Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Synpcc7942_0139 Synpcc7942_0139 acetolactate synthase 3 catalytic subunit
Query= BRENDA::P9WG41 (618 letters) >FitnessBrowser__SynE:Synpcc7942_0139 Length = 612 Score = 555 bits (1430), Expect = e-162 Identities = 305/573 (53%), Positives = 380/573 (66%), Gaps = 17/573 (2%) Query: 36 QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSK---KLRHVLVRHEQGAGHAA 92 Q+ TGA A+I SL + GV IFG PGGA+LP+YD L ++ +++H+LVRHEQGA HAA Sbjct: 10 QRATGAYALIDSLCQHGVKHIFGYPGGAILPIYDELHRAEAAGRVQHILVRHEQGAVHAA 69 Query: 93 SGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADI 152 Y+ TG VGVC ATSGPGATNLVT +A AQMDSIP+V +TGQV R IGTDAFQE DI Sbjct: 70 DAYSRATGEVGVCFATSGPGATNLVTGIATAQMDSIPMVVVTGQVPRTAIGTDAFQETDI 129 Query: 153 SGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPP-- 210 GIT+PI KH+++VR D+ R++AEAFHIA SGRPG VL+D+PKDV G F + P Sbjct: 130 YGITLPIVKHSYVVRDPRDMARIVAEAFHIAQSGRPGPVLIDVPKDV--GTEEFDYVPVA 187 Query: 211 --RMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIP 268 + LPGY+P T+ + RQ+ +A L+ AR+P+LYVGGG I A +LR AE +P Sbjct: 188 PGDIRLPGYRPTTRGNPRQIAQAIALVKVARRPLLYVGGGAITAGAHAELRAFAERFQLP 247 Query: 269 VVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAP 328 V TTLM +GAF + H LGM GMHGT A A+ DLLIA+G RFDDRVTGKLD FA Sbjct: 248 VTTTLMGKGAFDERHPLALGMLGMHGTAYANFAVSECDLLIAVGARFDDRVTGKLDEFAS 307 Query: 329 EAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHH-HIPGTIEMADWWAYLNG 387 +A+VIH DIDPAE+GKNR +VPIVGDV+ V+ EL+A W + Sbjct: 308 KAQVIHVDIDPAEVGKNRVPEVPIVGDVRQVLNELLARAEEQISADDATRTQPWLDRIAY 367 Query: 388 VRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWL 447 ++ YPL P LSP+ VI LGE A PDA F VGQHQMWAAQFI+ PR W+ Sbjct: 368 WKREYPLQI-PYYADVLSPQQVIHSLGE-AAPDAYFTTDVGQHQMWAAQFIK-NGPRRWI 424 Query: 448 NSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINN 507 +S GLGTMGF +PAAMGA++ALP V + GD M QEL T A IP+KV ++NN Sbjct: 425 SSAGLGTMGFGMPAAMGAQMALPDDTVICVAGDASILMNIQELGTLAQYNIPIKVVVVNN 484 Query: 508 GNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQA 567 G GMVRQWQ FY ERYS +++ +PDFVKLAEA G G+R +++ I + Sbjct: 485 GWQGMVRQWQEAFYDERYSNSNM---ERGMPDFVKLAEAFGIKGMRVSHPDELQAAIAEM 541 Query: 568 RAINDCPVVIDFIVGADAQVWPMVAAGTSNDEI 600 A D PV +D IV D +PMV +G SN ++ Sbjct: 542 LAF-DGPVFLDAIVKRDENCYPMVPSGHSNAQM 573 Lambda K H 0.319 0.136 0.414 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: 1138 Number of extensions: 55 Number of successful extensions: 7 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: 618 Length of database: 612 Length adjustment: 37 Effective length of query: 581 Effective length of database: 575 Effective search space: 334075 Effective search space used: 334075 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 Synpcc7942_0139 Synpcc7942_0139 (acetolactate synthase 3 catalytic 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.31079.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-266 869.9 0.1 4.1e-266 869.7 0.1 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0139 Synpcc7942_0139 acetolactate syn Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0139 Synpcc7942_0139 acetolactate synthase 3 catalytic subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 869.7 0.1 4.1e-266 4.1e-266 2 555 .. 13 575 .. 12 577 .. 0.98 Alignments for each domain: == domain 1 score: 869.7 bits; conditional E-value: 4.1e-266 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly....dselehilvrheqaaahaadGyarasGkvGv 66 +ga++l++sl ++gv+++fGyPGGa+lpiyd+l+ ++ ++hilvrheq+a+haad y+ra+G+vGv lcl|FitnessBrowser__SynE:Synpcc7942_0139 13 TGAYALIDSLCQHGVKHIFGYPGGAILPIYDELHraeaAGRVQHILVRHEQGAVHAADAYSRATGEVGV 81 79********************************9887789**************************** PP TIGR00118 67 vlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlp 135 ++atsGPGatnlvtgiata +ds+P+vv+tGqv++++iG+dafqe di Gitlp++khs++v++++d++ lcl|FitnessBrowser__SynE:Synpcc7942_0139 82 CFATSGPGATNLVTGIATAQMDSIPMVVVTGQVPRTAIGTDAFQETDIYGITLPIVKHSYVVRDPRDMA 150 ********************************************************************* PP TIGR00118 136 eilkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakk 202 +i+ eaf+ia++GrPGPvl+d+Pkdv ++e+++ ++ lpgy+pt++g+++qi++a+ l++ a++ lcl|FitnessBrowser__SynE:Synpcc7942_0139 151 RIVAEAFHIAQSGRPGPVLIDVPKDVGTEEFDYVPVapGDIRLPGYRPTTRGNPRQIAQAIALVKVARR 219 ********************************9877679****************************** PP TIGR00118 203 PvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlli 271 P+l+vGgG+i+a+a++el+ +aer+++pvtttl+G+Gaf+e hplalgmlGmhGt++an+avse+dlli lcl|FitnessBrowser__SynE:Synpcc7942_0139 220 PLLYVGGGAITAGAHAELRAFAERFQLPVTTTLMGKGAFDERHPLALGMLGMHGTAYANFAVSECDLLI 288 ********************************************************************* PP TIGR00118 272 avGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekke 336 avGarfddrvtg+l++fa++a++ih+didPae+gkn+ ++pivGd+++vl+ell++++e+ + + lcl|FitnessBrowser__SynE:Synpcc7942_0139 289 AVGARFDDRVTGKLDEFASKAQVIHVDIDPAEVGKNRVPEVPIVGDVRQVLNELLARAEEQisadDATR 357 *********************************************************999988764555 PP TIGR00118 337 ke.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404 ++ Wl++i+ wk+ey+l++ ++ + + Pq+vi++l + ++d a+ ttdvGqhqmwaaqf k+ pr++i lcl|FitnessBrowser__SynE:Synpcc7942_0139 358 TQpWLDRIAYWKREYPLQIPYYADVLSPQQVIHSLGEAAPD-AYFTTDVGQHQMWAAQFIKNG-PRRWI 424 567*************************************6.******************998.***** PP TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473 +s+GlGtmGfG+Paa+Ga++a p++tv++v+Gd+s+ mn+qel t+++y+ip+k+v++nn ++Gmv+qW lcl|FitnessBrowser__SynE:Synpcc7942_0139 425 SSAGLGTMGFGMPAAMGAQMALPDDTVICVAGDASILMNIQELGTLAQYNIPIKVVVVNNGWQGMVRQW 493 ********************************************************************* PP TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542 qe fy+erys+++++ ++pdfvklaea+G+kg+r+++p+el+++++e+l+ ++pv+ld v+++e+++P lcl|FitnessBrowser__SynE:Synpcc7942_0139 494 QEAFYDERYSNSNMERGMPDFVKLAEAFGIKGMRVSHPDELQAAIAEMLAFDGPVFLDAIVKRDENCYP 562 ********************************************************************* PP TIGR00118 543 mvapGagldelve 555 mv++G++++++++ lcl|FitnessBrowser__SynE:Synpcc7942_0139 563 MVPSGHSNAQMLG 575 **********986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (612 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: 11.41 // [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