Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_026595984.1 A3OQ_RS0117845 acetolactate synthase 3 large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000385335.1:WP_026595984.1 Length = 586 Score = 622 bits (1604), Expect = 0.0 Identities = 314/572 (54%), Positives = 406/572 (70%), Gaps = 5/572 (0%) Query: 16 APEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADG 75 A EM GAE++V AL ++ V+ ++GYPGGAVL IYD L +Q HILVRHEQ A HAA+G Sbjct: 2 AKEMTGAEMVVEALKDQDVDCLFGYPGGAVLPIYDALFQQNHVRHILVRHEQGAAHAAEG 61 Query: 76 YARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVG 135 YAR++GKVGV LVTSGPG TN +TG+ A +DSIP++ ITG VPTH IG DAFQECDTVG Sbjct: 62 YARSSGKVGVLLVTSGPGATNTITGLTDALMDSIPLICITGQVPTHLIGSDAFQECDTVG 121 Query: 136 ITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDM 195 ITR KHN+LV+ + DL + +AF++A GRPGPVV+DIPKDV Y P+ I+ Sbjct: 122 ITRHCTKHNYLVRSIEDLPRVLHEAFYVAQNGRPGPVVIDIPKDVQFATGAYIGPQHIEH 181 Query: 196 RSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNT 253 R+Y P G S +I +AVA++ A RP YTGGG++ + AS +R+L ALTG P+T+T Sbjct: 182 RTYKPQLFGDSAKIEQAVAMMAVARRPVFYTGGGIINSGLEASKLMRELVALTGFPITST 241 Query: 254 LMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARK 313 LMGLGA+P + K ++GMLGMHGTYEAN AM +CD++IA+GARFDDR+ G F+ +RK Sbjct: 242 LMGLGAYPASGKNWLGMLGMHGTYEANNAMHDCDLMIAVGARFDDRITGRLDAFSPGSRK 301 Query: 314 IIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRS 373 IHIDIDPSSI+K VKVD+ I+G+ VLQ++I + K L WW +I+ WR+ Sbjct: 302 -IHIDIDPSSINKNVKVDLGIIGDCTHVLQQMIEVWRHRGYKADPVHLDTWWREIDTWRA 360 Query: 374 VDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSG 432 L + +S ++IKPQY V++++ELTK D +I ++VGQHQMWAAQ + F++P W+ SG Sbjct: 361 RKSLSFKQSDKVIKPQYAVQRLYELTKNRDTYITTEVGQHQMWAAQHFHFEDPHHWMTSG 420 Query: 433 GLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYL 492 GLGTMG GLP A+G + A + VV I GEGSI M +QE+ST +QYD PVKI LNN YL Sbjct: 421 GLGTMGYGLPAAIGAQLAHRDALVVDIAGEGSILMNMQEMSTAVQYDLPVKIFILNNEYL 480 Query: 493 GMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRT 552 GMVRQWQE+ + RYSHSY +ALPDFVKLAEAYG G+R +D++ A+ E R Sbjct: 481 GMVRQWQELLHGGRYSHSYSEALPDFVKLAEAYGAHGIRCSDPADLDAAIMEMID-TPRP 539 Query: 553 VFLDFQTDPTENVWPMVQAGKGISEMLLGAED 584 V D D TEN PM+ +GK +EM+L D Sbjct: 540 VIFDCLVDKTENCLPMIPSGKAHNEMILPDTD 571 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: 964 Number of extensions: 27 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: 586 Length adjustment: 37 Effective length of query: 548 Effective length of database: 549 Effective search space: 300852 Effective search space used: 300852 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_026595984.1 A3OQ_RS0117845 (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.23264.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-245 799.1 0.0 1.1e-244 798.9 0.0 1.0 1 lcl|NCBI__GCF_000385335.1:WP_026595984.1 A3OQ_RS0117845 acetolactate synt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000385335.1:WP_026595984.1 A3OQ_RS0117845 acetolactate synthase 3 large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 798.9 0.0 1.1e-244 1.1e-244 1 555 [. 5 567 .. 5 569 .. 0.98 Alignments for each domain: == domain 1 score: 798.9 bits; conditional E-value: 1.1e-244 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 ++gae++ve+lk+++v+ +fGyPGGavlpiydal+ +++++hilvrheq+aahaa+Gyar+sGkvGv l lcl|NCBI__GCF_000385335.1:WP_026595984.1 5 MTGAEMVVEALKDQDVDCLFGYPGGAVLPIYDALFqQNHVRHILVRHEQGAAHAAEGYARSSGKVGVLL 73 79*********************************8899****************************** PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 +tsGPGatn++tg+++a +ds+Pl+ +tGqv+t+liGsdafqe+d +Git+ +tkh++lv++ edlp++ lcl|NCBI__GCF_000385335.1:WP_026595984.1 74 VTSGPGATNTITGLTDALMDSIPLICITGQVPTHLIGSDAFQECDTVGITRHCTKHNYLVRSIEDLPRV 142 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206 l+eaf++a+ GrPGPv++d+Pkdv+ a+ + ++++e ++ykp++ g+ ++i++a+ +++ a++Pv + lcl|NCBI__GCF_000385335.1:WP_026595984.1 143 LHEAFYVAQNGRPGPVVIDIPKDVQFATGAYIGPQHIEHRTYKPQLFGDSAKIEQAVAMMAVARRPVFY 211 ********************************************************************* PP TIGR00118 207 vGgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273 GgG+i + eas+ ++el+ + p+t+tl+GlGa+p+ ++ lgmlGmhGt+ean a++++dl+iav lcl|NCBI__GCF_000385335.1:WP_026595984.1 212 TGGGIINSglEASKLMRELVALTGFPITSTLMGLGAYPASGKNWLGMLGMHGTYEANNAMHDCDLMIAV 280 ******8844699******************************************************** PP TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338 Garfddr+tg l+ f+p ++ ihididP++i+knvkvd+ i+Gd+++vl+++++ +++ + + + lcl|NCBI__GCF_000385335.1:WP_026595984.1 281 GARFDDRITGRLDAFSPGSRKIHIDIDPSSINKNVKVDLGIIGDCTHVLQQMIEVWRHRgykaDPVHLD 349 ******************************************************998877666333344 PP TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfit 405 W+++i+ w++++ l+++++++ ikPq+ +++l++l+k+ ++++tt+vGqhqmwaaq+++++ p++++t lcl|NCBI__GCF_000385335.1:WP_026595984.1 350 tWWREIDTWRARKSLSFKQSDKVIKPQYAVQRLYELTKNrDTYITTEVGQHQMWAAQHFHFEDPHHWMT 418 5************************************9889**************************** PP TIGR00118 406 sgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474 sgGlGtmG+GlPaa+Ga++a+ ++ vv+++G+gs+ mn+qe+st+v+yd+pvki ilnne+lGmv+qWq lcl|NCBI__GCF_000385335.1:WP_026595984.1 419 SGGLGTMGYGLPAAIGAQLAHRDALVVDIAGEGSILMNMQEMSTAVQYDLPVKIFILNNEYLGMVRQWQ 487 ********************************************************************* PP TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPm 543 el++ +rys+++ ++ lpdfvklaeayG++gir ++p++l++++ e++ + +pv++d vdk+e++lPm lcl|NCBI__GCF_000385335.1:WP_026595984.1 488 ELLHGGRYSHSYSEA-LPDFVKLAEAYGAHGIRCSDPADLDAAIMEMIDTPRPVIFDCLVDKTENCLPM 555 *************95.***************************************************** PP TIGR00118 544 vapGagldelve 555 +++G++ +e++ lcl|NCBI__GCF_000385335.1:WP_026595984.1 556 IPSGKAHNEMIL 567 **********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (586 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: 13.05 // [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