Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate 3608378 Dshi_1779 acetolactate synthase, large subunit, biosynthetic type (RefSeq)
Query= metacyc::MONOMER-18810 (585 letters) >FitnessBrowser__Dino:3608378 Length = 585 Score = 609 bits (1571), Expect = e-179 Identities = 310/571 (54%), Positives = 400/571 (70%), Gaps = 6/571 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 +M GA+++V AL ++GV+ V+GYPGGAVL IYDE+ +Q + +HILVRHEQAA HAA+GYA Sbjct: 4 QMTGAQMVVQALKDQGVDTVFGYPGGAVLPIYDEIFQQNEIKHILVRHEQAATHAAEGYA 63 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 R+TGK GV LVTSGPG TNAVTGI A +DSIPMVV++G VPT IG DAFQE DTVGIT Sbjct: 64 RSTGKPGVVLVTSGPGATNAVTGITDALMDSIPMVVLSGQVPTFMIGNDAFQEADTVGIT 123 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RP KHN+LVK+ LA TI +AF +A +GRPGPV+VDIPKDV + Y P D R Sbjct: 124 RPCTKHNWLVKETDLLADTIHQAFHVATSGRPGPVLVDIPKDVQFASGTYVPPAKADTRH 183 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNTLM 255 Y P KG I V L++ AERP YTGGGV+ + AS LR+ A TG P+T+TLM Sbjct: 184 YQPRVKGDVAAITAMVELMETAERPIFYTGGGVINSGPAASQLLREFVAETGFPITSTLM 243 Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315 GLGA+P + + ++GMLGMHG YEAN+AM CDV+I IGARFDDR+ G A F+ +++K I Sbjct: 244 GLGAYPASGENWIGMLGMHGLYEANLAMHGCDVMINIGARFDDRITGRVADFSPESKK-I 302 Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375 HIDIDPSSI+K ++ D+PI+G++ VL++ + KA K + A+ WW QIE+WR+V Sbjct: 303 HIDIDPSSINKVIRTDVPIIGDIAHVLEDALRIWKARGRKTNKAAVKAWWTQIEEWRTVR 362 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG--DAFICSDVGQHQMWAAQFYKFDEPRRWINSGG 433 CL + S IKPQY ++++ LTK FI ++VGQHQMWAAQ+ FDEP RW+ SGG Sbjct: 363 CLDFKNSETTIKPQYAMQRLEALTKDHPKRFIATEVGQHQMWAAQYLGFDEPNRWMTSGG 422 Query: 434 LGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLG 493 LGTMG G P ++G++ A P+ V+ + GE S M +QE+ T +QY PVK LNN LG Sbjct: 423 LGTMGYGFPASIGVQVAHPDALVINVAGEASWLMNMQEMGTAIQYMLPVKQFILNNERLG 482 Query: 494 MVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTV 553 MVRQWQE+ + RYSHS+ DALPDFVKLAEA+G G+ + D++ A+ E D V Sbjct: 483 MVRQWQELLHGERYSHSWSDALPDFVKLAEAFGAKGILCKDPKDLDDAIMEMLEY-DGPV 541 Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLLGAED 584 D + EN +PM+ +G +EMLLG D Sbjct: 542 IFDCLVEKHENCFPMIPSGAPHNEMLLGEAD 572 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: 952 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: 585 Length of database: 585 Length adjustment: 37 Effective length of query: 548 Effective length of database: 548 Effective search space: 300304 Effective search space used: 300304 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 3608378 Dshi_1779 (acetolactate synthase, large subunit, biosynthetic type (RefSeq))
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.17471.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-237 775.6 0.2 1.5e-237 775.4 0.2 1.0 1 lcl|FitnessBrowser__Dino:3608378 Dshi_1779 acetolactate synthase, Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3608378 Dshi_1779 acetolactate synthase, large subunit, biosynthetic type (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 775.4 0.2 1.5e-237 1.5e-237 1 554 [. 5 567 .. 5 570 .. 0.97 Alignments for each domain: == domain 1 score: 775.4 bits; conditional E-value: 1.5e-237 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGat 76 ++ga+++v++lk++gv+tvfGyPGGavlpiyd+++ ++e++hilvrheqaa+haa+Gyar++Gk+Gvvl+tsGPGat lcl|FitnessBrowser__Dino:3608378 5 MTGAQMVVQALKDQGVDTVFGYPGGAVLPIYDEIFqQNEIKHILVRHEQAATHAAEGYARSTGKPGVVLVTSGPGAT 81 79*********************************999*************************************** PP TIGR00118 77 nlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPv 153 n+vtgi++a +ds+P+vvl+Gqv+t +iG+dafqe+d +Git+p+tkh++lvk+++ l+ ++++af++a++GrPGPv lcl|FitnessBrowser__Dino:3608378 82 NAVTGITDALMDSIPMVVLSGQVPTFMIGNDAFQEADTVGITRPCTKHNWLVKETDLLADTIHQAFHVATSGRPGPV 158 ***************************************************************************** PP TIGR00118 154 lvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiae..aseelkelaerlk 228 lvd+Pkdv+ a+ ++ ++k + + y+p+vkg+ + i + +el+e+a++P+ + GgGvi ++ as+ l+e++ ++ lcl|FitnessBrowser__Dino:3608378 159 LVDIPKDVQFASGTYVPPAKADTRHYQPRVKGDVAAITAMVELMETAERPIFYTGGGVINSGpaASQLLREFVAETG 235 ***********************************************************885448999********* PP TIGR00118 229 ipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeig 305 p+t+tl+GlGa+p+ ++ +gmlGmhG +eanla++ +d++i +Garfddr+tg +a f+pe+k ihididP++i+ lcl|FitnessBrowser__Dino:3608378 236 FPITSTLMGLGAYPASGENWIGMLGMHGLYEANLAMHGCDVMINIGARFDDRITGRVADFSPESKKIHIDIDPSSIN 312 ***************************************************************************** PP TIGR00118 306 knvkvdipivGdakkvleellkklkee....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkd. 376 k++++d+pi+Gd +vle+ l+ k++ +k + W+ +ieew++ +l ++++e++ikPq+ +++l l+kd lcl|FitnessBrowser__Dino:3608378 313 KVIRTDVPIIGDIAHVLEDALRIWKARgrktNKAAVKaWWTQIEEWRTVRCLDFKNSETTIKPQYAMQRLEALTKDh 389 *******************9987776655545555567**************************************7 PP TIGR00118 377 .eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstive 452 + +++t+vGqhqmwaaq++ +++p++++tsgGlGtmG+G+Pa++G++va+p++ v++v+G++s mn+qe+ t+ + lcl|FitnessBrowser__Dino:3608378 390 pKRFIATEVGQHQMWAAQYLGFDEPNRWMTSGGLGTMGYGFPASIGVQVAHPDALVINVAGEASWLMNMQEMGTAIQ 466 7789************************************************************************* PP TIGR00118 453 ydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvl 529 y +pvk ilnne lGmv+qWqel++ erys++ + lpdfvklaea+G+kgi ++p++l++++ e+le ++pv+ lcl|FitnessBrowser__Dino:3608378 467 YMLPVKQFILNNERLGMVRQWQELLHGERYSHSWSDA-LPDFVKLAEAFGAKGILCKDPKDLDDAIMEMLEYDGPVI 542 *********************************9995.*************************************** PP TIGR00118 530 ldvevdkeeevlPmvapGagldelv 554 +d v+k+e+++Pm+++Ga +e++ lcl|FitnessBrowser__Dino:3608378 543 FDCLVEKHENCFPMIPSGAPHNEML 567 ***********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (585 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: 11.98 // [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