Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_029622025.1 G7G_RS0114505 acetolactate synthase 3 large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000192475.1:WP_029622025.1 Length = 583 Score = 598 bits (1542), Expect = e-175 Identities = 306/567 (53%), Positives = 400/567 (70%), Gaps = 6/567 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 EM GA+++V AL ++GV+ V+GYPGGAVL IYDE+ Q HILVRHEQ AVHAA+GYA Sbjct: 4 EMTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFLQNDIRHILVRHEQGAVHAAEGYA 63 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 R+TGK GVALVTSGPG TNAVTG+ A LDSIP+VV+TG VPT IG DAFQE DTVGIT Sbjct: 64 RSTGKPGVALVTSGPGATNAVTGLTDALLDSIPIVVLTGQVPTFMIGSDAFQEADTVGIT 123 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RP KHN+LVKD LAAT+ +AF +A GRPGPV+VDIPKDV + +Y PK Sbjct: 124 RPCTKHNWLVKDTDSLAATMHEAFHVATAGRPGPVLVDIPKDVQFASGEYTTPKP-STSH 182 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNTLM 255 Y PV KG +I + VA ++ A++P YTGGGV+ + AS LR+L TG P+T+TLM Sbjct: 183 YQPVLKGDLEEITELVAAIETAKKPVFYTGGGVINSGPAASQLLRELVDATGFPITSTLM 242 Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315 GLGA+P + + ++GMLGMHG YEANMAM +CD++I IGARFDDR+ G F+ + K Sbjct: 243 GLGAYPASGENWIGMLGMHGLYEANMAMHDCDLMINIGARFDDRITGRIDAFSPNSIK-A 301 Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375 H+DIDPSSI+K ++VDIPIVG+V VL++++ KA K + +W +QI +WR V+ Sbjct: 302 HVDIDPSSINKVIRVDIPIVGDVAHVLEDILKVWKARGRKTDAANIKQWQDQINKWRKVN 361 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434 CL + S + IKPQY ++++ ELTK D ++ ++VGQHQMWAAQ+ F++P RW+ SGGL Sbjct: 362 CLAFTNSEKTIKPQYALQRLEELTKNHDRYVTTEVGQHQMWAAQYLGFEDPNRWMTSGGL 421 Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494 GTMG G P ++G++ A P+ V+ + GE S M +QE+ T QY PVK LNN LGM Sbjct: 422 GTMGYGFPASIGVQMAHPDALVINVAGEASWLMNMQEMGTAAQYRLPVKQFILNNERLGM 481 Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554 VRQWQE+ + RYSHS+ +ALPDFVKLAEA+G G+ +D++ A+ E D V Sbjct: 482 VRQWQELLHGERYSHSWSEALPDFVKLAEAFGAKGILCSDPADLDDAIMEMIDY-DGPVI 540 Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLG 581 D + EN +PM+ +GK +EMLLG Sbjct: 541 FDCVVEKHENCFPMIPSGKAHNEMLLG 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: 978 Number of extensions: 36 Number of successful extensions: 6 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: 583 Length adjustment: 36 Effective length of query: 549 Effective length of database: 547 Effective search space: 300303 Effective search space used: 300303 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_029622025.1 G7G_RS0114505 (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.3196982.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-238 778.1 0.2 2.6e-238 777.9 0.2 1.0 1 NCBI__GCF_000192475.1:WP_029622025.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000192475.1:WP_029622025.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 777.9 0.2 2.6e-238 2.6e-238 1 554 [. 5 565 .. 5 568 .. 0.97 Alignments for each domain: == domain 1 score: 777.9 bits; conditional E-value: 2.6e-238 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 ++ga+++v++lk++gv+tvfGyPGGavlpiyd+++ +++++hilvrheq+a+haa+Gyar++Gk+Gv+l+tsG NCBI__GCF_000192475.1:WP_029622025.1 5 MTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFlQNDIRHILVRHEQGAVHAAEGYARSTGKPGVALVTSG 77 79*********************************99************************************ PP TIGR00118 73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145 PGatn+vtg+++a lds+P+vvltGqv+t +iGsdafqe+d +Git+p+tkh++lvk+++ l+++++eaf++a NCBI__GCF_000192475.1:WP_029622025.1 78 PGATNAVTGLTDALLDSIPIVVLTGQVPTFMIGSDAFQEADTVGITRPCTKHNWLVKDTDSLAATMHEAFHVA 150 ************************************************************************* PP TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiae..a 216 ++GrPGPvlvd+Pkdv+ a+ e++++ k + y+p +kg+ i +++ +ie+akkPv + GgGvi ++ a NCBI__GCF_000192475.1:WP_029622025.1 151 TAGRPGPVLVDIPKDVQFASGEYTTP-KPSTSHYQPVLKGDLEEITELVAAIETAKKPVFYTGGGVINSGpaA 222 **********************9999.778899**********************************885448 PP TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289 s+ l+el++++ p+t+tl+GlGa+p+ ++ +gmlGmhG +ean+a++++dl+i +Garfddr+tg ++ f+ NCBI__GCF_000192475.1:WP_029622025.1 223 SQLLRELVDATGFPITSTLMGLGAYPASGENWIGMLGMHGLYEANMAMHDCDLMINIGARFDDRITGRIDAFS 295 999********************************************************************** PP TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldee 357 p++ h+didP++i+k+++vdipivGd+ +vle++lk k++ + +++ W ++i++w+k ++l++ ++ NCBI__GCF_000192475.1:WP_029622025.1 296 PNSIKAHVDIDPSSINKVIRVDIPIVGDVAHVLEDILKVWKARgrktDAANIKqWQDQINKWRKVNCLAFTNS 368 *************************************99888765553444445******************* PP TIGR00118 358 eesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpee 429 e++ikPq+ +++l +l+k+ + +vtt+vGqhqmwaaq++ ++ p++++tsgGlGtmG+G+Pa++G+++a+p++ NCBI__GCF_000192475.1:WP_029622025.1 369 EKTIKPQYALQRLEELTKNhDRYVTTEVGQHQMWAAQYLGFEDPNRWMTSGGLGTMGYGFPASIGVQMAHPDA 441 ****************998689*************************************************** PP TIGR00118 430 tvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502 v++v+G++s mn+qe+ t+++y +pvk ilnne lGmv+qWqel++ erys++ ++ lpdfvklaea+G NCBI__GCF_000192475.1:WP_029622025.1 442 LVINVAGEASWLMNMQEMGTAAQYRLPVKQFILNNERLGMVRQWQELLHGERYSHSWSEA-LPDFVKLAEAFG 513 ********************************************************9995.************ PP TIGR00118 503 vkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554 +kgi ++p++l++++ e++ ++pv++d +v+k+e+++Pm+++G++ +e++ NCBI__GCF_000192475.1:WP_029622025.1 514 AKGILCSDPADLDDAIMEMIDYDGPVIFDCVVEKHENCFPMIPSGKAHNEML 565 **************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (583 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 34.11 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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