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 CA265_RS15805 CA265_RS15805 acetolactate synthase, large subunit, biosynthetic type
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__Pedo557:CA265_RS15805 Length = 583 Score = 465 bits (1196), Expect = e-135 Identities = 249/556 (44%), Positives = 348/556 (62%), Gaps = 16/556 (2%) Query: 3 GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG--VEHLLCRHEQGAAMAAIGYARA 60 G+Q +++ L +GV T+FGYPGGAIMP+YDALYD +EH+L RHEQG AA G+ARA Sbjct: 26 GSQVLLNGLIEEGVTTIFGYPGGAIMPIYDALYDYADKLEHILVRHEQGGIHAAQGFARA 85 Query: 61 TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120 +G+ GV ATSGPGATNL+TGLADA +DS P+V ITGQV A +GTDAFQE DV+ ++ Sbjct: 86 SGEVGVVFATSGPGATNLVTGLADAQIDSTPLVCITGQVFAHLLGTDAFQETDVINITTP 145 Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180 TK ++ V +E+ ++A+AF +A SGRPGPVL+DI K+ QL + + Sbjct: 146 VTKWNYQVTDAKEIQEVLAKAFYIAKSGRPGPVLIDITKNAQLQLEEFPEYVKCNHIRSY 205 Query: 181 FPHAEV-----EQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLG 235 P +V EQA +++ A+KP + G GV + A + F+ T +PA T+ G G Sbjct: 206 RPKPKVRIEYIEQAAELINSAKKPFVLFGQGVILGSAEEEFKAFINKTGIPAAWTIMGEG 265 Query: 236 AVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDI 295 A+ +P +GMLGMHG N E D++IA+G RFDDRVTG+L+ +A A V+H+DI Sbjct: 266 AIPTSHPLNVGMLGMHGNYGPNVLTNEADVIIAIGMRFDDRVTGRLDKYAKQARVVHLDI 325 Query: 296 DPAEMNKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDH-------- 347 DPAE++K +A V + GD LP L +N+ + A+ R + D Sbjct: 326 DPAEIDKNVKAEVGVWGDCKETLPLLTNLVNENKHEDWLAKFRQYNQEEIDQVITPELYP 385 Query: 348 PGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGL 407 GD + +L+ +++ D V+ TDVGQHQM A ++ + ITS GLGTMGFGL Sbjct: 386 TGDEMTMGEVLRNINEICGGDAVIVTDVGQHQMVACRYAKFNNTRSNITSGGLGTMGFGL 445 Query: 408 PAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQL 467 PAA+GA+ P+ TV+ I GDG F M QELGT+ + +KI++L+N+ LGMVRQWQQL Sbjct: 446 PAAIGAKYGAPDKTVIAIIGDGGFQMTPQELGTIMQFGAAVKILILNNRFLGMVRQWQQL 505 Query: 468 FFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDEL 527 F +RYS +T +PDF+ LA ++ I + + + AL+TM+N +G YLL V + Sbjct: 506 FHDKRYSFVNIT-SPDFVALAKSYYIEASKVDERANLRQALETMINHEGSYLLEVMVGRE 564 Query: 528 ENVWPLVPPGASNSEM 543 NV+P+VP G S SE+ Sbjct: 565 NNVFPMVPQGMSVSEI 580 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: 766 Number of extensions: 31 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: 583 Length adjustment: 36 Effective length of query: 512 Effective length of database: 547 Effective search space: 280064 Effective search space used: 280064 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 CA265_RS15805 CA265_RS15805 (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.32053.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-213 696.1 1.3 1.8e-213 695.9 1.3 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS15805 CA265_RS15805 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS15805 CA265_RS15805 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 695.9 1.3 1.8e-213 1.8e-213 2 553 .. 25 580 .. 24 583 .] 0.96 Alignments for each domain: == domain 1 score: 695.9 bits; conditional E-value: 1.8e-213 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvv 67 +g+++l++ l +egv t+fGyPGGa++piydaly +++lehilvrheq+ +haa+G+arasG+vGvv lcl|FitnessBrowser__Pedo557:CA265_RS15805 25 TGSQVLLNGLIEEGVTTIFGYPGGAIMPIYDALYdyADKLEHILVRHEQGGIHAAQGFARASGEVGVV 92 6899******************************989******************************* PP TIGR00118 68 latsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlp 135 +atsGPGatnlvtg+a+a +ds+Plv +tGqv ++l+G+dafqe d++ it pvtk++++v++a+++ lcl|FitnessBrowser__Pedo557:CA265_RS15805 93 FATSGPGATNLVTGLADAQIDSTPLVCITGQVFAHLLGTDAFQETDVINITTPVTKWNYQVTDAKEIQ 160 ******************************************************************** PP TIGR00118 136 eilkeafeiastGrPGPvlvdlPkdvteaeieleve.ekvelpgykptvkghklqikkaleliekakk 202 e+l +af+ia++GrPGPvl+d+ k+ + + e++ + + ++++y+p+ k + i++a+eli++akk lcl|FitnessBrowser__Pedo557:CA265_RS15805 161 EVLAKAFYIAKSGRPGPVLIDITKNAQLQLEEFPEYvKCNHIRSYRPKPKVRIEYIEQAAELINSAKK 228 ***************************99999987746678*************************** PP TIGR00118 203 PvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadll 270 P +l G Gvi + a+ee+k + +++ ip + t++G Ga+p hpl +gmlGmhG + n+ +ead++ lcl|FitnessBrowser__Pedo557:CA265_RS15805 229 PFVLFGQGVILGSAEEEFKAFINKTGIPAAWTIMGEGAIPTSHPLNVGMLGMHGNYGPNVLTNEADVI 296 ******************************************************************** PP TIGR00118 271 iavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkeke 338 ia+G+rfddrvtg l+k+a++a+++h+didPaei+knvk+++ + Gd+k+ l l + ++e+++++ lcl|FitnessBrowser__Pedo557:CA265_RS15805 297 IAIGMRFDDRVTGRLDKYAKQARVVHLDIDPAEIDKNVKAEVGVWGDCKETLPLLTNLVNENKHED-- 362 ****************************************************99888888877777.. PP TIGR00118 339 Wlekieewkkeyilk.....ldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkpr 401 Wl+k +++ +e i + l + +++ +v++++ ++ ++a++ tdvGqhqm a ++ k++++r lcl|FitnessBrowser__Pedo557:CA265_RS15805 363 WLAKFRQYNQEEIDQvitpeLYPTGDEMTMGEVLRNINEICGGDAVIVTDVGQHQMVACRYAKFNNTR 430 *********9988762111133456789999************************************* PP TIGR00118 402 kfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGm 469 + itsgGlGtmGfGlPaa+Gak + p++tv+a+ Gdg+fqm+ qel ti++++ vki+ilnn++lGm lcl|FitnessBrowser__Pedo557:CA265_RS15805 431 SNITSGGLGTMGFGLPAAIGAKYGAPDKTVIAIIGDGGFQMTPQELGTIMQFGAAVKILILNNRFLGM 498 ******************************************************************** PP TIGR00118 470 vkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdke 537 v+qWq+lf+++rys ++++s pdfv+la++y +++ ++ ++++l ++l+ ++++++ +ll+v v +e lcl|FitnessBrowser__Pedo557:CA265_RS15805 499 VRQWQQLFHDKRYSFVNITS--PDFVALAKSYYIEASKVDERANLRQALETMINHEGSYLLEVMVGRE 564 ******************96..********************************************** PP TIGR00118 538 eevlPmvapGagldel 553 ++v+Pmv++G++++e+ lcl|FitnessBrowser__Pedo557:CA265_RS15805 565 NNVFPMVPQGMSVSEI 580 ************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (583 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 0.02s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 7.64 // [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