Align Acetolactate synthase isozyme 1 small subunit; EC 2.2.1.6; Acetohydroxy-acid synthase I small subunit; AHAS-I; ALS-I (uncharacterized)
to candidate WP_027722599.1 H589_RS0113930 acetolactate synthase small subunit
Query= curated2:P0ADG0 (96 letters) >NCBI__GCF_000425265.1:WP_027722599.1 Length = 88 Score = 81.6 bits (200), Expect = 2e-21 Identities = 37/78 (47%), Positives = 56/78 (71%) Query: 8 NVILELTVRNHPGVMTHVCGLFARRAFNVEGILCLPIQDSDKSHIWLLVNDDQRLEQMIS 67 N ++EL VRNH GVM+ + GLF+RR FN+EGI+C P+ D +S + L V D+ +LEQ++ Sbjct: 3 NYVIELLVRNHAGVMSQITGLFSRRNFNLEGIICGPVGDGGESRMILTVADNSKLEQILL 62 Query: 68 QIDKLEDVVKVQRNQSDP 85 Q++KL DV++V + P Sbjct: 63 QLEKLYDVLQVHKVDDHP 80 Lambda K H 0.324 0.137 0.410 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: 40 Number of extensions: 1 Number of successful extensions: 1 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: 96 Length of database: 88 Length adjustment: 9 Effective length of query: 87 Effective length of database: 79 Effective search space: 6873 Effective search space used: 6873 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (21.1 bits) S2: 39 (19.6 bits)
Align candidate WP_027722599.1 H589_RS0113930 (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.16529.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-21 62.6 0.1 2.4e-21 62.4 0.1 1.0 1 lcl|NCBI__GCF_000425265.1:WP_027722599.1 H589_RS0113930 acetolactate synt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000425265.1:WP_027722599.1 H589_RS0113930 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 62.4 0.1 2.4e-21 2.4e-21 3 79 .. 4 79 .. 2 87 .. 0.92 Alignments for each domain: == domain 1 score: 62.4 bits; conditional E-value: 2.4e-21 TIGR00119 3 hvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkv 73 v+++lv+n++Gv+s+++Glf+rr+fn+e ++ g + + srm ++v +d+ +eqi qlekl dvl+v lcl|NCBI__GCF_000425265.1:WP_027722599.1 4 YVIELLVRNHAGVMSQITGLFSRRNFNLEGIICGPVGDGGESRMILTV-ADNSKLEQILLQLEKLYDVLQV 73 699*****************************************7665.79999***************** PP TIGR00119 74 ldltes 79 ++++++ lcl|NCBI__GCF_000425265.1:WP_027722599.1 74 HKVDDH 79 998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (88 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: 4.78 // [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