Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013537219.1 THEAM_RS02375 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000185805.1:WP_013537219.1 Length = 579 Score = 625 bits (1612), Expect = 0.0 Identities = 317/568 (55%), Positives = 399/568 (70%), Gaps = 7/568 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 ++ GAEIL+ AL EGVE ++GYPGGAVL IYD L + +H L RHEQ A HAADGYA Sbjct: 2 KLSGAEILLRALELEGVEKIFGYPGGAVLDIYDRL-PFSPIKHYLTRHEQGAAHAADGYA 60 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 R TGKVGV TSGPG TN VTG+ATA +DS+P+V TGNVPT+ IG DAFQE DTVGIT Sbjct: 61 RVTGKVGVCFATSGPGATNLVTGLATAQIDSVPVVAFTGNVPTYMIGNDAFQEVDTVGIT 120 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKY---EYPKSID 194 RPI KHNFLVKDV++LA T+KKAF+IA TGRPG V+VD+PKDV+R + EY + Sbjct: 121 RPITKHNFLVKDVKELADTVKKAFYIARTGRPGVVLVDLPKDVTRELADFFEEEYKSPVQ 180 Query: 195 MRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTL 254 +RSY PV KGH GQI++A + AERP +Y GGG V + A+D + +LA + P+ TL Sbjct: 181 IRSYKPVLKGHPGQIKRAAKAIASAERPVLYIGGGTVSSGAADLVVKLAEVANIPMVATL 240 Query: 255 MGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKI 314 MGL A PG F+GMLGMHGTY ANMA+Q CD+LIA+GARFDDRV G + F A K+ Sbjct: 241 MGLTAVPGDHPFFLGMLGMHGTYAANMAVQECDLLIAVGARFDDRVTGKLSEFAPNA-KV 299 Query: 315 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKR--EALAKWWEQIEQWR 372 IHIDID + I K VDIPIVG+ K VL+EL+ +++ K + KW ++ W Sbjct: 300 IHIDIDSAEIGKNRAVDIPIVGDAKLVLEELLPEVEKQVAKNREFYGVREKWIVKVRSWA 359 Query: 373 SVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSG 432 L Y+ S +IKPQ+V+EKIWE+TKG+A I +DVGQHQMW AQFYKF PR+ + SG Sbjct: 360 ERYPLWYEPSDRVIKPQFVIEKIWEVTKGEAIITTDVGQHQMWTAQFYKFRFPRQLVTSG 419 Query: 433 GLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYL 492 GLGTMG GLP A+G K P+K V I+G+GS QM +QE+ T + Y+ P+K+ +NN +L Sbjct: 420 GLGTMGFGLPAAVGAKVGRPDKTVFCISGDGSFQMNMQEVVTAVHYNIPIKVAIINNSFL 479 Query: 493 GMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRT 552 GMVRQWQ I YD YS ++D PDFV+L EA G VG+R E+ +VE L+EA + DR Sbjct: 480 GMVRQWQGIFYDRNYSQVHLDVQPDFVRLVEAMGAVGLRAERPQEVEEVLKEAMAINDRP 539 Query: 553 VFLDFQTDPTENVWPMVQAGKGISEMLL 580 V +DF D E+V+PMV G + EM+L Sbjct: 540 VVIDFIVDREEDVFPMVPPGGALHEMIL 567 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: 983 Number of extensions: 35 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: 585 Length of database: 579 Length adjustment: 36 Effective length of query: 549 Effective length of database: 543 Effective search space: 298107 Effective search space used: 298107 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_013537219.1 THEAM_RS02375 (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.13132.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-257 841.5 0.3 1.7e-257 841.3 0.3 1.0 1 lcl|NCBI__GCF_000185805.1:WP_013537219.1 THEAM_RS02375 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185805.1:WP_013537219.1 THEAM_RS02375 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 841.3 0.3 1.7e-257 1.7e-257 1 555 [. 3 567 .. 3 569 .. 0.97 Alignments for each domain: == domain 1 score: 841.3 bits; conditional E-value: 1.7e-257 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 l+gaeil+++l+ egve++fGyPGGavl+iyd+l s ++h l+rheq+aahaadGyar++GkvGv++a lcl|NCBI__GCF_000185805.1:WP_013537219.1 3 LSGAEILLRALELEGVEKIFGYPGGAVLDIYDRLPFSPIKHYLTRHEQGAAHAADGYARVTGKVGVCFA 71 68******************************************************************* PP TIGR00118 70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138 tsGPGatnlvtg+ata +dsvP+v++tG v+t +iG+dafqe+d +Git+p+tkh+flvk++++l+ ++ lcl|NCBI__GCF_000185805.1:WP_013537219.1 72 TSGPGATNLVTGLATAQIDSVPVVAFTGNVPTYMIGNDAFQEVDTVGITRPITKHNFLVKDVKELADTV 140 ********************************************************************* PP TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaei...eleveekvelpgykptvkghklqikkaleliekakkPv 204 k+af+ia tGrPG vlvdlPkdvt++ e e+++ v++++ykp +kgh+ qik+a+++i++a++Pv lcl|NCBI__GCF_000185805.1:WP_013537219.1 141 KKAFYIARTGRPGVVLVDLPKDVTRELAdffEEEYKSPVQIRSYKPVLKGHPGQIKRAAKAIASAERPV 209 ***********************998651115566799******************************* PP TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273 l++GgG + ++a + +++lae ++ip+++tl+Gl a+p dhp +lgmlGmhGt++an+av+e+dlliav lcl|NCBI__GCF_000185805.1:WP_013537219.1 210 LYIGGGTVSSGAADLVVKLAEVANIPMVATLMGLTAVPGDHPFFLGMLGMHGTYAANMAVQECDLLIAV 278 ********************************************************************* PP TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.......ekk 335 Garfddrvtg+l++fap+ak+ihidid aeigkn++vdipivGdak vleell +++++ lcl|NCBI__GCF_000185805.1:WP_013537219.1 279 GARFDDRVTGKLSEFAPNAKVIHIDIDSAEIGKNRAVDIPIVGDAKLVLEELLPEVEKQvaknrefYGV 347 *****************************************************9999997754433122 PP TIGR00118 336 ekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404 ++W+ k+++w ++y+l+++ ++ ikPq vi+++++++k+eai+ttdvGqhqmw+aqfyk++ pr+ + lcl|NCBI__GCF_000185805.1:WP_013537219.1 348 REKWIVKVRSWAERYPLWYEPSDRVIKPQFVIEKIWEVTKGEAIITTDVGQHQMWTAQFYKFRFPRQLV 416 346****************************************************************** PP TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473 tsgGlGtmGfGlPaa+Gakv+ p++tv +++Gdgsfqmn+qe+ t+v+y+ip+k+ i+nn++lGmv+qW lcl|NCBI__GCF_000185805.1:WP_013537219.1 417 TSGGLGTMGFGLPAAVGAKVGRPDKTVFCISGDGSFQMNMQEVVTAVHYNIPIKVAIINNSFLGMVRQW 485 ********************************************************************* PP TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevl 541 q +fy++ ys+++l +pdfv+l ea+G++g+r e+p+e+ee lkea++ + +pv++d+ vd+ee+v+ lcl|NCBI__GCF_000185805.1:WP_013537219.1 486 QGIFYDRNYSQVHLDV-QPDFVRLVEAMGAVGLRAERPQEVEEVLKEAMAINdRPVVIDFIVDREEDVF 553 ***************6.********************************99879*************** PP TIGR00118 542 PmvapGagldelve 555 Pmv+pG++l+e++ lcl|NCBI__GCF_000185805.1:WP_013537219.1 554 PMVPPGGALHEMIL 567 ************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (579 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 8.19 // [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