Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_052666289.1 NITAL_RS11145 acetolactate synthase small subunit
Query= BRENDA::P9WKJ3 (168 letters) >NCBI__GCF_000969705.1:WP_052666289.1 Length = 177 Score = 181 bits (458), Expect = 8e-51 Identities = 92/159 (57%), Positives = 121/159 (76%) Query: 6 HTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTPLEQITK 65 HTLSVLVE+KPGVL RVA +F+RR +NI SLAVG T+ SR+T+VV E LEQI K Sbjct: 7 HTLSVLVENKPGVLTRVAGMFARRNYNIHSLAVGPTDDPRVSRLTLVVGTEAVQLEQIIK 66 Query: 66 QLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPESLTV 125 QLNKL++V+KIVE ++ +V REL L+KV DA +R Q+IE +FRAN++DV +SLT+ Sbjct: 67 QLNKLVHVLKIVELEEGDTVERELQLVKVACDAATRGQIIELAQVFRANIVDVDHDSLTI 126 Query: 126 EATGNRGKLEALLRVLEPFGIREIAQSGMVSLSRGPRGI 164 EA G+ KL AL+ +LEPFGIRE+ +SG ++L+RG R I Sbjct: 127 EAAGDPDKLGALVDLLEPFGIREMVRSGRIALARGTRSI 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: 107 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: 177 Length adjustment: 18 Effective length of query: 150 Effective length of database: 159 Effective search space: 23850 Effective search space used: 23850 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: 44 (21.6 bits)
Align candidate WP_052666289.1 NITAL_RS11145 (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.21597.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-64 202.7 0.8 1.9e-64 202.5 0.8 1.0 1 lcl|NCBI__GCF_000969705.1:WP_052666289.1 NITAL_RS11145 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000969705.1:WP_052666289.1 NITAL_RS11145 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 202.5 0.8 1.9e-64 1.9e-64 2 157 .. 6 161 .. 5 162 .. 0.99 Alignments for each domain: == domain 1 score: 202.5 bits; conditional E-value: 1.9e-64 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdv 70 +h+lsvlven+pGvL+rv+G+farr++ni+sl+vg t+++ +sr+t+vv ++ +eqi+kql+klv+v lcl|NCBI__GCF_000969705.1:WP_052666289.1 6 QHTLSVLVENKPGVLTRVAGMFARRNYNIHSLAVGPTDDPRVSRLTLVVGTEAVQLEQIIKQLNKLVHV 74 8******************************************************************** PP TIGR00119 71 lkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllk 139 lk+++l+e ++v+rel lvkv + +r +i+el+++fr+++vDv +dsl++e +g++dk+ a+++ll+ lcl|NCBI__GCF_000969705.1:WP_052666289.1 75 LKIVELEEGDTVERELQLVKVACDAATRGQIIELAQVFRANIVDVDHDSLTIEAAGDPDKLGALVDLLE 143 ********************************************************************* PP TIGR00119 140 efgikevarsGlvalsrg 157 +fgi+e++rsG +al+rg lcl|NCBI__GCF_000969705.1:WP_052666289.1 144 PFGIREMVRSGRIALARG 161 *****************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (177 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: 5.85 // [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