Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate GFF1987 PGA1_c20210 acetolactate synthase isozyme 3 large subunit
Query= metacyc::MONOMER-18810 (585 letters) >FitnessBrowser__Phaeo:GFF1987 Length = 583 Score = 598 bits (1543), Expect = e-175 Identities = 310/570 (54%), Positives = 397/570 (69%), Gaps = 6/570 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 EM GA+++V AL ++GV+ V+GYPGGAVL IYDE+ Q HILVRHEQ AVHAA+GYA Sbjct: 4 EMTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFLQNDIRHILVRHEQGAVHAAEGYA 63 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 R+TGK GV LVTSGPG TNAVTG+ A LDSIP+VV+TG VPT IG DAFQE DTVGIT Sbjct: 64 RSTGKPGVVLVTSGPGATNAVTGLTDALLDSIPLVVLTGQVPTFMIGSDAFQEADTVGIT 123 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RP KHN+LVKD LA T+ +AF +A GRPGPV++DIPKDV Y+ PK Sbjct: 124 RPCTKHNWLVKDTEKLAGTLHEAFHVATAGRPGPVLIDIPKDVQFATGTYQDPKPA-ASH 182 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255 Y P KG I + VA ++ A+RP YTGGGV+ + AS LR+L A TG PVT+TLM Sbjct: 183 YQPPVKGDLEAITELVAAMETAKRPVFYTGGGVINSGPGASQLLRELVAATGIPVTSTLM 242 Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315 GLGA+P + K ++GMLGMHG YEANMAM +CD++I IGARFDDR+ G F+ + K Sbjct: 243 GLGAYPASGKNWLGMLGMHGLYEANMAMHDCDLMINIGARFDDRITGRLDAFSPNSTK-A 301 Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375 HIDIDPSSI+K ++VDIPIVG++ VL++++ K+ K A+AKW EQI +WR + Sbjct: 302 HIDIDPSSINKVIRVDIPIVGDIGHVLEDVLKVWKSRGRKVDSAAIAKWQEQITEWRDIR 361 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434 CL Y S IKPQY +E++ LTK + +I ++VGQHQMWAAQ+ F++P RW+ SGGL Sbjct: 362 CLAYTASESTIKPQYALERLEALTKDRNRYITTEVGQHQMWAAQYLGFEDPNRWMTSGGL 421 Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494 GTMG G P ++G++ A P+ V+ + GE S M +QE+ T +QY PVK LNN LGM Sbjct: 422 GTMGYGTPASLGVQVAHPDALVINVAGEASWLMNMQEMGTAVQYRLPVKQFILNNERLGM 481 Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554 VRQWQE+ + RYSHS+ +ALPDFVKLAEA+G G+ + D++ A+ E D V Sbjct: 482 VRQWQELLHGERYSHSWSEALPDFVKLAEAFGAKGIICKDPKDLDDAIMEMLDY-DGPVI 540 Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAED 584 D + EN +PM+ +GK +EMLLG D Sbjct: 541 FDCLVEKHENCFPMIPSGKAHNEMLLGEAD 570 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: 987 Number of extensions: 40 Number of successful extensions: 6 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: 583 Length adjustment: 36 Effective length of query: 549 Effective length of database: 547 Effective search space: 300303 Effective search space used: 300303 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 GFF1987 PGA1_c20210 (acetolactate synthase isozyme 3 large 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.25529.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-236 770.7 0.0 4.6e-236 770.5 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF1987 PGA1_c20210 acetolactate synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF1987 PGA1_c20210 acetolactate synthase isozyme 3 large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 770.5 0.0 4.6e-236 4.6e-236 1 554 [. 5 565 .. 5 568 .. 0.97 Alignments for each domain: == domain 1 score: 770.5 bits; conditional E-value: 4.6e-236 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGa 75 ++ga+++v++lk++gv+tvfGyPGGavlpiyd+++ +++++hilvrheq+a+haa+Gyar++Gk+Gvvl+tsGPGa lcl|FitnessBrowser__Phaeo:GFF1987 5 MTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFlQNDIRHILVRHEQGAVHAAEGYARSTGKPGVVLVTSGPGA 80 79*********************************99*************************************** PP TIGR00118 76 tnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPG 151 tn+vtg+++a lds+PlvvltGqv+t +iGsdafqe+d +Git+p+tkh++lvk++e l+ +l+eaf++a++GrPG lcl|FitnessBrowser__Phaeo:GFF1987 81 TNAVTGLTDALLDSIPLVVLTGQVPTFMIGSDAFQEADTVGITRPCTKHNWLVKDTEKLAGTLHEAFHVATAGRPG 156 **************************************************************************** PP TIGR00118 152 PvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviia..easeelkelae 225 Pvl+d+Pkdv+ a+ +++ + k y+p vkg+ i +++ ++e+ak+Pv + GgGvi + +as+ l+el+ lcl|FitnessBrowser__Phaeo:GFF1987 157 PVLIDIPKDVQFATGTYQDP-KPAASHYQPPVKGDLEAITELVAAMETAKRPVFYTGGGVINSgpGASQLLRELVA 231 *************9999988.667899**********************************8733699******** PP TIGR00118 226 rlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididP 301 ++ ipvt+tl+GlGa+p+ ++ lgmlGmhG +ean+a++++dl+i +Garfddr+tg l+ f+p+++ hididP lcl|FitnessBrowser__Phaeo:GFF1987 232 ATGIPVTSTLMGLGAYPASGKNWLGMLGMHGLYEANMAMHDCDLMINIGARFDDRITGRLDAFSPNSTKAHIDIDP 307 **************************************************************************** PP TIGR00118 302 aeigknvkvdipivGdakkvleellkklkee.....ekkekeWlekieewkkeyilkldeeeesikPqkvikelsk 372 ++i+k+++vdipivGd +vle++lk k++ + +W e+i+ew++ +l++ +e++ikPq+ +++l lcl|FitnessBrowser__Phaeo:GFF1987 308 SSINKVIRVDIPIVGDIGHVLEDVLKVWKSRgrkvdSAAIAKWQEQITEWRDIRCLAYTASESTIKPQYALERLEA 383 *************************99888776553333445********************************** PP TIGR00118 373 llkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqel 447 l+kd + ++tt+vGqhqmwaaq++ ++ p++++tsgGlGtmG+G Pa+lG++va+p++ v++v+G++s mn+qe+ lcl|FitnessBrowser__Phaeo:GFF1987 384 LTKDrNRYITTEVGQHQMWAAQYLGFEDPNRWMTSGGLGTMGYGTPASLGVQVAHPDALVINVAGEASWLMNMQEM 459 ***9889********************************************************************* PP TIGR00118 448 stiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkeale 523 t+v+y +pvk ilnne lGmv+qWqel++ erys++ ++ lpdfvklaea+G+kgi ++p++l++++ e+l lcl|FitnessBrowser__Phaeo:GFF1987 460 GTAVQYRLPVKQFILNNERLGMVRQWQELLHGERYSHSWSEA-LPDFVKLAEAFGAKGIICKDPKDLDDAIMEMLD 534 **************************************9995.********************************* PP TIGR00118 524 skepvlldvevdkeeevlPmvapGagldelv 554 ++pv++d v+k+e+++Pm+++G++ +e++ lcl|FitnessBrowser__Phaeo:GFF1987 535 YDGPVIFDCLVEKHENCFPMIPSGKAHNEML 565 *****************************98 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 10.01 // [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