Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate GFF4652 PS417_23805 acetolactate synthase 3 regulatory subunit
Query= BRENDA::P00894 (163 letters) >FitnessBrowser__WCS417:GFF4652 Length = 163 Score = 210 bits (534), Expect = 1e-59 Identities = 102/162 (62%), Positives = 137/162 (84%), Gaps = 1/162 (0%) Query: 1 MRRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTVGDEKVLEQI 60 MR I+S+LLENE GALSRV+GLFSQR YNIESLTVAPT+DPTLSR+T+ TVG ++V+EQI Sbjct: 1 MRHIISLLLENEPGALSRVVGLFSQRNYNIESLTVAPTEDPTLSRLTLTTVGHDEVIEQI 60 Query: 61 EKQLHKLVDVLRVSELGQGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSLY 120 K L+KL++V+++ +L + AH+ERE+MLVK++A+G R E+KR T+I+RGQI+DV+ S+Y Sbjct: 61 TKNLNKLIEVVKLVDLSESAHIERELMLVKVKATGAQRAEIKRTTDIYRGQIVDVSASVY 120 Query: 121 TVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRGDKIM 162 TVQL GTS KLD+F+ SI A I+E RSGV G++RGDK++ Sbjct: 121 TVQLTGTSDKLDSFIQSI-GTASILETVRSGVTGIARGDKVL 161 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: 125 Number of extensions: 2 Number of successful extensions: 2 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: 163 Length adjustment: 18 Effective length of query: 145 Effective length of database: 145 Effective search space: 21025 Effective search space used: 21025 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 GFF4652 PS417_23805 (acetolactate synthase 3 regulatory subunit)
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.2493.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-67 210.2 2.3 9.1e-67 210.0 2.3 1.0 1 lcl|FitnessBrowser__WCS417:GFF4652 PS417_23805 acetolactate synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF4652 PS417_23805 acetolactate synthase 3 regulatory subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 210.0 2.3 9.1e-67 9.1e-67 1 158 [] 1 158 [. 1 158 [. 0.99 Alignments for each domain: == domain 1 score: 210.0 bits; conditional E-value: 9.1e-67 TIGR00119 1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvld 75 ++h++s+l+enepG+Lsrv+Glf++r++niesltv+ te+++lsr+t+++ g+d+v+eqi+k l+kl++v+k +d lcl|FitnessBrowser__WCS417:GFF4652 1 MRHIISLLLENEPGALSRVVGLFSQRNYNIESLTVAPTEDPTLSRLTLTTVGHDEVIEQITKNLNKLIEVVKLVD 75 69************************************************************************* PP TIGR00119 76 lteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevarsG 150 l+es++++rel+lvkv+a+g +r+eik++t+i+rg++vDvs + ++v+l+g++dk+++f++++ +i+e +rsG lcl|FitnessBrowser__WCS417:GFF4652 76 LSESAHIERELMLVKVKATGAQRAEIKRTTDIYRGQIVDVSASVYTVQLTGTSDKLDSFIQSIGTASILETVRSG 150 *************************************************************************** PP TIGR00119 151 lvalsrge 158 +++++rg+ lcl|FitnessBrowser__WCS417:GFF4652 151 VTGIARGD 158 ******85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (163 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.42 // [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