Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_012853872.1 TCUR_RS17510 acetolactate synthase small subunit
Query= BRENDA::P9WKJ3 (168 letters) >NCBI__GCF_000024385.1:WP_012853872.1 Length = 174 Score = 229 bits (583), Expect = 2e-65 Identities = 116/159 (72%), Positives = 138/159 (86%) Query: 6 HTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTPLEQITK 65 HTLSVLVE+KPG+LARVAALFSRRGFNI+SLAVG TE + SRMTIVV+ ED PLEQ+TK Sbjct: 4 HTLSVLVENKPGILARVAALFSRRGFNIDSLAVGTTEHPEISRMTIVVNVEDHPLEQVTK 63 Query: 66 QLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPESLTV 125 QLNKL+NV+KIVE D SV REL L+KV+ADA +RSQV+E V LFRA V+DV+PE++T+ Sbjct: 64 QLNKLVNVLKIVELDPSSSVQRELILVKVRADAETRSQVLETVQLFRAKVVDVAPEAVTI 123 Query: 126 EATGNRGKLEALLRVLEPFGIREIAQSGMVSLSRGPRGI 164 EATGNR KLEAL+RVLEPFGI+E+ QSGMV++ RG R I Sbjct: 124 EATGNRDKLEALIRVLEPFGIKELVQSGMVAIGRGARSI 162 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: 144 Number of extensions: 2 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: 174 Length adjustment: 18 Effective length of query: 150 Effective length of database: 156 Effective search space: 23400 Effective search space used: 23400 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_012853872.1 TCUR_RS17510 (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.29429.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-66 209.0 2.9 2.1e-66 208.8 2.9 1.0 1 lcl|NCBI__GCF_000024385.1:WP_012853872.1 TCUR_RS17510 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_012853872.1 TCUR_RS17510 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 208.8 2.9 2.1e-66 2.1e-66 2 157 .. 3 158 .. 2 159 .. 0.99 Alignments for each domain: == domain 1 score: 208.8 bits; conditional E-value: 2.1e-66 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdv 70 +h+lsvlven+pG+L+rv+ lf+rrgfni+sl+vg+te++++srmtivv+++d+ +eq++kql+klv+v lcl|NCBI__GCF_000024385.1:WP_012853872.1 3 RHTLSVLVENKPGILARVAALFSRRGFNIDSLAVGTTEHPEISRMTIVVNVEDHPLEQVTKQLNKLVNV 71 8******************************************************************** PP TIGR00119 71 lkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllk 139 lk+++l+ s++v+rel+lvkv+a +e+r+++ e+++ fr++vvDv+++++++e +g+ dk++a++++l+ lcl|NCBI__GCF_000024385.1:WP_012853872.1 72 LKIVELDPSSSVQRELILVKVRADAETRSQVLETVQLFRAKVVDVAPEAVTIEATGNRDKLEALIRVLE 140 ********************************************************************* PP TIGR00119 140 efgikevarsGlvalsrg 157 +fgike+++sG+va+ rg lcl|NCBI__GCF_000024385.1:WP_012853872.1 141 PFGIKELVQSGMVAIGRG 158 ***************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (174 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: 7.69 // [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