Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate 3608380 Dshi_1781 acetolactate synthase, small subunit (RefSeq)
Query= BRENDA::P00894 (163 letters) >FitnessBrowser__Dino:3608380 Length = 190 Score = 128 bits (321), Expect = 6e-35 Identities = 75/156 (48%), Positives = 104/156 (66%), Gaps = 3/156 (1%) Query: 5 LSVLLENESGALSRVIGLFSQRGYNIESLTVAPTD-DPTLSRMTIQTVGDEKVLEQIEKQ 63 L+V+++NE+G L+RVIGLFS RGYNIESLTVA D + SR+TI T G +V+EQI+ Q Sbjct: 31 LAVVVDNEAGVLARVIGLFSGRGYNIESLTVAEIDHEGHRSRITIVTTGTPQVIEQIKAQ 90 Query: 64 LHKLVDVLRVSELG-QGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSLYTV 122 L ++V V V +L +GA VERE+ L K+ +G R E R EIFR ++D T + Sbjct: 91 LARMVPVHEVHDLTVEGASVERELALFKVAGTGDKRIEALRLAEIFRANVVDSTLQSFVF 150 Query: 123 QLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRG 158 ++ GT K+DAF +R + + E+AR+GV LSRG Sbjct: 151 EITGTPAKIDAFGELMRPLG-LTEIARTGVAALSRG 185 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: 104 Number of extensions: 5 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: 190 Length adjustment: 19 Effective length of query: 144 Effective length of database: 171 Effective search space: 24624 Effective search space used: 24624 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: 44 (21.6 bits)
Align candidate 3608380 Dshi_1781 (acetolactate synthase, small subunit (RefSeq))
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.18270.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-54 170.3 0.5 1.8e-54 170.1 0.5 1.0 1 lcl|FitnessBrowser__Dino:3608380 Dshi_1781 acetolactate synthase, Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3608380 Dshi_1781 acetolactate synthase, small subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 170.1 0.5 1.8e-54 1.8e-54 2 157 .. 28 185 .. 27 186 .. 0.97 Alignments for each domain: == domain 1 score: 170.1 bits; conditional E-value: 1.8e-54 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteek.dlsrmtivvegddkvveqiekqleklvdvlkvldlt 77 +h+l+v+v+ne+GvL+rv+Glf+ rg+niesltv+e +++ + sr+tiv++g +v+eqi+ ql ++v+v +v+dlt lcl|FitnessBrowser__Dino:3608380 28 THTLAVVVDNEAGVLARVIGLFSGRGYNIESLTVAEIDHEgHRSRITIVTTGTPQVIEQIKAQLARMVPVHEVHDLT 104 79**********************************9987257*********************************9 PP TIGR00119 78 .eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevarsGlva 153 e ++v+rel+l kv +g +r e +l+eifr++vvD + +s++ e++g++ ki+af +l++++g+ e+ar+G+ a lcl|FitnessBrowser__Dino:3608380 105 vEGASVERELALFKVAGTGDKRIEALRLAEIFRANVVDSTLQSFVFEITGTPAKIDAFGELMRPLGLTEIARTGVAA 181 57799************************************************************************ PP TIGR00119 154 lsrg 157 lsrg lcl|FitnessBrowser__Dino:3608380 182 LSRG 185 ***8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (190 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 4.88 // [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