Align acetohydroxy-acid synthase small subunit (EC 2.2.1.6) (characterized)
to candidate WP_092483545.1 BM299_RS09935 acetolactate synthase small subunit
Query= metacyc::MONOMER-11901 (169 letters) >NCBI__GCF_900115975.1:WP_092483545.1 Length = 165 Score = 164 bits (414), Expect = 9e-46 Identities = 83/165 (50%), Positives = 117/165 (70%), Gaps = 1/165 (0%) Query: 4 THIISVLVLNKPGVLQRISGLFTRRWYNISSITGGSTDSTDISRMTIVVKGDDKVVEQVV 63 TH ++VLVLNKPGVL RI+GL +RR +NI SI G T+ DI+R+T+VV GD+ V+EQV+ Sbjct: 2 THTLAVLVLNKPGVLARIAGLLSRRVFNIESIAAGYTEEPDITRITLVVNGDEHVLEQVI 61 Query: 64 KQLNKLIEVIKVIDLDEEECVERELCLIKIYAPTESSKSQVIQYANIFRGNIVDLSQESL 123 QL+KL++VIK+ L++ E +EREL LIK+ A E + ++ IFR NIVD+ +E++ Sbjct: 62 HQLSKLVDVIKITRLEDRESIERELALIKVKADPE-KRRDIVDIVEIFRANIVDVGKETM 120 Query: 124 TVQITGDKTKISAFIKLVKPMGIKEISRTGLTALMRGPKILKSNK 168 +QI GD+ KISAF +++ GI E+ RTG AL R P+ K K Sbjct: 121 VIQIIGDEQKISAFTHVLEHQGIVEMVRTGKIALSRQPQAAKDGK 165 Lambda K H 0.317 0.134 0.362 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: 85 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: 169 Length of database: 165 Length adjustment: 18 Effective length of query: 151 Effective length of database: 147 Effective search space: 22197 Effective search space used: 22197 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_092483545.1 BM299_RS09935 (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.14487.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-64 201.1 6.4 5.8e-64 200.9 6.4 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092483545.1 BM299_RS09935 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092483545.1 BM299_RS09935 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 200.9 6.4 5.8e-64 5.8e-64 1 157 [. 1 157 [. 1 158 [. 0.99 Alignments for each domain: == domain 1 score: 200.9 bits; conditional E-value: 5.8e-64 TIGR00119 1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvd 69 ++h+l+vlv n+pGvL+r++Gl++rr fnies++ g tee+d++r+t+vv+gd++v+eq+++ql+klvd lcl|NCBI__GCF_900115975.1:WP_092483545.1 1 MTHTLAVLVLNKPGVLARIAGLLSRRVFNIESIAAGYTEEPDITRITLVVNGDEHVLEQVIHQLSKLVD 69 689****************************************************************** PP TIGR00119 70 vlkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkll 138 v+k++ l+++e+++rel+l+kv+a +e+r +i++++eifr+++vDv ++++++++ g+e+kisaf ++l lcl|NCBI__GCF_900115975.1:WP_092483545.1 70 VIKITRLEDRESIERELALIKVKADPEKRRDIVDIVEIFRANIVDVGKETMVIQIIGDEQKISAFTHVL 138 ********************************************************************* PP TIGR00119 139 kefgikevarsGlvalsrg 157 ++ gi+e++r+G++alsr+ lcl|NCBI__GCF_900115975.1:WP_092483545.1 139 EHQGIVEMVRTGKIALSRQ 157 ******************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (165 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: 5.58 // [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