Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_034992592.1 DL88_RS04520 acetolactate synthase 3 large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000745425.1:WP_034992592.1 Length = 586 Score = 617 bits (1592), Expect = 0.0 Identities = 312/565 (55%), Positives = 407/565 (72%), Gaps = 5/565 (0%) Query: 19 MIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYAR 78 M GA+++V AL ++GV+ ++GYPGGAVL IYD L +Q H+LVRHEQ AVHAA+GYAR Sbjct: 5 MTGAQMVVEALKDQGVDTIFGYPGGAVLPIYDALFQQNAIRHVLVRHEQGAVHAAEGYAR 64 Query: 79 ATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITR 138 +TG+ GV LVTSGPG TNAVTG+ A LDSIP+V ITG VPTH IG DAFQECDTVGITR Sbjct: 65 STGRAGVVLVTSGPGATNAVTGLTDAMLDSIPLVCITGQVPTHLIGSDAFQECDTVGITR 124 Query: 139 PIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSY 198 KHN+LV+ V DL + +AF++A GRPGPVV+DIPKDV Y P +I+ ++Y Sbjct: 125 HCTKHNYLVRQVEDLPRILHEAFYVAQHGRPGPVVIDIPKDVQFALGAYAGPANIEHKTY 184 Query: 199 NPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLMG 256 P KG +I +A++ + A+RP YTGGGV+ + A+ LR+L +TG P+T+TLMG Sbjct: 185 KPAFKGDLARIDEALSWIAAAKRPIFYTGGGVINSGPEAAALLRELVNMTGAPITSTLMG 244 Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316 LGA+P +S Q++GMLGMHGTYEAN AM +CD++IAIGARFDDR+ G F+ +RK IH Sbjct: 245 LGAYPASSPQWLGMLGMHGTYEANNAMHDCDLMIAIGARFDDRITGRIDAFSPGSRK-IH 303 Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDC 376 IDIDPSSI+K VKVD+ IVG+ VL++++A+ K + AL KWW +I+ WR+ Sbjct: 304 IDIDPSSINKIVKVDLGIVGDCTQVLRDMVARWKERKLSCDPAALEKWWREIDHWRARKS 363 Query: 377 LKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435 L Y S+E+IKPQ+ +++++ELT+ D +I ++VGQHQMWAAQ Y F+EP RW+ SGGLG Sbjct: 364 LAYRPSNEVIKPQHAIQRLYELTRARDTYISTEVGQHQMWAAQHYHFEEPNRWMTSGGLG 423 Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495 TMG GLP A+G + A P+ V+ I GE SI M IQELST +Q+ PVKI LNN Y+GMV Sbjct: 424 TMGYGLPAAIGAQMAHPDSLVIDIAGEASILMNIQELSTAVQFRLPVKIFILNNQYMGMV 483 Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555 RQWQE+ + RYS SY +ALPDFVKLAEAYG G+R + ++ A+ E + V L Sbjct: 484 RQWQELLHGGRYSQSYSEALPDFVKLAEAYGCHGIRCADPASLDAAILEMID-TPKPVLL 542 Query: 556 DFQTDPTENVWPMVQAGKGISEMLL 580 D D EN PM+ +GK +EM+L Sbjct: 543 DCIVDREENCLPMIPSGKAHNEMIL 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: 956 Number of extensions: 29 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_034992592.1 DL88_RS04520 (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.22087.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-245 802.3 0.0 1.3e-245 802.1 0.0 1.0 1 lcl|NCBI__GCF_000745425.1:WP_034992592.1 DL88_RS04520 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_034992592.1 DL88_RS04520 acetolactate synthase 3 large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 802.1 0.0 1.3e-245 1.3e-245 1 555 [. 5 567 .. 5 569 .. 0.98 Alignments for each domain: == domain 1 score: 802.1 bits; conditional E-value: 1.3e-245 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 ++ga+++ve+lk++gv+t+fGyPGGavlpiydal+ ++ ++h+lvrheq+a+haa+Gyar++G++Gvvl lcl|NCBI__GCF_000745425.1:WP_034992592.1 5 MTGAQMVVEALKDQGVDTIFGYPGGAVLPIYDALFqQNAIRHVLVRHEQGAVHAAEGYARSTGRAGVVL 73 79*********************************8899****************************** PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 +tsGPGatn+vtg+++a+lds+Plv +tGqv+t+liGsdafqe+d +Git+ +tkh++lv+++edlp+i lcl|NCBI__GCF_000745425.1:WP_034992592.1 74 VTSGPGATNAVTGLTDAMLDSIPLVCITGQVPTHLIGSDAFQECDTVGITRHCTKHNYLVRQVEDLPRI 142 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206 l+eaf++a+ GrPGPv++d+Pkdv+ a + ++++e ++ykp kg+ ++i +al i++ak+P+ + lcl|NCBI__GCF_000745425.1:WP_034992592.1 143 LHEAFYVAQHGRPGPVVIDIPKDVQFALGAYAGPANIEHKTYKPAFKGDLARIDEALSWIAAAKRPIFY 211 ********************************************************************* PP TIGR00118 207 vGgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273 GgGvi + ea + l+el++++ +p+t+tl+GlGa+p+ p+ lgmlGmhGt+ean a++++dl+ia+ lcl|NCBI__GCF_000745425.1:WP_034992592.1 212 TGGGVINSgpEAAALLRELVNMTGAPITSTLMGLGAYPASSPQWLGMLGMHGTYEANNAMHDCDLMIAI 280 ******873368899****************************************************** PP TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338 Garfddr+tg ++ f+p ++ ihididP++i+k+vkvd+ ivGd+++vl++++++ ke+ + e lcl|NCBI__GCF_000745425.1:WP_034992592.1 281 GARFDDRITGRIDAFSPGSRKIHIDIDPSSINKIVKVDLGIVGDCTQVLRDMVARWKERklscDPAALE 349 ******************************************************999987777444444 PP TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfit 405 W+++i++w++++ l++ ++e ikPq+ i++l++l++ +++++t+vGqhqmwaaq+y++++p++++t lcl|NCBI__GCF_000745425.1:WP_034992592.1 350 kWWREIDHWRARKSLAYRPSNEVIKPQHAIQRLYELTRArDTYISTEVGQHQMWAAQHYHFEEPNRWMT 418 4***********************************98779**************************** PP TIGR00118 406 sgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474 sgGlGtmG+GlPaa+Ga++a+p++ v++++G++s+ mn+qelst+v++ +pvki ilnn+++Gmv+qWq lcl|NCBI__GCF_000745425.1:WP_034992592.1 419 SGGLGTMGYGLPAAIGAQMAHPDSLVIDIAGEASILMNIQELSTAVQFRLPVKIFILNNQYMGMVRQWQ 487 ********************************************************************* PP TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPm 543 el++ +rys+++ ++ lpdfvklaeayG +gir ++p+ l++++ e++ + +pvlld vd+ee++lPm lcl|NCBI__GCF_000745425.1:WP_034992592.1 488 ELLHGGRYSQSYSEA-LPDFVKLAEAYGCHGIRCADPASLDAAILEMIDTPKPVLLDCIVDREENCLPM 555 *************95.***************************************************** PP TIGR00118 544 vapGagldelve 555 +++G++ +e++ lcl|NCBI__GCF_000745425.1:WP_034992592.1 556 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: 12.96 // [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