Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate Ga0059261_0068 Ga0059261_0068 acetolactate synthase, large subunit (EC 2.2.1.6)
Query= metacyc::MONOMER-18810 (585 letters) >FitnessBrowser__Korea:Ga0059261_0068 Length = 581 Score = 608 bits (1567), Expect = e-178 Identities = 316/571 (55%), Positives = 393/571 (68%), Gaps = 7/571 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 E GA+IL+ A + GVE ++GYPGGAVL IYD + +QTK HILVRHEQAA HAA+GYA Sbjct: 3 EKSGADILIEAFNDLGVEVIFGYPGGAVLPIYDAIFQQTKIRHILVRHEQAATHAAEGYA 62 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 RATGK GV LVTSGPG TNAVTGI A +DSIPMVVITG VP+H IG DAFQE DTVGIT Sbjct: 63 RATGKPGVVLVTSGPGATNAVTGITDALMDSIPMVVITGQVPSHLIGSDAFQEADTVGIT 122 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 R KHN+LVKD L + + +AF IA +GRPGPVV+DIPKDV +Y P I ++ Sbjct: 123 RHCTKHNYLVKDPAHLGSIVHEAFHIATSGRPGPVVIDIPKDVQIATARYSKPGPIQHKT 182 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255 Y P K I AV +L AERP YTGGGV+ + AS LR+LA +TG PVT+TLM Sbjct: 183 YRPQVKADKALIESAVEMLAAAERPVFYTGGGVINSGPQASQLLRELARITGAPVTSTLM 242 Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315 GLGAFP +S Q++GMLGMHGTYEAN AM D+++AIGARFDDRV G F ARK I Sbjct: 243 GLGAFPASSDQWLGMLGMHGTYEANYAMNQADLIVAIGARFDDRVTGRLDAFAPHARK-I 301 Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375 HIDID SS++K V+VD+PIV +V L+++I KA + R L++WW +IE WR+V Sbjct: 302 HIDIDRSSMNKTVRVDLPIVADVGHALEDMIRIWKAR--QHPRPDLSEWWSRIEGWRAVK 359 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDA-FICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434 CL + S I PQ + +WE T+ A I ++VGQHQMWAAQ + F+ P +W+ SGGL Sbjct: 360 CLDFPEDSNEIMPQRAIRALWEATRDQAPIITTEVGQHQMWAAQHFHFESPNKWLTSGGL 419 Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494 GTMG GLP A+G + P+ V+ I GE SIQM IQEL+T QY PVKI LNN Y+GM Sbjct: 420 GTMGYGLPAAIGAQLGHPDALVIDIAGEASIQMNIQELATATQYRLPVKIFILNNEYMGM 479 Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554 VRQWQE+ Y +RYS SY DALPDFVKL EAYG G+R+E ++ + A D V Sbjct: 480 VRQWQELTYSSRYSESYSDALPDFVKLGEAYGWEGIRIEGKDQLDDGI-AAMLAHDGPVI 538 Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585 +D + N +PM+ +G ++MLL + ++ Sbjct: 539 VDCRVAKLANCFPMIPSGAAHTDMLLQSAEV 569 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: 951 Number of extensions: 37 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: 581 Length adjustment: 36 Effective length of query: 549 Effective length of database: 545 Effective search space: 299205 Effective search space used: 299205 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 Ga0059261_0068 Ga0059261_0068 (acetolactate synthase, large subunit (EC 2.2.1.6))
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.30969.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-243 795.4 0.1 1.6e-243 795.1 0.1 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0068 Ga0059261_0068 acetolactate synt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0068 Ga0059261_0068 acetolactate synthase, large subunit (EC 2.2.1.6) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 795.1 0.1 1.6e-243 1.6e-243 2 555 .. 5 564 .. 4 566 .. 0.97 Alignments for each domain: == domain 1 score: 795.1 bits; conditional E-value: 1.6e-243 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 +ga+il+e++++ gve++fGyPGGavlpiyda++ + +++hilvrheqaa+haa+Gyara+Gk+Gvvl+ lcl|FitnessBrowser__Korea:Ga0059261_0068 5 SGADILIEAFNDLGVEVIFGYPGGAVLPIYDAIFqQTKIRHILVRHEQAATHAAEGYARATGKPGVVLV 73 79********************************999******************************** PP TIGR00118 70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138 tsGPGatn+vtgi++a +ds+P+vv+tGqv+++liGsdafqe+d +Git+ +tkh++lvk+++ l +i+ lcl|FitnessBrowser__Korea:Ga0059261_0068 74 TSGPGATNAVTGITDALMDSIPMVVITGQVPSHLIGSDAFQEADTVGITRHCTKHNYLVKDPAHLGSIV 142 ********************************************************************* PP TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207 +eaf+ia++GrPGPv++d+Pkdv+ a+ +++++ ++ ++y+p+vk++k+ i+ a+e++++a++Pv + lcl|FitnessBrowser__Korea:Ga0059261_0068 143 HEAFHIATSGRPGPVVIDIPKDVQIATARYSKPGPIQHKTYRPQVKADKALIESAVEMLAAAERPVFYT 211 ********************************************************************* PP TIGR00118 208 GgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274 GgGvi + +as+ l+ela + +pvt+tl+GlGafp+ + lgmlGmhGt+ean+a+++adl++a+G lcl|FitnessBrowser__Korea:Ga0059261_0068 212 GGGVINSgpQASQLLRELARITGAPVTSTLMGLGAFPASSDQWLGMLGMHGTYEANYAMNQADLIVAIG 280 *****87336999******************************************************** PP TIGR00118 275 arfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee..ekkeke.Wl 340 arfddrvtg l+ fap+a+ ihidid ++++k+v+vd+piv d+ + le++++ k++ + + W+ lcl|FitnessBrowser__Korea:Ga0059261_0068 281 ARFDDRVTGRLDAFAPHARKIHIDIDRSSMNKTVRVDLPIVADVGHALEDMIRIWKARqhPRPDLSeWW 349 ***************************************************9976665444555545** PP TIGR00118 341 ekieewkkeyilkldeeeesikPqkvikelskllkdea.ivttdvGqhqmwaaqfyktkkprkfitsgG 408 ++ie w++ ++l + e++++i Pq+ i++l++ ++d+a i+tt+vGqhqmwaaq++++++p+k++tsgG lcl|FitnessBrowser__Korea:Ga0059261_0068 350 SRIEGWRAVKCLDFPEDSNEIMPQRAIRALWEATRDQApIITTEVGQHQMWAAQHFHFESPNKWLTSGG 418 ***********************************976599**************************** PP TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477 lGtmG+GlPaa+Ga++++p++ v++++G++s+qmn+qel+t+++y +pvki ilnne++Gmv+qWqel lcl|FitnessBrowser__Korea:Ga0059261_0068 419 LGTMGYGLPAAIGAQLGHPDALVIDIAGEASIQMNIQELATATQYRLPVKIFILNNEYMGMVRQWQELT 487 ********************************************************************* PP TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvap 546 y+ ryse++ + lpdfvkl eayG +girie +++l++ ++ +l++++pv++d +v+k ++++Pm+++ lcl|FitnessBrowser__Korea:Ga0059261_0068 488 YSSRYSESYSDA-LPDFVKLGEAYGWEGIRIEGKDQLDDGIAAMLAHDGPVIVDCRVAKLANCFPMIPS 555 **********95.******************************************************** PP TIGR00118 547 Gagldelve 555 Ga+ ++++ lcl|FitnessBrowser__Korea:Ga0059261_0068 556 GAAHTDMLL 564 *****9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (581 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 0.02s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 7.97 // [ok]
This GapMind analysis is from Apr 09 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