Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013460347.1 SULKU_RS07495 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000183725.1:WP_013460347.1 Length = 564 Score = 575 bits (1481), Expect = e-168 Identities = 288/563 (51%), Positives = 385/563 (68%), Gaps = 5/563 (0%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 ++ GA++++ AL E VE V+GYPGGA++ +YDE++KQ F+HIL RHEQAAVHAA+GYA Sbjct: 2 QISGAQMVIEALIAEEVEVVFGYPGGAIMNVYDEIYKQRSFQHILTRHEQAAVHAAEGYA 61 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 +ATGKVGVA++TSGPG TN VTG+A AY+DSIP+VVI+G VP IG DAFQE D VGI+ Sbjct: 62 KATGKVGVAMITSGPGFTNGVTGMADAYMDSIPLVVISGQVPMSLIGTDAFQEIDAVGIS 121 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RP KHN+LV D DL +K+AF+IA TGRPGPV VDIPKDV+ ++Y K +++ + Sbjct: 122 RPCTKHNYLVTDAADLPRVLKEAFYIARTGRPGPVHVDIPKDVTAQIATFDYSKEVELET 181 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257 Y P KG++ QI+KA+ + A+RP +Y GGG++ ANA++ +R+ + +T P T M Sbjct: 182 YKPTTKGNARQIKKAIEAIASAKRPLLYLGGGIINANAAELVREFSKMTQIPAVETFMAR 241 Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317 G + MLGMHG+Y ANMAM D++I +GARFDDRV G + F A +IIH+ Sbjct: 242 GTLRYDDPLLISMLGMHGSYAANMAMSETDLVIGLGARFDDRVTGKLSEFAKNA-QIIHV 300 Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377 DIDP+S+SK V PIVG+VK+VL+++I K I P R A W I + + L Sbjct: 301 DIDPASVSKLVHAHFPIVGDVKNVLEQMIPLAK-EQIDPAR--YASWHNTIANFNKLHPL 357 Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437 Y + +KPQ+VVE+I +L DA I +DVGQHQMW AQFY F PR+W++SGGLGTM Sbjct: 358 SYTEEGDRLKPQWVVERIGQLLGDDANISTDVGQHQMWTAQFYPFTRPRQWVSSGGLGTM 417 Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497 G G P AMG+K+A E+ + ITG+GSI M IQEL T ++Y+ PV LNN +LGMVRQ Sbjct: 418 GFGFPAAMGVKRADMERVSINITGDGSILMNIQELMTAVEYELPVINVILNNNFLGMVRQ 477 Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557 WQ + YD R+S + + PDFVKL EA+G VG RV + + AL++A K+ +D Sbjct: 478 WQTLFYDKRHSSTDLSIQPDFVKLVEAFGGVGYRVTTKEEFDAALKDAVE-KNVVAIIDV 536 Query: 558 QTDPTENVWPMVQAGKGISEMLL 580 + ENV PMV AG + M+L Sbjct: 537 VVNRFENVLPMVPAGGSLFNMML 559 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: 862 Number of extensions: 31 Number of successful extensions: 4 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: 564 Length adjustment: 36 Effective length of query: 549 Effective length of database: 528 Effective search space: 289872 Effective search space used: 289872 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_013460347.1 SULKU_RS07495 (acetolactate synthase, large subunit, biosynthetic type)
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.5992.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-248 809.2 3.1 1e-247 809.0 3.1 1.0 1 lcl|NCBI__GCF_000183725.1:WP_013460347.1 SULKU_RS07495 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183725.1:WP_013460347.1 SULKU_RS07495 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 809.0 3.1 1e-247 1e-247 2 555 .. 4 559 .. 3 561 .. 0.99 Alignments for each domain: == domain 1 score: 809.0 bits; conditional E-value: 1e-247 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 +ga++++e+l +e+ve+vfGyPGGa++++yd++y + ++hil+rheqaa+haa+Gya+a+GkvGv++ lcl|NCBI__GCF_000183725.1:WP_013460347.1 4 SGAQMVIEALIAEEVEVVFGYPGGAIMNVYDEIYkQRSFQHILTRHEQAAVHAAEGYAKATGKVGVAMI 72 89********************************8899******************************* PP TIGR00118 70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138 tsGPG tn vtg+a+ay+ds+Plvv++Gqv+ sliG+dafqeid +Gi++p+tkh++lv++a+dlp++l lcl|NCBI__GCF_000183725.1:WP_013460347.1 73 TSGPGFTNGVTGMADAYMDSIPLVVISGQVPMSLIGTDAFQEIDAVGISRPCTKHNYLVTDAADLPRVL 141 ********************************************************************* PP TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207 keaf+ia tGrPGPv+vd+Pkdvt++ +++++++vel +ykpt+kg+ +qikka+e+i++ak+P+l+ lcl|NCBI__GCF_000183725.1:WP_013460347.1 142 KEAFYIARTGRPGPVHVDIPKDVTAQIATFDYSKEVELETYKPTTKGNARQIKKAIEAIASAKRPLLYL 210 ********************************************************************* PP TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276 GgG+i a+a e ++e++++++ip + t++ G++ d+pl + mlGmhG+++an+a+se+dl+i++Gar lcl|NCBI__GCF_000183725.1:WP_013460347.1 211 GGGIINANAAELVREFSKMTQIPAVETFMARGTLRYDDPLLISMLGMHGSYAANMAMSETDLVIGLGAR 279 ********************************************************************* PP TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee..ekkekeWleki 343 fddrvtg+l++fa++a+iih+didPa+++k v+++ pivGd+k+vle+++ +ke+ + W + i lcl|NCBI__GCF_000183725.1:WP_013460347.1 280 FDDRVTGKLSEFAKNAQIIHVDIDPASVSKLVHAHFPIVGDVKNVLEQMIPLAKEQidPARYASWHNTI 348 ***************************************************9999975455556***** PP TIGR00118 344 eewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtm 412 +++ k ++l++ ee + +kPq v++++ +ll d+a ++tdvGqhqmw+aqfy++++pr++++sgGlGtm lcl|NCBI__GCF_000183725.1:WP_013460347.1 349 ANFNKLHPLSYTEEGDRLKPQWVVERIGQLLGDDANISTDVGQHQMWTAQFYPFTRPRQWVSSGGLGTM 417 ********************************************************************* PP TIGR00118 413 GfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeer 481 GfG+Paa+G+k a e +++tGdgs+ mn+qel t+vey++pv+ vilnn++lGmv+qWq lfy++r lcl|NCBI__GCF_000183725.1:WP_013460347.1 418 GFGFPAAMGVKRADMERVSINITGDGSILMNIQELMTAVEYELPVINVILNNNFLGMVRQWQTLFYDKR 486 ********************************************************************* PP TIGR00118 482 ysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagl 550 +s+t l+ +pdfvkl ea+G +g r++++ee +++lk+a+e++ +++dv+v++ e+vlPmv+ G++l lcl|NCBI__GCF_000183725.1:WP_013460347.1 487 HSSTDLSI-QPDFVKLVEAFGGVGYRVTTKEEFDAALKDAVEKNVVAIIDVVVNRFENVLPMVPAGGSL 554 *******6.************************************************************ PP TIGR00118 551 delve 555 +++ lcl|NCBI__GCF_000183725.1:WP_013460347.1 555 FNMML 559 99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (564 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: 10.50 // [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