Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate AZOBR_RS06565 AZOBR_RS06565 acetolactate synthase
Query= BRENDA::P00894 (163 letters) >FitnessBrowser__azobra:AZOBR_RS06565 Length = 168 Score = 125 bits (314), Expect = 3e-34 Identities = 70/159 (44%), Positives = 108/159 (67%), Gaps = 3/159 (1%) Query: 2 RRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPT-LSRMTIQTVGDEKVLEQI 60 + ++VL++NE G L+RVIGLFS RGYNIESLTVA ++ LSR+T+ T G V+EQI Sbjct: 7 KHTIAVLVDNEPGVLARVIGLFSGRGYNIESLTVAEVNNADHLSRITLVTSGTRMVVEQI 66 Query: 61 EKQLHKLVDVLRVSEL-GQGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSL 119 + QL +LV V +V +L +G VERE+ LVK+ +G R E R +IF+ +++D T + Sbjct: 67 KAQLDRLVPVHKVHDLTDEGPSVERELALVKVAGTGERRIEALRLADIFKAKVVDATLTS 126 Query: 120 YTVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRG 158 + +L GT+ ++D F+ + + +VE +R+GVV +S+G Sbjct: 127 FVFELTGTTAEVDDFVGLMAQLG-LVEASRTGVVAMSKG 164 Lambda K H 0.318 0.136 0.360 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: 85 Number of extensions: 8 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: 163 Length of database: 168 Length adjustment: 18 Effective length of query: 145 Effective length of database: 150 Effective search space: 21750 Effective search space used: 21750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 43 (21.2 bits)
Align candidate AZOBR_RS06565 AZOBR_RS06565 (acetolactate synthase)
to HMM TIGR00119 (ilvN: acetolactate synthase, small subunit (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/TIGR00119.hmm # target sequence database: /tmp/gapView.10920.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00119 [M=158] Accession: TIGR00119 Description: acolac_sm: acetolactate synthase, small subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-54 170.4 1.2 1.7e-54 170.2 1.2 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS06565 AZOBR_RS06565 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS06565 AZOBR_RS06565 acetolactate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 170.2 1.2 1.7e-54 1.7e-54 2 157 .. 7 164 .. 6 165 .. 0.96 Alignments for each domain: == domain 1 score: 170.2 bits; conditional E-value: 1.7e-54 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgetee.kdlsrmtivvegddkvveqiekqleklvd 69 kh+++vlv+nepGvL+rv+Glf+ rg+niesltv+e ++ ++lsr+t+v++g vveqi+ ql++lv+ lcl|FitnessBrowser__azobra:AZOBR_RS06565 7 KHTIAVLVDNEPGVLARVIGLFSGRGYNIESLTVAEVNNaDHLSRITLVTSGTRMVVEQIKAQLDRLVP 75 8**********************************9877256*************************** PP TIGR00119 70 vlkvldltes.eivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkl 137 v kv+dlt++ +v+rel+lvkv +ge+r e +l++if+++vvD + +s++ el+g+ ++ f+ l lcl|FitnessBrowser__azobra:AZOBR_RS06565 76 VHKVHDLTDEgPSVERELALVKVAGTGERRIEALRLADIFKAKVVDATLTSFVFELTGTTAEVDDFVGL 144 *******965389******************************************************** PP TIGR00119 138 lkefgikevarsGlvalsrg 157 ++++g++e +r+G+va+s+g lcl|FitnessBrowser__azobra:AZOBR_RS06565 145 MAQLGLVEASRTGVVAMSKG 164 *****************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (168 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 4.19 // [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