Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate AZOBR_RS06560 AZOBR_RS06560 acetolactate synthase
Query= metacyc::MONOMER-18810 (585 letters) >FitnessBrowser__azobra:AZOBR_RS06560 Length = 587 Score = 633 bits (1633), Expect = 0.0 Identities = 311/570 (54%), Positives = 411/570 (72%), Gaps = 4/570 (0%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 ++ GA+I++ AL ++GV+ ++GYPGGAVL IYD + +Q +HILVRHEQAAVHAA+GYA Sbjct: 5 KLTGAQIVIKALKDQGVDIIFGYPGGAVLPIYDAIFQQNDIKHILVRHEQAAVHAAEGYA 64 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 R+TGKVG LVTSGPG TNAVTG+ A DSIP+V ++G VPTH IG DAFQE DT GIT Sbjct: 65 RSTGKVGCVLVTSGPGATNAVTGLLDALCDSIPLVCLSGQVPTHLIGNDAFQEADTTGIT 124 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RP KHN+LVKDV LA T+ +AF++A +GRPGPV+VDIPKDV Y P + ++ Sbjct: 125 RPCTKHNYLVKDVNQLARTMHEAFYVARSGRPGPVLVDIPKDVQFADGTYIPPTEVKHKT 184 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNTLM 255 Y P K ++ +A+ L+ A+RP YTGGGVV A A+ L Q +TG P+T+TLM Sbjct: 185 YRPQVKPEIARVEEAIELIATAKRPIFYTGGGVVNAGPIAAKLLTQFVKMTGFPITSTLM 244 Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315 GLGAFP + Q++GMLGMHGTYEAN+AM NCDV+I IGARFDDRV G + F ++K I Sbjct: 245 GLGAFPASDPQWLGMLGMHGTYEANLAMYNCDVMINIGARFDDRVTGKLSEFAPGSKK-I 303 Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375 H+DIDPSSI+K V VDIPIVG+ VL+++I KA + + AL +WW Q+E WR+ + Sbjct: 304 HVDIDPSSINKNVAVDIPIVGDAGAVLEDMIRIWKARQKRADQTALKEWWGQVEGWRARN 363 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434 CL Y+R+ +IKPQY +E++ E +G + ++ ++VGQHQMWAAQF FDEP RW+ SGGL Sbjct: 364 CLNYNRTEAVIKPQYALERLREALRGKNHYVTTEVGQHQMWAAQFLPFDEPNRWMTSGGL 423 Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494 GTMG GLP A+G + A P+ VV ++GE S M +QE+ T +QY PVKI LNN Y+GM Sbjct: 424 GTMGYGLPAAIGAQLAHPDAIVVDVSGEASFLMNMQEIGTAVQYRAPVKIFILNNKYMGM 483 Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554 VRQWQE+ + +RYS+SY +ALPDFVKLAE++G VG+R ++V+ + + + DR Sbjct: 484 VRQWQELLHGSRYSNSYSEALPDFVKLAESWGCVGLRATTVAEVDEVIEKMLAVTDRPCI 543 Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAED 584 +D DP EN +PM+ GK +E+L G ED Sbjct: 544 IDIAVDPKENCFPMIPGGKAHNEILFGPED 573 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: 946 Number of extensions: 24 Number of successful extensions: 4 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: 587 Length adjustment: 37 Effective length of query: 548 Effective length of database: 550 Effective search space: 301400 Effective search space used: 301400 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 AZOBR_RS06560 AZOBR_RS06560 (acetolactate synthase)
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.11632.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-244 796.9 0.1 5.7e-244 796.6 0.1 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS06560 AZOBR_RS06560 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS06560 AZOBR_RS06560 acetolactate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 796.6 0.1 5.7e-244 5.7e-244 1 554 [. 6 568 .. 6 570 .. 0.97 Alignments for each domain: == domain 1 score: 796.6 bits; conditional E-value: 5.7e-244 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 l+ga+i++++lk++gv+++fGyPGGavlpiyda++ +++++hilvrheqaa+haa+Gyar++GkvG+vl lcl|FitnessBrowser__azobra:AZOBR_RS06560 6 LTGAQIVIKALKDQGVDIIFGYPGGAVLPIYDAIFqQNDIKHILVRHEQAAVHAAEGYARSTGKVGCVL 74 68*********************************999******************************* PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 +tsGPGatn+vtg+++a ds+Plv l+Gqv+t+liG+dafqe+d +Git+p+tkh++lvk++++l+++ lcl|FitnessBrowser__azobra:AZOBR_RS06560 75 VTSGPGATNAVTGLLDALCDSIPLVCLSGQVPTHLIGNDAFQEADTTGITRPCTKHNYLVKDVNQLART 143 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206 ++eaf++a +GrPGPvlvd+Pkdv+ a+ ++ +++v+ ++y+p+vk++ +++++a+eli++ak+P+ + lcl|FitnessBrowser__azobra:AZOBR_RS06560 144 MHEAFYVARSGRPGPVLVDIPKDVQFADGTYIPPTEVKHKTYRPQVKPEIARVEEAIELIATAKRPIFY 212 ********************************************************************* PP TIGR00118 207 vGgGviiae..aseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273 GgGv+ a+ a + l+++++++ p+t+tl+GlGafp+ +p+ lgmlGmhGt+eanla+ ++d++i + lcl|FitnessBrowser__azobra:AZOBR_RS06560 213 TGGGVVNAGpiAAKLLTQFVKMTGFPITSTLMGLGAFPASDPQWLGMLGMHGTYEANLAMYNCDVMINI 281 ******998668999****************************************************** PP TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338 Garfddrvtg+l++fap +k ih+didP++i+knv+vdipivGda vle++++ k++ +++ + lcl|FitnessBrowser__azobra:AZOBR_RS06560 282 GARFDDRVTGKLSEFAPGSKKIHVDIDPSSINKNVAVDIPIVGDAGAVLEDMIRIWKARqkraDQTALK 350 ****************************************************98666554455334444 PP TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfit 405 W+ ++e w+++++l+++++e ikPq+ +++l + l++ + +vtt+vGqhqmwaaqf+++++p++++t lcl|FitnessBrowser__azobra:AZOBR_RS06560 351 eWWGQVEGWRARNCLNYNRTEAVIKPQYALERLREALRGkNHYVTTEVGQHQMWAAQFLPFDEPNRWMT 419 5**********************************9998689*************************** PP TIGR00118 406 sgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474 sgGlGtmG+GlPaa+Ga++a+p++ vv+v+G++sf mn+qe+ t+v+y pvki ilnn+++Gmv+qWq lcl|FitnessBrowser__azobra:AZOBR_RS06560 420 SGGLGTMGYGLPAAIGAQLAHPDAIVVDVSGEASFLMNMQEIGTAVQYRAPVKIFILNNKYMGMVRQWQ 488 ********************************************************************* PP TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlP 542 el++ rys+++ ++ lpdfvklae++G +g+r ++ +e++e ++++l+++ +p ++d+ vd +e+++P lcl|FitnessBrowser__azobra:AZOBR_RS06560 489 ELLHGSRYSNSYSEA-LPDFVKLAESWGCVGLRATTVAEVDEVIEKMLAVTdRPCIIDIAVDPKENCFP 556 ************995.*******************************997669**************** PP TIGR00118 543 mvapGagldelv 554 m++ G++ +e++ lcl|FitnessBrowser__azobra:AZOBR_RS06560 557 MIPGGKAHNEIL 568 *********986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (587 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.37 // [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