Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012505327.1 PAES_RS03725 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000020625.1:WP_012505327.1 Length = 573 Score = 585 bits (1507), Expect = e-171 Identities = 293/564 (51%), Positives = 383/564 (67%), Gaps = 9/564 (1%) Query: 19 MIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYAR 78 M G+EIL L E VEY++GYPGGA+L +Y+ L+ +HILVRHEQ A H A+GYAR Sbjct: 8 MNGSEILFECLRREHVEYIFGYPGGALLQVYETLYDVKDIKHILVRHEQGAAHMAEGYAR 67 Query: 79 ATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITR 138 ATGK G+ LVTSGPG TN VTGI AY+DS PMVV TG VP++ IG DAFQE D VGITR Sbjct: 68 ATGKPGIVLVTSGPGATNTVTGITNAYMDSSPMVVFTGQVPSNLIGNDAFQEADIVGITR 127 Query: 139 PIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSY 198 PI KHNFLVKDV+DLA TI+KAF++A GRPGPV+VD+PKDV + C +++PK+ID+R + Sbjct: 128 PITKHNFLVKDVKDLALTIRKAFYLATHGRPGPVLVDLPKDVMNSECIFDWPKTIDIRGF 187 Query: 199 NPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLG 258 P K H Q++KA ++ A++P +Y GGGV+ A AS+ELR+LA PVT TL GLG Sbjct: 188 KPTIKTHENQVKKAAKMIAKAKKPLLYVGGGVIAAEASEELRKLAIAQNIPVTMTLQGLG 247 Query: 259 AFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHID 318 AFPG +GMLGMHGTY AN A+ NCD+LI++GARFDDRV G F + A K IH D Sbjct: 248 AFPGNDPLSMGMLGMHGTYWANQAVNNCDLLISVGARFDDRVTGKTETFATHAYK-IHND 306 Query: 319 IDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPK-REALAKWWEQIEQWRSVDCL 377 IDP++I K +KVD+P+VG+ K LQ ++ D PK +E W +IE+WRS L Sbjct: 307 IDPTNIDKNIKVDLPVVGDAKQFLQGIL------DALPKTKENRKPWLAEIEKWRSQCPL 360 Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437 Y + +K ++V+E++ T GDA I +DVGQHQMW +Q+Y F PR + SGGLGTM Sbjct: 361 TYTIDDDSLKTEFVIEEVSRQTHGDAVITTDVGQHQMWTSQYYSFRNPRSILTSGGLGTM 420 Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497 G GLP A+G ++ VV G+G M IQEL T + Y P+KI +NN +LGMVRQ Sbjct: 421 GYGLPAAIGAAFGVHDRPVVLFCGDGGFMMNIQELVTAVYYKLPIKIFLINNNFLGMVRQ 480 Query: 498 WQEIEYDNRYSHSYM-DALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLD 556 WQE+ + +YS + + D+ PDF+++ EA+G R E + A+ EA D F++ Sbjct: 481 WQELFHQEKYSFTDLEDSNPDFIRVVEAFGCKARRAENPEEARQAISEALAYNDGPCFVE 540 Query: 557 FQTDPTENVWPMVQAGKGISEMLL 580 F+ + V+PMV AG IS+MLL Sbjct: 541 FRVVKKDMVFPMVPAGASISDMLL 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: 916 Number of extensions: 34 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: 573 Length adjustment: 36 Effective length of query: 549 Effective length of database: 537 Effective search space: 294813 Effective search space used: 294813 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_012505327.1 PAES_RS03725 (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.11039.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-248 809.0 0.0 1.1e-247 808.8 0.0 1.0 1 lcl|NCBI__GCF_000020625.1:WP_012505327.1 PAES_RS03725 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020625.1:WP_012505327.1 PAES_RS03725 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 808.8 0.0 1.1e-247 1.1e-247 1 554 [. 8 563 .. 8 566 .. 0.99 Alignments for each domain: == domain 1 score: 808.8 bits; conditional E-value: 1.1e-247 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 ++g+eil e l++e ve++fGyPGGa+l++y++ly ++++hilvrheq+aah+a+Gyara+Gk+G+vl lcl|NCBI__GCF_000020625.1:WP_012505327.1 8 MNGSEILFECLRREHVEYIFGYPGGALLQVYETLYdVKDIKHILVRHEQGAAHMAEGYARATGKPGIVL 76 789********************************889******************************* PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 +tsGPGatn+vtgi++ay+ds+P+vv+tGqv+++liG+dafqe+di+Git+p+tkh+flvk+++dl+ + lcl|NCBI__GCF_000020625.1:WP_012505327.1 77 VTSGPGATNTVTGITNAYMDSSPMVVFTGQVPSNLIGNDAFQEADIVGITRPITKHNFLVKDVKDLALT 145 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206 +++af++a+ GrPGPvlvdlPkdv+++e+ ++ +++++++g+kpt+k+h++q+kka+++i+kakkP+l+ lcl|NCBI__GCF_000020625.1:WP_012505327.1 146 IRKAFYLATHGRPGPVLVDLPKDVMNSECIFDWPKTIDIRGFKPTIKTHENQVKKAAKMIAKAKKPLLY 214 ********************************************************************* PP TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275 vGgGvi+aeaseel++la +++ipvt+tl+GlGafp ++pl++gmlGmhGt+ an av+++dlli+vGa lcl|NCBI__GCF_000020625.1:WP_012505327.1 215 VGGGVIAAEASEELRKLAIAQNIPVTMTLQGLGAFPGNDPLSMGMLGMHGTYWANQAVNNCDLLISVGA 283 ********************************************************************* PP TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekie 344 rfddrvtg+ ++fa++a ih didP++i+kn+kvd+p+vGdak+ l+ +l++l +++++ k Wl++ie lcl|NCBI__GCF_000020625.1:WP_012505327.1 284 RFDDRVTGKTETFATHAYKIHNDIDPTNIDKNIKVDLPVVGDAKQFLQGILDALPKTKENRKPWLAEIE 352 ********************************************************9999988****** PP TIGR00118 345 ewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmG 413 +w+++++l++ +++s+k vi+e+s++++++a++ttdvGqhqmw++q+y++++pr+ +tsgGlGtmG lcl|NCBI__GCF_000020625.1:WP_012505327.1 353 KWRSQCPLTYTIDDDSLKTEFVIEEVSRQTHGDAVITTDVGQHQMWTSQYYSFRNPRSILTSGGLGTMG 421 ********************************************************************* PP TIGR00118 414 fGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeery 482 +GlPaa+Ga ++ + vv +Gdg+f+mn+qel t+v y++p+ki ++nn++lGmv+qWqelf++e+y lcl|NCBI__GCF_000020625.1:WP_012505327.1 422 YGLPAAIGAAFGVHDRPVVLFCGDGGFMMNIQELVTAVYYKLPIKIFLINNNFLGMVRQWQELFHQEKY 490 ********************************************************************* PP TIGR00118 483 setklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagl 550 s t l+ ++pdf+++ ea+G k+ r e+pee+ ++++eal+ + +p +++++v k++ v+Pmv+ Ga++ lcl|NCBI__GCF_000020625.1:WP_012505327.1 491 SFTDLEDSNPDFIRVVEAFGCKARRAENPEEARQAISEALAYNdGPCFVEFRVVKKDMVFPMVPAGASI 559 ****************************************98879************************ PP TIGR00118 551 delv 554 ++++ lcl|NCBI__GCF_000020625.1:WP_012505327.1 560 SDML 563 *997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (573 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: 7.61 // [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