Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_015818963.1 TERTU_RS04690 acetolactate synthase 3 large subunit
Query= BRENDA::P00893 (574 letters) >NCBI__GCF_000023025.1:WP_015818963.1 Length = 578 Score = 726 bits (1874), Expect = 0.0 Identities = 353/580 (60%), Positives = 441/580 (76%), Gaps = 8/580 (1%) Query: 1 MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60 ME LSG ++++RSL D+GV+ VFGYPGGA L IYDA+ + HVLVRHEQAA H ADG Sbjct: 1 MEKLSGGDILIRSLADEGVETVFGYPGGAALHIYDAIFRQKQVKHVLVRHEQAATHAADG 60 Query: 61 LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120 AR+TG+ GVVLVTSGPGATNAITGIATAYMDSIP+VV+SGQV + IG DAFQE DMVG Sbjct: 61 YARSTGKTGVVLVTSGPGATNAITGIATAYMDSIPMVVISGQVVSDKIGEDAFQETDMVG 120 Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180 +SRP+VKHSFLVK +DI + +KKAF++A++GRPGPVV+D+PKDI NP +K+ Y +PE + Sbjct: 121 VSRPIVKHSFLVKDQKDIAETVKKAFYIASTGRPGPVVIDIPKDITNPVDKVEYHYPEKI 180 Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240 +RSY P + GH GQIK+A+Q ++ A++P++Y GGG + QL + LN PV + Sbjct: 181 KLRSYTPASKGHSGQIKKAVQLMLTARRPMIYAGGGVVQGNASAQLTAIAQMLNFPVTNT 240 Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300 LMGLGA+P T RQ LGMLGMHGT EAN MH+ADVIFAVG RFDDR TN +K+CP+A + Sbjct: 241 LMGLGAYPGTDRQFLGMLGMHGTVEANTAMHHADVIFAVGARFDDRVTNTPSKFCPSAKI 300 Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360 +H+DIDP SISKTV ADIPIVG VL++ML LL++ + I WW++I++WR R Sbjct: 301 IHVDIDPASISKTVAADIPIVGPVESVLDEMLSLLNETNERPDAKAIAGWWKEIDEWRNR 360 Query: 361 QCL----KYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWIN 416 + +YDT + + PQ V+ L+ +T GDAYV SDVGQHQMF+A YY FDKPRRWIN Sbjct: 361 YGILTKPRYDTSGDMLMPQEVVRALFEVTNGDAYVCSDVGQHQMFSAQYYQFDKPRRWIN 420 Query: 417 SGGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNR 476 SGGLGTMGFGLPAA+GV+MA + V CVTG+GSIQM IQELST QY LPV ++ LNN+ Sbjct: 421 SGGLGTMGFGLPAAMGVQMAHRDAVVACVTGEGSIQMCIQELSTCTQYHLPVKIICLNNQ 480 Query: 477 YLGMVKQWQDMIYSGRHSQS-YMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQV 535 LGMVKQWQDM Y R+S+S Y SLPDFV+L +AYGHVG++++ EL++KL E Sbjct: 481 ALGMVKQWQDMQYDSRYSESLYEDSLPDFVKLMDAYGHVGMRVTKRDELKAKLEECF--A 538 Query: 536 RNNRLVFVDVTVDGSEHVYPMQIR-GGGMDEMWLSKTERT 574 +R VF+D+ VD EHVYPMQ+ G M +MWLSKTERT Sbjct: 539 MKDRCVFMDIYVDPKEHVYPMQVAPNGSMRDMWLSKTERT 578 Lambda K H 0.319 0.135 0.403 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: 982 Number of extensions: 29 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: 574 Length of database: 578 Length adjustment: 36 Effective length of query: 538 Effective length of database: 542 Effective search space: 291596 Effective search space used: 291596 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 WP_015818963.1 TERTU_RS04690 (acetolactate synthase 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.22586.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-258 842.9 2.2 6.1e-258 842.7 2.2 1.0 1 lcl|NCBI__GCF_000023025.1:WP_015818963.1 TERTU_RS04690 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023025.1:WP_015818963.1 TERTU_RS04690 acetolactate synthase 3 large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 842.7 2.2 6.1e-258 6.1e-258 1 556 [. 4 573 .. 4 574 .. 0.96 Alignments for each domain: == domain 1 score: 842.7 bits; conditional E-value: 6.1e-258 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 l+g++il++sl +egvetvfGyPGGa l+iyda++ +++++h+lvrheqaa+haadGyar++Gk+Gvvl lcl|NCBI__GCF_000023025.1:WP_015818963.1 4 LSGGDILIRSLADEGVETVFGYPGGAALHIYDAIFrQKQVKHVLVRHEQAATHAADGYARSTGKTGVVL 72 689********************************9999****************************** PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 +tsGPGatn++tgiatay+ds+P+vv++Gqv ++ iG+dafqe d++G+++p++khsflvk+ +d++e+ lcl|NCBI__GCF_000023025.1:WP_015818963.1 73 VTSGPGATNAITGIATAYMDSIPMVVISGQVVSDKIGEDAFQETDMVGVSRPIVKHSFLVKDQKDIAET 141 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvtea..eieleveekvelpgykptvkghklqikkaleliekakkPv 204 +k+af+iastGrPGPv++d+Pkd+t++ ++e++++ek++l++y p kgh qikka++l+ +a++P+ lcl|NCBI__GCF_000023025.1:WP_015818963.1 142 VKKAFYIASTGRPGPVVIDIPKDITNPvdKVEYHYPEKIKLRSYTPASKGHSGQIKKAVQLMLTARRPM 210 *************************97224555666********************************* PP TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273 +++GgGv++++as++l+ +a++l+ pvt tl+GlGa+p +++++lgmlGmhGt ean+a+++ad+++av lcl|NCBI__GCF_000023025.1:WP_015818963.1 211 IYAGGGVVQGNASAQLTAIAQMLNFPVTNTLMGLGAYPGTDRQFLGMLGMHGTVEANTAMHHADVIFAV 279 ********************************************************************* PP TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338 Garfddrvt+ +kf+p akiih+didPa+i+k+v++dipivG +++vl+e+l+ l+e+ + k + lcl|NCBI__GCF_000023025.1:WP_015818963.1 280 GARFDDRVTNTPSKFCPSAKIIHVDIDPASISKTVAADIPIVGPVESVLDEMLSLLNETnerpDAKAIA 348 *******************************************************99987655445555 PP TIGR00118 339 .Wlekieewkkey....ilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprk 402 W+++i+ew+++y +++d++ + + Pq+v+++l ++++++a+v +dvGqhqm++aq+y+++kpr+ lcl|NCBI__GCF_000023025.1:WP_015818963.1 349 gWWKEIDEWRNRYgiltKPRYDTSGDMLMPQEVVRALFEVTNGDAYVCSDVGQHQMFSAQYYQFDKPRR 417 8**********9832222358888999****************************************** PP TIGR00118 403 fitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvk 471 +i+sgGlGtmGfGlPaa+G+++a+ ++ v +vtG+gs+qm +qelst+++y++pvki++lnn+ lGmvk lcl|NCBI__GCF_000023025.1:WP_015818963.1 418 WINSGGLGTMGFGLPAAMGVQMAHRDAVVACVTGEGSIQMCIQELSTCTQYHLPVKIICLNNQALGMVK 486 ********************************************************************* PP TIGR00118 472 qWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeee 539 qWq++ y+ ryse+ + +lpdfvkl +ayG++g+r++k++el++kl+e +++k + v++d+ vd +e+ lcl|NCBI__GCF_000023025.1:WP_015818963.1 487 QWQDMQYDSRYSESLYEDSLPDFVKLMDAYGHVGMRVTKRDELKAKLEECFAMKdRCVFMDIYVDPKEH 555 *************************************************99988689************ PP TIGR00118 540 vlPmv.apGagldelvee 556 v+Pm+ ap +++ +++ + lcl|NCBI__GCF_000023025.1:WP_015818963.1 556 VYPMQvAPNGSMRDMWLS 573 ****62678889999865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (578 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.17 // [ok]
This GapMind analysis is from Apr 10 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