Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_029935908.1 N746_RS0108915 acetolactate synthase 3 large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000711195.1:WP_029935908.1 Length = 565 Score = 767 bits (1981), Expect = 0.0 Identities = 372/564 (65%), Positives = 446/564 (79%), Gaps = 2/564 (0%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTK-FEHILVRHEQAAVHAADGY 76 E+ GA+IL+H L +EGVE++WGYPGGA L IYD L K +HILVRHEQAAVHAADGY Sbjct: 2 ELTGAQILIHFLEDEGVEHIWGYPGGAALPIYDALDTDAKELKHILVRHEQAAVHAADGY 61 Query: 77 ARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGI 136 AR+TGK GV LVTSGPG TN VTGIATA++DS P++VITG V T IG DAFQE DTVGI Sbjct: 62 ARSTGKPGVVLVTSGPGATNTVTGIATAHMDSTPLIVITGQVATDMIGLDAFQEVDTVGI 121 Query: 137 TRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMR 196 TRPIVKHNFLVKDV DLA T+KKAF+IA TGRPGPVV+DIPKDV YEYP+ +++R Sbjct: 122 TRPIVKHNFLVKDVNDLAMTLKKAFYIATTGRPGPVVIDIPKDVQNATSTYEYPQEVELR 181 Query: 197 SYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMG 256 SY PV KGH+GQI+KAV ++ AERP YTGGGVV+ S+EL +L G+P+T TLMG Sbjct: 182 SYLPVVKGHTGQIKKAVEMMLSAERPIFYTGGGVVMGEGSEELVKLVKSLGYPITQTLMG 241 Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316 LGAFP KQ +GMLGMHGTYEAN+AM +CDVLIAIG+RFDDRV GN A F A KIIH Sbjct: 242 LGAFPADDKQNIGMLGMHGTYEANLAMHHCDVLIAIGSRFDDRVTGNIAKFCPTA-KIIH 300 Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDC 376 +DIDP+SISK V VDIPIVG V+ V+QE+ Q+ + KP +AL WW QI++WR+VDC Sbjct: 301 VDIDPASISKNVVVDIPIVGPVQQVVQEMNTQLAKLNKKPDSQALQAWWSQIDEWRNVDC 360 Query: 377 LKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGT 436 LKYD + IKPQ V+ +WE+T GDA++ +DVGQHQM+AAQ+Y F++PRRWINSGGLGT Sbjct: 361 LKYDTTGSKIKPQAAVQAVWEVTNGDAYVTADVGQHQMFAAQYYTFNKPRRWINSGGLGT 420 Query: 437 MGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVR 496 MG GLP AMG++ A+P+ V+ ITGEGSIQM IQELSTCLQY P+K+ LNNG+LGMVR Sbjct: 421 MGFGLPAAMGVQMAYPDATVLCITGEGSIQMNIQELSTCLQYGLPIKVVCLNNGFLGMVR 480 Query: 497 QWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLD 556 QWQE YD RYS SYMD+LPDFVKL EAYGHVG+R++ ++ L EAF LKD+ VF+D Sbjct: 481 QWQEFFYDRRYSMSYMDSLPDFVKLTEAYGHVGVRIDDPKTMKKQLEEAFALKDKFVFID 540 Query: 557 FQTDPTENVWPMVQAGKGISEMLL 580 TD ENV+PM+ AG G +EM+L Sbjct: 541 IITDQQENVYPMIPAGAGQNEMIL 564 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: 1025 Number of extensions: 36 Number of successful extensions: 3 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: 565 Length adjustment: 36 Effective length of query: 549 Effective length of database: 529 Effective search space: 290421 Effective search space used: 290421 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_029935908.1 N746_RS0108915 (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.19105.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-265 866.4 5.3 4.6e-265 866.3 5.3 1.0 1 lcl|NCBI__GCF_000711195.1:WP_029935908.1 N746_RS0108915 acetolactate synt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711195.1:WP_029935908.1 N746_RS0108915 acetolactate synthase 3 large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 866.3 5.3 4.6e-265 4.6e-265 1 555 [. 3 564 .. 3 565 .] 0.98 Alignments for each domain: == domain 1 score: 866.3 bits; conditional E-value: 4.6e-265 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvv 67 l+ga+il++ l++egve+++GyPGGa lpiydal ++el+hilvrheqaa+haadGyar++Gk+Gvv lcl|NCBI__GCF_000711195.1:WP_029935908.1 3 LTGAQILIHFLEDEGVEHIWGYPGGAALPIYDALDtdAKELKHILVRHEQAAVHAADGYARSTGKPGVV 71 68********************************988899***************************** PP TIGR00118 68 latsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpe 136 l+tsGPGatn+vtgiata++ds+Pl+v+tGqvat++iG dafqe+d +Git+p++kh+flvk+++dl+ lcl|NCBI__GCF_000711195.1:WP_029935908.1 72 LVTSGPGATNTVTGIATAHMDSTPLIVITGQVATDMIGLDAFQEVDTVGITRPIVKHNFLVKDVNDLAM 140 ********************************************************************* PP TIGR00118 137 ilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvl 205 +lk+af+ia+tGrPGPv++d+Pkdv++a+ ++e++++vel++y p vkgh+ qikka+e++ +a++P+ lcl|NCBI__GCF_000711195.1:WP_029935908.1 141 TLKKAFYIATTGRPGPVVIDIPKDVQNATSTYEYPQEVELRSYLPVVKGHTGQIKKAVEMMLSAERPIF 209 ********************************************************************* PP TIGR00118 206 lvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274 + GgGv+++e+seel++l++ l p+t+tl+GlGafp+d+++ +gmlGmhGt+eanla++++d+lia+G lcl|NCBI__GCF_000711195.1:WP_029935908.1 210 YTGGGVVMGEGSEELVKLVKSLGYPITQTLMGLGAFPADDKQNIGMLGMHGTYEANLAMHHCDVLIAIG 278 ********************************************************************* PP TIGR00118 275 arfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke. 338 rfddrvtgn+akf+p akiih+didPa+i+knv vdipivG +++v++e+ ++l + +++ + lcl|NCBI__GCF_000711195.1:WP_029935908.1 279 SRFDDRVTGNIAKFCPTAKIIHVDIDPASISKNVVVDIPIVGPVQQVVQEMNTQLAKLnkkpDSQALQa 347 ***************************************************988877755554445567 PP TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407 W+++i+ew++ +lk+d++ ++ikPq+ +++++++++++a+vt+dvGqhqm+aaq+y+++kpr++i+sg lcl|NCBI__GCF_000711195.1:WP_029935908.1 348 WWSQIDEWRNVDCLKYDTTGSKIKPQAAVQAVWEVTNGDAYVTADVGQHQMFAAQYYTFNKPRRWINSG 416 ********************************************************************* PP TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476 GlGtmGfGlPaa+G+++a p++tv+++tG+gs+qmn+qelst+ +y++p+k+v+lnn +lGmv+qWqe+ lcl|NCBI__GCF_000711195.1:WP_029935908.1 417 GLGTMGFGLPAAMGVQMAYPDATVLCITGEGSIQMNIQELSTCLQYGLPIKVVCLNNGFLGMVRQWQEF 485 ********************************************************************* PP TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmv 544 fy++rys +++ s lpdfvkl+eayG++g+ri +p+ ++++l+ea++ k + v++d+ d++e+v+Pm+ lcl|NCBI__GCF_000711195.1:WP_029935908.1 486 FYDRRYSMSYMDS-LPDFVKLTEAYGHVGVRIDDPKTMKKQLEEAFALKdKFVFIDIITDQQENVYPMI 553 ************5.*******************************9987689***************** PP TIGR00118 545 apGagldelve 555 + Gag +e++ lcl|NCBI__GCF_000711195.1:WP_029935908.1 554 PAGAGQNEMIL 564 *********85 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 12.05 // [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