Align Probable acetolactate synthase small subunit; EC 2.2.1.6; Acetohydroxy-acid synthase small subunit; AHAS; ALS (uncharacterized)
to candidate WP_078716656.1 B5D49_RS05445 acetolactate synthase small subunit
Query= curated2:O28555 (159 letters) >NCBI__GCF_900167125.1:WP_078716656.1 Length = 159 Score = 121 bits (303), Expect = 6e-33 Identities = 60/159 (37%), Positives = 100/159 (62%), Gaps = 1/159 (0%) Query: 1 MKHTIAVLVENKPGVLARVAGLFRRRGFNIESLTVGTTERDDLSRMTIVVEGDDKVVEQV 60 MKHT++ LV N+PGVLA +A F NI S+ G TE D+SRM I +E + + + ++ Sbjct: 1 MKHTLSALVRNEPGVLAHMARHFGEAKLNINSIACGETENPDISRMVIRIEANPERISRI 60 Query: 61 IKQLNKLIETIKVSEITESS-VERELCLIRVHAPPEKRGEIVELTNIFRARIVDVSRDSF 119 +++ L I+V +++ V+REL LI+V PE +I+++ +FRA +V + + S Sbjct: 61 TERMQALDVVIQVDDLSRKEFVDRELALIKVALTPEDTAQIMQIFEVFRADVVGMGQRSV 120 Query: 120 IIEVTGDEDKVSAFIDLMRQYGIKELARTGKVAMVRGNK 158 +E+TGDE +V I +++ YGI + RTG +A+ RG++ Sbjct: 121 TVELTGDEARVDGLIKMLKPYGILSMCRTGTIALKRGDE 159 Lambda K H 0.319 0.137 0.365 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: 72 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: 159 Length of database: 159 Length adjustment: 17 Effective length of query: 142 Effective length of database: 142 Effective search space: 20164 Effective search space used: 20164 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: 43 (21.2 bits)
Align candidate WP_078716656.1 B5D49_RS05445 (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.7809.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-47 147.5 0.6 1.8e-47 147.4 0.6 1.0 1 lcl|NCBI__GCF_900167125.1:WP_078716656.1 B5D49_RS05445 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900167125.1:WP_078716656.1 B5D49_RS05445 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 147.4 0.6 1.8e-47 1.8e-47 1 158 [] 1 158 [. 1 158 [. 0.99 Alignments for each domain: == domain 1 score: 147.4 bits; conditional E-value: 1.8e-47 TIGR00119 1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvd 69 +kh+ls+lv+nepGvL+ ++ f + + ni+s++ gete++d+srm i +e++ + + +i+ +++ l lcl|NCBI__GCF_900167125.1:WP_078716656.1 1 MKHTLSALVRNEPGVLAHMARHFGEAKLNINSIACGETENPDISRMVIRIEANPERISRITERMQALDV 69 69******************************************************************* PP TIGR00119 70 vlkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkll 138 v++v dl+ +e v+rel+l+kv +++e+ ++i+++ e+fr+ vv + + s++vel+g+e +++ ++k+l lcl|NCBI__GCF_900167125.1:WP_078716656.1 70 VIQVDDLSRKEFVDRELALIKVALTPEDTAQIMQIFEVFRADVVGMGQRSVTVELTGDEARVDGLIKML 138 ********************************************************************* PP TIGR00119 139 kefgikevarsGlvalsrge 158 k++gi+ + r+G++al rg+ lcl|NCBI__GCF_900167125.1:WP_078716656.1 139 KPYGILSMCRTGTIALKRGD 158 ******************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (159 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: 4.68 // [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