQEVDTYGISIPITKHNYLVRNIAELPQVMSDAF 155 *********************************************************************** PP TIGR00118 143 eiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGvii 213 ia++GrPGPv +d+Pkdv++a+iel+ + + +p+ + + +++a+ +i++a++Pvl+ GgGvi lcl|FitnessBrowser__Koxy:BWI76_RS27815 156 RIAQSGRPGPVWIDIPKDVQAATIELDALPEPGARMAAPEF--DSASVREAAAMINAAQRPVLYLGGGVI- 223 *************************9998776666666655..56789*********************9. PP TIGR00118 214 aeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgn 284 +a+e++++lae++++p t+tl+ lG +p+ hpl+lgmlGmhG++ +n+ ++eadll+ +Garfddr g+ lcl|FitnessBrowser__Koxy:BWI76_RS27815 224 -NAPEHIRQLAEKANLPTTQTLMALGMLPKAHPLSLGMLGMHGARSTNFILQEADLLVVLGARFDDRAIGK 293 .57999***************************************************************** PP TIGR00118 285 lakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkld 355 ++f+p+akiih+did +e+gk+ +++++i Gd+ +vle+l+ +++++ ++ Wl+ ++++++e + ++ lcl|FitnessBrowser__Koxy:BWI76_RS27815 294 TEQFCPNAKIIHVDIDRSELGKIKQAHVAIQGDVGEVLEQLIPQVEAQPRSA--WLQLVADLQREFPCTIP 362 **********************************************999998..***************** PP TIGR00118 356 eeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvak 426 +e++++ +i+++ ++deaivttdvGqhqmw+aq y+ ++pr+++tsgGlGtmGfGlPaa+Ga +a+ lcl|FitnessBrowser__Koxy:BWI76_RS27815 363 QEQDPLSHYGLINAVAACVDDEAIVTTDVGQHQMWVAQAYPLNRPRQWLTSGGLGTMGFGLPAAVGAALAN 433 *********************************************************************** PP TIGR00118 427 peetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvkl 497 p+ +v++ +Gdgs++mn+qe++t++e +++vki+++nne lG+v+q q+lfy++ +++ ++ +f+++ lcl|FitnessBrowser__Koxy:BWI76_RS27815 434 PQRKVICFSGDGSLMMNIQEMATAAENQLDVKIILMNNEALGLVYQQQSLFYKQGVFAATYP-GMVNFMQI 503 *****************************************************999888877.59****** PP TIGR00118 498 aeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555 a ++G+++ ++++++ +++l+ ++ +p+l+ v++d ee+v+Pmv+pGa+++e+v+ lcl|FitnessBrowser__Koxy:BWI76_RS27815 504 ASGFGLQTCDLNNEADPQAALQAIIDRPGPALIHVRIDAEEKVYPMVPPGAANTEMVG 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 11.65 // [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