Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_106718131.1 CU100_RS18730 acetolactate synthase 3 large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_003010935.1:WP_106718131.1 Length = 601 Score = 649 bits (1675), Expect = 0.0 Identities = 324/584 (55%), Positives = 429/584 (73%), Gaps = 5/584 (0%) Query: 3 SAEFSHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHIL 62 +AE ++S+SS EM GAE++V AL ++GV ++GYPGGAVL IYDEL +Q + HIL Sbjct: 2 TAEKLASESHSSQRREMTGAEMVVQALIDQGVTDIFGYPGGAVLPIYDELFQQDRINHIL 61 Query: 63 VRHEQAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHA 122 VRHEQ A HAA+GYAR+TGKVGV LVTSGPG TNAVT + A +DSIP+V I+G VPT Sbjct: 62 VRHEQGAGHAAEGYARSTGKVGVMLVTSGPGATNAVTPLQDALMDSIPLVCISGQVPTSL 121 Query: 123 IGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSR 182 IG DAFQECDTVGITRP KHN+LVKDV DLA + +AF +A TGRPGPV+VD+PKDV Sbjct: 122 IGSDAFQECDTVGITRPCTKHNWLVKDVNDLARVLHEAFHVAKTGRPGPVLVDVPKDVQF 181 Query: 183 NACKYEYPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELR 240 Y P+ SY+P +G I++AVAL+ A+RP IY+GGGV+ + AS LR Sbjct: 182 ATGIYTPPEVSPRTSYHPRIQGDIEAIKQAVALMLTAKRPVIYSGGGVINSGNEASKLLR 241 Query: 241 QLAALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRV 300 +L LT P+T+TLMGLGA+P + K ++GMLGMHGTYEANM M +CDV++ IGARFDDR+ Sbjct: 242 ELVELTNFPITSTLMGLGAYPASGKNWLGMLGMHGTYEANMTMHDCDVMVNIGARFDDRI 301 Query: 301 IGNPAHFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREA 360 G + F+ ++K IHIDIDPSSI+K V+VD+P++G+V VL+++I I+AS KP +A Sbjct: 302 TGRISGFSPNSKK-IHIDIDPSSINKAVRVDVPVIGDVAHVLEDMIRLIRASSTKPDEKA 360 Query: 361 LAKWWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQF 419 + WW QI++WRS L Y R+ ++I PQY +E+++ LTK D +I ++VGQHQMWAAQF Sbjct: 361 MGAWWSQIDKWRSRKSLSYTRNKDVIMPQYALERLYALTKDRDTYITTEVGQHQMWAAQF 420 Query: 420 YKFDEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYD 479 Y F++P RW+ SGGLGTMG GLP A+G++ A P+ V+ I G+ S+QM +QE+S +QY+ Sbjct: 421 YHFEKPNRWMTSGGLGTMGYGLPAALGVQIAHPDSLVIDIAGDASVQMNMQEMSAAVQYE 480 Query: 480 TPVKICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVE 539 P+KI LNN Y+GMVRQWQ++ + NR SHSY +ALPDFVKLAEAYG G+R EK D++ Sbjct: 481 APIKIFILNNQYMGMVRQWQQLLHGNRLSHSYTEALPDFVKLAEAYGGHGIRCEKPGDLD 540 Query: 540 PALREAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAE 583 A++E +K + V D + N +PM+ +GK +EMLL E Sbjct: 541 DAIQEMIDVK-KPVLFDCRVANLANCFPMIPSGKAHNEMLLPDE 583 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: 936 Number of extensions: 32 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: 601 Length adjustment: 37 Effective length of query: 548 Effective length of database: 564 Effective search space: 309072 Effective search space used: 309072 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_106718131.1 CU100_RS18730 (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.400993.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-246 804.6 0.1 2.5e-246 804.4 0.1 1.0 1 NCBI__GCF_003010935.1:WP_106718131.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106718131.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 804.4 0.1 2.5e-246 2.5e-246 1 555 [. 18 580 .. 18 582 .. 0.97 Alignments for each domain: == domain 1 score: 804.4 bits; conditional E-value: 2.5e-246 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 ++gae++v++l ++gv +fGyPGGavlpiyd+l+ ++ ++hilvrheq+a haa+Gyar++GkvGv+l+tsG NCBI__GCF_003010935.1:WP_106718131.1 18 MTGAEMVVQALIDQGVTDIFGYPGGAVLPIYDELFqQDRINHILVRHEQGAGHAAEGYARSTGKVGVMLVTSG 90 79*********************************9999********************************** PP TIGR00118 73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145 PGatn+vt++ +a +ds+Plv ++Gqv+tsliGsdafqe+d +Git+p+tkh++lvk+++dl+++l+eaf++a NCBI__GCF_003010935.1:WP_106718131.1 91 PGATNAVTPLQDALMDSIPLVCISGQVPTSLIGSDAFQECDTVGITRPCTKHNWLVKDVNDLARVLHEAFHVA 163 ************************************************************************* PP TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviia..ea 216 +tGrPGPvlvd+Pkdv+ a+ ++ +e +y+p+++g+ ik+a+ l+ +ak+Pv++ GgGvi + ea NCBI__GCF_003010935.1:WP_106718131.1 164 KTGRPGPVLVDVPKDVQFATGIYTPPEVSPRTSYHPRIQGDIEAIKQAVALMLTAKRPVIYSGGGVINSgnEA 236 ********************999999888899***********************************763369 PP TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289 s+ l+el+e ++ p+t+tl+GlGa+p+ ++ lgmlGmhGt+ean++++++d+++ +Garfddr+tg ++ f+ NCBI__GCF_003010935.1:WP_106718131.1 237 SKLLRELVELTNFPITSTLMGLGAYPASGKNWLGMLGMHGTYEANMTMHDCDVMVNIGARFDDRITGRISGFS 309 9************************************************************************ PP TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldee 357 p++k ihididP++i+k v+vd+p++Gd+ +vle++++ +++ ++k + W+++i++w++++ l++ ++ NCBI__GCF_003010935.1:WP_106718131.1 310 PNSKKIHIDIDPSSINKAVRVDVPVIGDVAHVLEDMIRLIRASstkpDEKAMGaWWSQIDKWRSRKSLSYTRN 382 **************************************9998866553333336******************* PP TIGR00118 358 eesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpee 429 ++ i Pq+ +++l+ l+kd ++++tt+vGqhqmwaaqfy+++kp++++tsgGlGtmG+GlPaalG+++a+p++ NCBI__GCF_003010935.1:WP_106718131.1 383 KDVIMPQYALERLYALTKDrDTYITTEVGQHQMWAAQFYHFEKPNRWMTSGGLGTMGYGLPAALGVQIAHPDS 455 ******************999**************************************************** PP TIGR00118 430 tvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502 v++++Gd+s+qmn+qe+s++v+y+ p+ki ilnn+++Gmv+qWq+l++ +r s+++ ++ lpdfvklaeayG NCBI__GCF_003010935.1:WP_106718131.1 456 LVIDIAGDASVQMNMQEMSAAVQYEAPIKIFILNNQYMGMVRQWQQLLHGNRLSHSYTEA-LPDFVKLAEAYG 527 ***********************************************************5.************ PP TIGR00118 503 vkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555 +gir ekp +l+++++e++ +k+pvl+d +v++ ++++Pm+++G++ +e++ NCBI__GCF_003010935.1:WP_106718131.1 528 GHGIRCEKPGDLDDAIQEMIDVKKPVLFDCRVANLANCFPMIPSGKAHNEMLL 580 **************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (601 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: 35.49 // [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