Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_012606634.1 AFE_RS03535 acetolactate synthase small subunit
Query= BRENDA::P00894 (163 letters) >NCBI__GCF_000021485.1:WP_012606634.1 Length = 161 Score = 193 bits (490), Expect = 1e-54 Identities = 96/160 (60%), Positives = 128/160 (80%), Gaps = 1/160 (0%) Query: 1 MRRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTVGDEKVLEQI 60 MR I+S+LLENE+GALSRV GLFS RGYNIE++TVAPT DP++SRMT+ T G ++++EQ+ Sbjct: 1 MRHIISILLENEAGALSRVAGLFSARGYNIEAMTVAPTHDPSISRMTVATRGSDEIMEQV 60 Query: 61 EKQLHKLVDVLRVSELGQGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSLY 120 KQL+KLV+V+RV +L +G H+ERE+MLVK+ A G R+EVKR ++IFRG+IIDVT Y Sbjct: 61 LKQLNKLVEVVRVHDLTEGPHIERELMLVKVHAMGPDREEVKRLSDIFRGRIIDVTDRSY 120 Query: 121 TVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRGDK 160 T++L GT KLDAF+ S+ D ++EV RSG +SRG K Sbjct: 121 TMELTGTGEKLDAFIQSL-DPGMVIEVVRSGASAISRGAK 159 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: 113 Number of extensions: 3 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: 161 Length adjustment: 18 Effective length of query: 145 Effective length of database: 143 Effective search space: 20735 Effective search space used: 20735 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 WP_012606634.1 AFE_RS03535 (acetolactate synthase small 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.32710.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-66 209.8 0.3 1.2e-66 209.7 0.3 1.0 1 lcl|NCBI__GCF_000021485.1:WP_012606634.1 AFE_RS03535 acetolactate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021485.1:WP_012606634.1 AFE_RS03535 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 209.7 0.3 1.2e-66 1.2e-66 1 157 [. 1 157 [. 1 158 [. 0.99 Alignments for each domain: == domain 1 score: 209.7 bits; conditional E-value: 1.2e-66 TIGR00119 1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvd 69 ++h++s+l+ene+G+Lsrv+Glf++rg+nie++tv+ t ++ +srmt+ ++g d+++eq+ kql+klv+ lcl|NCBI__GCF_000021485.1:WP_012606634.1 1 MRHIISILLENEAGALSRVAGLFSARGYNIEAMTVAPTHDPSISRMTVATRGSDEIMEQVLKQLNKLVE 69 69******************************************************************* PP TIGR00119 70 vlkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkll 138 v++v+dlte +++rel+lvkv+a+g +r+e+k+l +ifrgr++Dv++ s+++el+g+ +k++af+++l lcl|NCBI__GCF_000021485.1:WP_012606634.1 70 VVRVHDLTEGPHIERELMLVKVHAMGPDREEVKRLSDIFRGRIIDVTDRSYTMELTGTGEKLDAFIQSL 138 ********************************************************************* PP TIGR00119 139 kefgikevarsGlvalsrg 157 + + ev+rsG a+srg lcl|NCBI__GCF_000021485.1:WP_012606634.1 139 DPGMVIEVVRSGASAISRG 157 ******************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (161 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 4.70 // [ok]
This GapMind analysis is from Apr 10 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