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 351605 BT2077 acetolactate synthase large subunit (NCBI ptt file)
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__Btheta:351605 Length = 565 Score = 478 bits (1231), Expect = e-139 Identities = 253/558 (45%), Positives = 360/558 (64%), Gaps = 15/558 (2%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYD--GGVEHLLCRHEQGAAMAAIGYA 58 + GA+ ++ +L QGV T+FGYPGG+IMP +DALYD + H+L RHEQGAA AA GYA Sbjct: 6 ITGAEAMMRSLEHQGVTTIFGYPGGSIMPTFDALYDHQNTLNHILVRHEQGAAHAAQGYA 65 Query: 59 RATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLS 118 R +GK GVC+ TSGPGATN ITG+ADA++DS P+V I GQV F+GTDAFQEVD++G++ Sbjct: 66 RVSGKVGVCLVTSGPGATNTITGIADAMIDSTPIVVIAGQVGTGFLGTDAFQEVDLVGIT 125 Query: 119 LACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTT-VEN 177 K S+ ++ E++ +A AF +A SGRPGPV++D K+ Q+ EP + + Sbjct: 126 QPIAKWSYQIRRAEDVAWAIARAFYIASSGRPGPVVLDFAKNAQVEKTKYEPTKQEFIRS 185 Query: 178 EVTFPHAE---VEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGL 234 V P + V+ A +++ A++P++ VG GV + A LR F+ MPA CTL GL Sbjct: 186 YVPVPDTDEESVKAAAELINNAERPLVLVGQGVELGSAQEELRIFIEKADMPAGCTLLGL 245 Query: 235 GAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMD 294 A+ D+P GMLGMHG N +CD+LIAVG RFDDRVTG L T+A A VIH D Sbjct: 246 SALPTDHPLNKGMLGMHGNLGPNINTNKCDVLIAVGMRFDDRVTGNLATYAKQAKVIHFD 305 Query: 295 IDPAEMNKLRQAHVALQGDLNALLPALQQPLNQ------YDWQQHCAQLRDEHSWRYD-H 347 IDPAE+NK + +A+ GD L A+ L + D + + +E R + H Sbjct: 306 IDPAEVNKNVKVDIAVLGDCKKTLAAVTGLLKKNRHTEWVDSFKEYEAVEEEKVIRPELH 365 Query: 348 PG-DAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFG 406 P D++ +++ +S+ + ++ TDVGQ+QM +A++ +TR + +TS GLGTMGFG Sbjct: 366 PATDSLSMGEVVRAVSEATRHEAILVTDVGQNQMISARYFKYTRERSIVTSGGLGTMGFG 425 Query: 407 LPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQ 466 LPAA+GA RP+ TV GDG MN+QELGT+ ++ P+KI+ L+N LG VRQWQ Sbjct: 426 LPAAIGATFGRPDRTVCVFMGDGGLQMNIQELGTIMEQKAPVKIICLNNNYLGNVRQWQA 485 Query: 467 LFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDE 526 +FF RYS T + NPD++ +ASA+ I + + +++++AA+D ML++DG +LL + E Sbjct: 486 MFFNRRYSFTPML-NPDYMKIASAYDIPSKRVFSREELKAAIDEMLSTDGAFLLEACVVE 544 Query: 527 LENVWPLVPPGASNSEML 544 NV P+ PPG S ++ML Sbjct: 545 EGNVLPMTPPGGSVNQML 562 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: 771 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: 565 Length adjustment: 36 Effective length of query: 512 Effective length of database: 529 Effective search space: 270848 Effective search space used: 270848 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 351605 BT2077 (acetolactate synthase large subunit (NCBI ptt file))
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.6965.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-211 689.3 0.3 2e-211 689.2 0.3 1.0 1 lcl|FitnessBrowser__Btheta:351605 BT2077 acetolactate synthase lar Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:351605 BT2077 acetolactate synthase large subunit (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 689.2 0.3 2e-211 2e-211 2 555 .. 7 563 .. 6 565 .] 0.97 Alignments for each domain: == domain 1 score: 689.2 bits; conditional E-value: 2e-211 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlatsGPGa 75 +gae++++sl+++gv t+fGyPGG+++p +daly ++ l+hilvrheq+aahaa+Gyar+sGkvGv+l+tsGPGa lcl|FitnessBrowser__Btheta:351605 7 TGAEAMMRSLEHQGVTTIFGYPGGSIMPTFDALYdhQNTLNHILVRHEQGAAHAAQGYARVSGKVGVCLVTSGPGA 82 89********************************88899************************************* PP TIGR00118 76 tnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPG 151 tn++tgia+a++ds+P+vv++Gqv t +G+dafqe+d++Git+p+ k+s+++++aed++ + +af+ias+GrPG lcl|FitnessBrowser__Btheta:351605 83 TNTITGIADAMIDSTPIVVIAGQVGTGFLGTDAFQEVDLVGITQPIAKWSYQIRRAEDVAWAIARAFYIASSGRPG 158 **************************************************************************** PP TIGR00118 152 PvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerl 227 Pv++d+ k+ + +++++e +++ +++y p +++ +k+a+eli++a++P++lvG Gv + a+eel+ + e++ lcl|FitnessBrowser__Btheta:351605 159 PVVLDFAKNAQVEKTKYEPTKQEFIRSYVPVPDTDEESVKAAAELINNAERPLVLVGQGVELGSAQEELRIFIEKA 234 **************************************************************************** PP TIGR00118 228 kipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPae 303 ++p +tllGl a+p dhpl gmlGmhG n+ +++d+liavG+rfddrvtgnla++a++ak+ih+didPae lcl|FitnessBrowser__Btheta:351605 235 DMPAGCTLLGLSALPTDHPLNKGMLGMHGNLGPNINTNKCDVLIAVGMRFDDRVTGNLATYAKQAKVIHFDIDPAE 310 **************************************************************************** PP TIGR00118 304 igknvkvdipivGdakkvleellkklkeeekkekeWlekieewkk...eyilk..ldeeeesikPqkvikelskll 374 ++knvkvdi++ Gd+kk l+ + lk+++++e W+++ +e+ + e++++ l+ +s+ +v++++s+ + lcl|FitnessBrowser__Btheta:351605 311 VNKNVKVDIAVLGDCKKTLAAVTGLLKKNRHTE--WVDSFKEYEAveeEKVIRpeLHPATDSLSMGEVVRAVSEAT 384 ***********************9999887777..999999987521144444337777889************** PP TIGR00118 375 kdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelsti 450 ++eai+ tdvGq+qm +a+++k+++ r+ +tsgGlGtmGfGlPaa+Ga + p+ tv +Gdg++qmn+qel ti lcl|FitnessBrowser__Btheta:351605 385 RHEAILVTDVGQNQMISARYFKYTRERSIVTSGGLGTMGFGLPAAIGATFGRPDRTVCVFMGDGGLQMNIQELGTI 460 **************************************************************************** PP TIGR00118 451 veydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeske 526 +e + pvki++lnn++lG v+qWq +f+++rys t + + pd++k+a ay + + r+ ++eel+++++e+l++++ lcl|FitnessBrowser__Btheta:351605 461 MEQKAPVKIICLNNNYLGNVRQWQAMFFNRRYSFTPMLN--PDYMKIASAYDIPSKRVFSREELKAAIDEMLSTDG 534 **************************************7..*********************************** PP TIGR00118 527 pvlldvevdkeeevlPmvapGagldelve 555 ll+ v +e +vlPm +pG+++++++ lcl|FitnessBrowser__Btheta:351605 535 AFLLEACVVEEGNVLPMTPPGGSVNQMLL 563 **************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (565 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: 12.44 // [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