Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_013009759.1 DACET_RS02090 acetolactate synthase small subunit
Query= BRENDA::P9WKJ3 (168 letters) >NCBI__GCF_000025725.1:WP_013009759.1 Length = 165 Score = 151 bits (382), Expect = 5e-42 Identities = 74/163 (45%), Positives = 113/163 (69%) Query: 6 HTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTPLEQITK 65 HT+SVLVE+K GVL+R++ LFS RG+NIESL+V T + S MTIV + + +EQI K Sbjct: 3 HTISVLVENKFGVLSRISGLFSGRGYNIESLSVNKTMDVNISTMTIVTTGDADVIEQIIK 62 Query: 66 QLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPESLTV 125 QL KL+NV+++ + + + RE+ L+KV+ + +RS++ V FRA +D++ SL + Sbjct: 63 QLRKLVNVLRVRDVSEMEHIEREMMLVKVRTEKSTRSEIFNVVGTFRAKTVDITNNSLVI 122 Query: 126 EATGNRGKLEALLRVLEPFGIREIAQSGMVSLSRGPRGIGTAK 168 E TG+RGK+ A L+VLEP+GI E+ ++G ++LSRG + K Sbjct: 123 EITGDRGKILAFLKVLEPYGIIEVVRTGAIALSRGSKATSDFK 165 Lambda K H 0.315 0.131 0.347 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: 101 Number of extensions: 4 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: 168 Length of database: 165 Length adjustment: 18 Effective length of query: 150 Effective length of database: 147 Effective search space: 22050 Effective search space used: 22050 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 (21.6 bits) S2: 43 (21.2 bits)
Align candidate WP_013009759.1 DACET_RS02090 (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.20691.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-63 200.0 7.9 1.2e-63 199.9 7.9 1.0 1 lcl|NCBI__GCF_000025725.1:WP_013009759.1 DACET_RS02090 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025725.1:WP_013009759.1 DACET_RS02090 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 199.9 7.9 1.2e-63 1.2e-63 1 157 [. 1 157 [. 1 158 [. 0.99 Alignments for each domain: == domain 1 score: 199.9 bits; conditional E-value: 1.2e-63 TIGR00119 1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvd 69 ++h++svlven+ GvLsr+sGlf+ rg+niesl v +t + ++s mtiv++gd +v+eqi+kql+klv+ lcl|NCBI__GCF_000025725.1:WP_013009759.1 1 MRHTISVLVENKFGVLSRISGLFSGRGYNIESLSVNKTMDVNISTMTIVTTGDADVIEQIIKQLRKLVN 69 69******************************************************************* PP TIGR00119 70 vlkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkll 138 vl+v+d++e e+++re++lvkv++ ++r+ei +++ +fr++ vD++++sl++e++g+ +ki aflk+l lcl|NCBI__GCF_000025725.1:WP_013009759.1 70 VLRVRDVSEMEHIEREMMLVKVRTEKSTRSEIFNVVGTFRAKTVDITNNSLVIEITGDRGKILAFLKVL 138 ********************************************************************* PP TIGR00119 139 kefgikevarsGlvalsrg 157 +++gi ev+r+G +alsrg lcl|NCBI__GCF_000025725.1:WP_013009759.1 139 EPYGIIEVVRTGAIALSRG 157 ******************8 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.70 // [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